Starting phenix.real_space_refine on Mon Sep 30 01:24:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1q_23115/09_2024/7l1q_23115.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1q_23115/09_2024/7l1q_23115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1q_23115/09_2024/7l1q_23115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1q_23115/09_2024/7l1q_23115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1q_23115/09_2024/7l1q_23115.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1q_23115/09_2024/7l1q_23115.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 78 5.16 5 C 15235 2.51 5 N 4214 2.21 5 O 4653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 250 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24204 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3636 Classifications: {'peptide': 474} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 451} Chain: "B" Number of atoms: 3643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3643 Classifications: {'peptide': 475} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 452} Chain: "C" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3649 Classifications: {'peptide': 476} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 453} Chain: "D" Number of atoms: 3621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3621 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3622 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3629 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2211 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 271} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.03, per 1000 atoms: 0.62 Number of scatterers: 24204 At special positions: 0 Unit cell: (141.12, 120.96, 131.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 18 15.00 Mg 6 11.99 O 4653 8.00 N 4214 7.00 C 15235 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.77 Conformation dependent library (CDL) restraints added in 3.0 seconds 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5690 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 22 sheets defined 47.3% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.764A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.508A pdb=" N GLY A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 288 No H-bonds generated for 'chain 'A' and resid 287 through 288' Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.686A pdb=" N ILE A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 372 through 394 removed outlier: 3.728A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 399 removed outlier: 4.429A pdb=" N PHE A 398 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 399 " --> pdb=" O ALA A 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 395 through 399' Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.566A pdb=" N GLN A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 443 through 447 removed outlier: 4.338A pdb=" N ASP A 447 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.658A pdb=" N PHE A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A 457 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 removed outlier: 3.629A pdb=" N LEU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.827A pdb=" N ASN A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LYS A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.595A pdb=" N ARG B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 removed outlier: 3.648A pdb=" N TYR B 220 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 removed outlier: 3.503A pdb=" N LEU B 237 " --> pdb=" O PRO B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 253 removed outlier: 3.739A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.570A pdb=" N GLU B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 338 removed outlier: 3.832A pdb=" N ILE B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 358 through 362 Processing helix chain 'B' and resid 372 through 380 removed outlier: 4.013A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 399 removed outlier: 3.825A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 421 removed outlier: 3.622A pdb=" N ALA B 411 " --> pdb=" O GLN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 449 through 468 removed outlier: 3.888A pdb=" N ARG B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLN B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.627A pdb=" N LYS B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 38 removed outlier: 4.543A pdb=" N GLY C 37 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.891A pdb=" N VAL C 178 " --> pdb=" O GLY C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 217 through 221 removed outlier: 4.166A pdb=" N TYR C 220 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR C 221 " --> pdb=" O LEU C 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 217 through 221' Processing helix chain 'C' and resid 231 through 237 removed outlier: 3.767A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 253 removed outlier: 4.089A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 4.000A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 328 through 338 Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 372 through 397 removed outlier: 3.583A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 429 through 442 removed outlier: 3.796A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 467 removed outlier: 3.626A pdb=" N LYS C 458 " --> pdb=" O ARG C 454 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.535A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 179 Processing helix chain 'D' and resid 191 through 205 removed outlier: 3.523A pdb=" N GLY D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN D 196 " --> pdb=" O THR D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 211 removed outlier: 4.214A pdb=" N LYS D 210 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR D 211 " --> pdb=" O ILE D 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 207 through 211' Processing helix chain 'D' and resid 221 through 244 removed outlier: 3.605A pdb=" N VAL D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 Processing helix chain 'D' and resid 280 through 291 removed outlier: 3.877A pdb=" N GLU D 284 " --> pdb=" O THR D 280 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 323 removed outlier: 4.288A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.517A pdb=" N ALA D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 379 Processing helix chain 'D' and resid 380 through 387 Processing helix chain 'D' and resid 388 through 392 Processing helix chain 'D' and resid 393 through 410 Processing helix chain 'D' and resid 416 through 421 removed outlier: 4.068A pdb=" N PHE D 420 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 444 through 448 removed outlier: 4.334A pdb=" N HIS D 447 " --> pdb=" O LYS D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 458 through 470 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 164 through 178 Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 221 through 242 removed outlier: 4.381A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 269 Processing helix chain 'E' and resid 280 through 290 removed outlier: 3.654A pdb=" N LEU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 325 removed outlier: 3.952A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 387 removed outlier: 4.019A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 392 Processing helix chain 'E' and resid 393 through 410 Processing helix chain 'E' and resid 415 through 421 removed outlier: 4.230A pdb=" N GLN E 419 " --> pdb=" O HIS E 415 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE E 420 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 443 Processing helix chain 'E' and resid 444 through 448 removed outlier: 4.362A pdb=" N HIS E 447 " --> pdb=" O LYS E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 454 removed outlier: 3.695A pdb=" N ARG E 454 " --> pdb=" O ASP E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.560A pdb=" N LYS E 467 " --> pdb=" O VAL E 463 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.504A pdb=" N LEU F 92 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 145 Processing helix chain 'F' and resid 163 through 176 removed outlier: 3.666A pdb=" N LEU F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 205 Processing helix chain 'F' and resid 206 through 210 removed outlier: 3.503A pdb=" N SER F 209 " --> pdb=" O GLY F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 243 removed outlier: 3.506A pdb=" N ARG F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.917A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 292 removed outlier: 3.912A pdb=" N GLU F 284 " --> pdb=" O THR F 280 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE F 292 " --> pdb=" O LEU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 322 removed outlier: 3.634A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 removed outlier: 3.547A pdb=" N ALA F 336 " --> pdb=" O GLU F 332 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 388 removed outlier: 3.748A pdb=" N VAL F 366 " --> pdb=" O GLU F 362 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU F 379 " --> pdb=" O GLN F 375 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 6.161A pdb=" N SER F 393 " --> pdb=" O ASP F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 410 removed outlier: 3.774A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 420 removed outlier: 3.891A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 458 through 469 Processing helix chain 'G' and resid 7 through 62 removed outlier: 4.164A pdb=" N THR G 12 " --> pdb=" O ARG G 8 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) Proline residue: G 47 - end of helix removed outlier: 4.178A pdb=" N GLY G 62 " --> pdb=" O ASN G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 111 removed outlier: 3.764A pdb=" N VAL G 98 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 148 through 165 removed outlier: 3.676A pdb=" N ILE G 152 " --> pdb=" O SER G 148 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE G 155 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 287 removed outlier: 3.768A pdb=" N CYS G 215 " --> pdb=" O SER G 211 " (cutoff:3.500A) Proline residue: G 221 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 34 removed outlier: 6.305A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 39 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN A 65 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 76 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLY A 61 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.462A pdb=" N VAL A 256 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N LEU A 316 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL A 258 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 35 removed outlier: 6.348A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ARG B 93 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.230A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.344A pdb=" N VAL B 108 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 258 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N PHE B 318 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR B 260 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N GLU B 320 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 28 through 33 removed outlier: 6.090A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN C 65 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 99 Processing sheet with id=AB1, first strand: chain 'C' and resid 107 through 108 removed outlier: 3.998A pdb=" N LEU C 257 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 10 removed outlier: 3.976A pdb=" N ARG D 5 " --> pdb=" O LYS D 17 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB4, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.261A pdb=" N PHE D 96 " --> pdb=" O PHE D 215 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLN D 217 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 10 removed outlier: 3.696A pdb=" N ARG E 5 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASN E 28 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA E 29 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.591A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR E 301 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA E 305 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS E 153 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N THR E 329 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY E 155 " --> pdb=" O THR E 329 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU E 331 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE E 157 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 4 through 10 removed outlier: 4.020A pdb=" N ARG F 5 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE F 44 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS F 34 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 85 through 86 Processing sheet with id=AC1, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.611A pdb=" N PHE F 96 " --> pdb=" O PHE F 215 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N GLN F 217 " --> pdb=" O PHE F 96 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY F 189 " --> pdb=" O GLY F 216 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA F 305 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS F 153 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N THR F 329 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY F 155 " --> pdb=" O THR F 329 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU F 331 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE F 157 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 133 through 134 removed outlier: 4.640A pdb=" N GLU F 133 " --> pdb=" O LYS F 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 136 through 140 removed outlier: 7.916A pdb=" N ILE G 137 " --> pdb=" O TYR G 116 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ILE G 118 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP G 139 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL G 120 " --> pdb=" O ASP G 139 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR G 79 " --> pdb=" O ALA G 117 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE G 119 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N TYR G 81 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE G 121 " --> pdb=" O TYR G 81 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL G 83 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE G 84 " --> pdb=" O TYR G 174 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU G 171 " --> pdb=" O LEU G 191 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 176 through 177 1143 hydrogen bonds defined for protein. 3267 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: 8.51 Time building geometry restraints manager: 6.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4497 1.32 - 1.44: 5579 1.44 - 1.57: 14350 1.57 - 1.69: 28 1.69 - 1.81: 154 Bond restraints: 24608 Sorted by residual: bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.476 -0.088 1.00e-02 1.00e+04 7.83e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.13e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.18e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.93e+01 bond pdb=" C8 ATP B 600 " pdb=" N7 ATP B 600 " ideal model delta sigma weight residual 1.310 1.365 -0.055 1.00e-02 1.00e+04 3.03e+01 ... (remaining 24603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.19: 32987 4.19 - 8.37: 364 8.37 - 12.56: 11 12.56 - 16.74: 3 16.74 - 20.93: 5 Bond angle restraints: 33370 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 118.94 20.93 1.00e+00 1.00e+00 4.38e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.65 20.18 1.00e+00 1.00e+00 4.07e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 121.88 17.99 1.00e+00 1.00e+00 3.24e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 122.90 16.97 1.00e+00 1.00e+00 2.88e+02 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 122.97 16.90 1.00e+00 1.00e+00 2.86e+02 ... (remaining 33365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.19: 13819 21.19 - 42.39: 997 42.39 - 63.58: 176 63.58 - 84.78: 45 84.78 - 105.97: 7 Dihedral angle restraints: 15044 sinusoidal: 6152 harmonic: 8892 Sorted by residual: dihedral pdb=" C THR B 204 " pdb=" N THR B 204 " pdb=" CA THR B 204 " pdb=" CB THR B 204 " ideal model delta harmonic sigma weight residual -122.00 -137.70 15.70 0 2.50e+00 1.60e-01 3.95e+01 dihedral pdb=" CA GLU C 284 " pdb=" C GLU C 284 " pdb=" N ALA C 285 " pdb=" CA ALA C 285 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA GLY C 35 " pdb=" C GLY C 35 " pdb=" N ASP C 36 " pdb=" CA ASP C 36 " ideal model delta harmonic sigma weight residual 180.00 151.80 28.20 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 15041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3338 0.101 - 0.203: 466 0.203 - 0.304: 28 0.304 - 0.406: 6 0.406 - 0.507: 2 Chirality restraints: 3840 Sorted by residual: chirality pdb=" CA THR B 204 " pdb=" N THR B 204 " pdb=" C THR B 204 " pdb=" CB THR B 204 " both_signs ideal model delta sigma weight residual False 2.53 2.02 0.51 2.00e-01 2.50e+01 6.42e+00 chirality pdb=" CA HIS A 425 " pdb=" N HIS A 425 " pdb=" C HIS A 425 " pdb=" CB HIS A 425 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CA ARG C 454 " pdb=" N ARG C 454 " pdb=" C ARG C 454 " pdb=" CB ARG C 454 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 3837 not shown) Planarity restraints: 4349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 296 " -0.348 9.50e-02 1.11e+02 1.61e-01 3.64e+01 pdb=" NE ARG B 296 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG B 296 " 0.084 2.00e-02 2.50e+03 pdb=" NH1 ARG B 296 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG B 296 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 435 " 0.336 9.50e-02 1.11e+02 1.55e-01 3.04e+01 pdb=" NE ARG D 435 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG D 435 " -0.074 2.00e-02 2.50e+03 pdb=" NH1 ARG D 435 " 0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG D 435 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 161 " 0.129 9.50e-02 1.11e+02 7.38e-02 2.83e+01 pdb=" NE ARG A 161 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 161 " 0.087 2.00e-02 2.50e+03 pdb=" NH1 ARG A 161 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG A 161 " -0.024 2.00e-02 2.50e+03 ... (remaining 4346 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 24 2.43 - 3.04: 14858 3.04 - 3.66: 34419 3.66 - 4.28: 51443 4.28 - 4.90: 88052 Nonbonded interactions: 188796 Sorted by model distance: nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.807 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 501 " model vdw 2.058 2.170 nonbonded pdb=" O1G ATP B 600 " pdb="MG MG B 601 " model vdw 2.067 2.170 nonbonded pdb=" OE1 GLU E 194 " pdb="MG MG E 502 " model vdw 2.151 2.170 nonbonded pdb=" O2G ATP E 501 " pdb="MG MG E 502 " model vdw 2.161 2.170 ... (remaining 188791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 499) selection = (chain 'B' and resid 27 through 499) selection = (chain 'C' and resid 27 through 499) } ncs_group { reference = (chain 'D' and resid 2 through 470) selection = (chain 'E' and resid 2 through 470) selection = (chain 'F' and resid 2 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 51.850 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 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 : 0.008 0.105 24608 Z= 0.525 Angle : 1.295 20.929 33370 Z= 0.838 Chirality : 0.068 0.507 3840 Planarity : 0.011 0.161 4349 Dihedral : 15.526 105.970 9354 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.70 % Favored : 96.13 % Rotamer: Outliers : 2.54 % Allowed : 12.24 % Favored : 85.22 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3104 helix: -0.40 (0.13), residues: 1253 sheet: -0.16 (0.22), residues: 500 loop : -0.63 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS C 425 PHE 0.057 0.005 PHE A 236 TYR 0.054 0.007 TYR C 438 ARG 0.089 0.011 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1062 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ILE cc_start: 0.7669 (mm) cc_final: 0.7371 (tt) REVERT: A 190 ASN cc_start: 0.7620 (m-40) cc_final: 0.7234 (m-40) REVERT: A 214 LYS cc_start: 0.7555 (tttt) cc_final: 0.7302 (tttt) REVERT: A 333 ASN cc_start: 0.7541 (t0) cc_final: 0.7303 (t0) REVERT: A 415 ARG cc_start: 0.7852 (mtt90) cc_final: 0.7505 (mtt90) REVERT: A 417 VAL cc_start: 0.8583 (t) cc_final: 0.8352 (m) REVERT: A 420 LEU cc_start: 0.8207 (mp) cc_final: 0.7912 (mt) REVERT: A 432 LYS cc_start: 0.7861 (mttt) cc_final: 0.7137 (mtpp) REVERT: A 456 PHE cc_start: 0.7658 (t80) cc_final: 0.7399 (t80) REVERT: B 32 ILE cc_start: 0.8331 (tt) cc_final: 0.7889 (tt) REVERT: B 45 ASP cc_start: 0.6433 (p0) cc_final: 0.6207 (p0) REVERT: B 88 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7909 (p) REVERT: B 150 ILE cc_start: 0.8228 (mt) cc_final: 0.7330 (mt) REVERT: B 154 ASP cc_start: 0.7528 (m-30) cc_final: 0.7204 (m-30) REVERT: B 175 LYS cc_start: 0.7543 (mtmm) cc_final: 0.7065 (mtmm) REVERT: B 184 ILE cc_start: 0.7744 (mt) cc_final: 0.7505 (tp) REVERT: B 230 GLN cc_start: 0.6724 (mm-40) cc_final: 0.6459 (mm-40) REVERT: B 243 VAL cc_start: 0.7452 (m) cc_final: 0.7237 (t) REVERT: B 373 LYS cc_start: 0.7641 (ttmt) cc_final: 0.7149 (ttmt) REVERT: B 377 LYS cc_start: 0.7910 (mttp) cc_final: 0.7596 (mttp) REVERT: B 424 LEU cc_start: 0.7913 (tp) cc_final: 0.7657 (tp) REVERT: B 452 ASP cc_start: 0.6625 (m-30) cc_final: 0.6388 (t0) REVERT: B 470 HIS cc_start: 0.7689 (p90) cc_final: 0.7414 (p-80) REVERT: C 202 GLU cc_start: 0.6807 (tt0) cc_final: 0.6550 (tt0) REVERT: C 206 ARG cc_start: 0.7191 (ttt180) cc_final: 0.6851 (tpp-160) REVERT: C 227 SER cc_start: 0.7186 (p) cc_final: 0.6584 (p) REVERT: C 434 VAL cc_start: 0.7791 (m) cc_final: 0.7445 (p) REVERT: C 452 ASP cc_start: 0.7178 (m-30) cc_final: 0.6960 (m-30) REVERT: C 474 HIS cc_start: 0.6663 (t70) cc_final: 0.6315 (t70) REVERT: C 480 ASP cc_start: 0.6697 (t0) cc_final: 0.6357 (t0) REVERT: D 18 PHE cc_start: 0.7504 (m-80) cc_final: 0.7130 (m-80) REVERT: D 35 LYS cc_start: 0.7908 (ttmt) cc_final: 0.7700 (ttmt) REVERT: D 44 ILE cc_start: 0.7474 (tp) cc_final: 0.7230 (tp) REVERT: D 45 ASP cc_start: 0.6683 (t0) cc_final: 0.6178 (t0) REVERT: D 66 SER cc_start: 0.6800 (t) cc_final: 0.6524 (m) REVERT: D 104 ASP cc_start: 0.7583 (p0) cc_final: 0.6976 (p0) REVERT: D 191 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6678 (mtt180) REVERT: D 213 MET cc_start: 0.7084 (mtp) cc_final: 0.6867 (mtp) REVERT: D 271 MET cc_start: 0.6352 (mtt) cc_final: 0.5522 (mtt) REVERT: D 275 VAL cc_start: 0.8418 (t) cc_final: 0.8096 (t) REVERT: D 308 VAL cc_start: 0.8668 (t) cc_final: 0.8432 (m) REVERT: D 333 ARG cc_start: 0.6760 (ttm110) cc_final: 0.6558 (ttm110) REVERT: D 334 LYS cc_start: 0.7477 (ttpt) cc_final: 0.7167 (ttpt) REVERT: D 401 HIS cc_start: 0.6358 (t70) cc_final: 0.5405 (t70) REVERT: D 405 ARG cc_start: 0.7057 (mpt180) cc_final: 0.6646 (mpt180) REVERT: D 441 LEU cc_start: 0.8432 (mt) cc_final: 0.8190 (mp) REVERT: D 464 GLU cc_start: 0.7391 (tp30) cc_final: 0.7023 (tp30) REVERT: E 10 MET cc_start: 0.5754 (mtp) cc_final: 0.5433 (mtp) REVERT: E 44 ILE cc_start: 0.6401 (tp) cc_final: 0.6162 (tp) REVERT: E 92 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6627 (mt) REVERT: E 101 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6551 (mp0) REVERT: E 136 GLU cc_start: 0.5764 (tt0) cc_final: 0.5480 (tt0) REVERT: E 168 ILE cc_start: 0.8685 (mm) cc_final: 0.8453 (mm) REVERT: E 197 ASP cc_start: 0.6279 (t0) cc_final: 0.6020 (t0) REVERT: E 201 GLU cc_start: 0.6676 (tp30) cc_final: 0.6202 (tp30) REVERT: E 207 VAL cc_start: 0.7471 (t) cc_final: 0.7196 (p) REVERT: E 372 GLN cc_start: 0.7623 (mt0) cc_final: 0.7305 (mt0) REVERT: E 389 MET cc_start: 0.7091 (mmm) cc_final: 0.6845 (mmm) REVERT: E 405 ARG cc_start: 0.7391 (mpt180) cc_final: 0.7188 (mpt180) REVERT: E 410 LEU cc_start: 0.8395 (mt) cc_final: 0.8175 (mt) REVERT: E 411 SER cc_start: 0.7834 (m) cc_final: 0.7548 (p) REVERT: E 419 GLN cc_start: 0.7452 (pt0) cc_final: 0.6862 (pm20) REVERT: E 432 GLU cc_start: 0.6463 (mm-30) cc_final: 0.5443 (mm-30) REVERT: E 450 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6320 (pm20) REVERT: E 453 PHE cc_start: 0.7865 (m-80) cc_final: 0.7590 (m-80) REVERT: E 469 MET cc_start: 0.5663 (mmm) cc_final: 0.5352 (mmm) REVERT: F 38 ASN cc_start: 0.7681 (t0) cc_final: 0.7258 (t0) REVERT: F 39 GLU cc_start: 0.6959 (pp20) cc_final: 0.6727 (pp20) REVERT: F 47 THR cc_start: 0.6921 (t) cc_final: 0.6711 (p) REVERT: F 77 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.5684 (mt) REVERT: F 240 ARG cc_start: 0.5653 (OUTLIER) cc_final: 0.5324 (ppt90) REVERT: F 241 ASP cc_start: 0.7103 (m-30) cc_final: 0.6702 (m-30) REVERT: F 285 MET cc_start: 0.6887 (ttp) cc_final: 0.6530 (ttt) REVERT: F 331 LEU cc_start: 0.7754 (mt) cc_final: 0.7352 (mt) REVERT: F 366 VAL cc_start: 0.7550 (t) cc_final: 0.7017 (p) REVERT: F 377 TYR cc_start: 0.7842 (t80) cc_final: 0.7493 (t80) REVERT: F 438 LYS cc_start: 0.7942 (tttt) cc_final: 0.7651 (tttt) REVERT: F 456 VAL cc_start: 0.6235 (p) cc_final: 0.5750 (m) REVERT: G 12 THR cc_start: 0.8066 (p) cc_final: 0.7845 (t) REVERT: G 19 LYS cc_start: 0.8018 (mptt) cc_final: 0.7731 (mptt) REVERT: G 43 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8253 (ttpt) REVERT: G 48 TYR cc_start: 0.7508 (t80) cc_final: 0.7266 (t80) REVERT: G 49 MET cc_start: 0.7640 (mmt) cc_final: 0.7430 (mmt) REVERT: G 70 MET cc_start: 0.7766 (mmp) cc_final: 0.7475 (mmp) REVERT: G 97 ASN cc_start: 0.7656 (m-40) cc_final: 0.6845 (m-40) REVERT: G 148 SER cc_start: 0.8579 (m) cc_final: 0.8346 (p) REVERT: G 149 PHE cc_start: 0.6840 (t80) cc_final: 0.6640 (t80) REVERT: G 222 GLN cc_start: 0.7570 (mt0) cc_final: 0.7337 (mt0) REVERT: G 265 TYR cc_start: 0.7740 (t80) cc_final: 0.7035 (t80) REVERT: G 269 ARG cc_start: 0.7140 (ttp80) cc_final: 0.6762 (ttp80) REVERT: G 270 GLN cc_start: 0.7319 (mt0) cc_final: 0.6930 (mt0) REVERT: G 275 GLN cc_start: 0.7426 (tp40) cc_final: 0.6321 (tp40) REVERT: G 279 GLU cc_start: 0.6698 (mm-30) cc_final: 0.6452 (mm-30) outliers start: 65 outliers final: 13 residues processed: 1101 average time/residue: 0.4131 time to fit residues: 667.6559 Evaluate side-chains 1004 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 984 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 322 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 158 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 chunk 281 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 113 GLN A 185 ASN A 215 HIS ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 426 GLN ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 HIS A 474 HIS B 470 HIS B 474 HIS B 488 ASN C 69 ASN C 185 ASN D 33 GLN D 200 HIS D 259 GLN D 372 GLN D 419 GLN E 33 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN E 177 GLN E 259 GLN E 287 GLN E 371 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN F 33 GLN F 174 ASN F 196 ASN F 217 GLN F 287 GLN F 304 GLN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN F 363 HIS F 423 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN G 184 GLN G 266 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24608 Z= 0.290 Angle : 0.744 18.306 33370 Z= 0.395 Chirality : 0.050 0.347 3840 Planarity : 0.006 0.061 4349 Dihedral : 9.514 87.605 3611 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 5.47 % Allowed : 19.78 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3104 helix: 0.54 (0.14), residues: 1280 sheet: 0.20 (0.23), residues: 496 loop : -0.71 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS F 53 PHE 0.028 0.003 PHE A 236 TYR 0.022 0.002 TYR G 103 ARG 0.012 0.001 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 992 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.7451 (t) cc_final: 0.6821 (m) REVERT: A 62 MET cc_start: 0.6627 (ptp) cc_final: 0.6417 (ptp) REVERT: A 87 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6567 (mm-30) REVERT: A 164 ARG cc_start: 0.6655 (mtm110) cc_final: 0.6447 (mtm-85) REVERT: A 190 ASN cc_start: 0.7544 (m-40) cc_final: 0.7152 (m-40) REVERT: A 272 GLU cc_start: 0.6833 (tt0) cc_final: 0.6580 (tt0) REVERT: A 333 ASN cc_start: 0.7573 (t0) cc_final: 0.7355 (t0) REVERT: A 363 VAL cc_start: 0.7701 (p) cc_final: 0.7460 (t) REVERT: A 365 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6874 (mtt-85) REVERT: A 415 ARG cc_start: 0.7847 (mtt90) cc_final: 0.7511 (mtt90) REVERT: A 417 VAL cc_start: 0.8533 (t) cc_final: 0.8331 (m) REVERT: A 424 LEU cc_start: 0.7903 (tp) cc_final: 0.7055 (tp) REVERT: A 432 LYS cc_start: 0.8022 (mttt) cc_final: 0.7360 (mtpp) REVERT: A 448 ILE cc_start: 0.7400 (mp) cc_final: 0.7082 (mp) REVERT: A 456 PHE cc_start: 0.7664 (t80) cc_final: 0.7359 (t80) REVERT: B 80 THR cc_start: 0.7966 (p) cc_final: 0.7694 (m) REVERT: B 88 VAL cc_start: 0.8098 (t) cc_final: 0.7876 (p) REVERT: B 93 ARG cc_start: 0.6385 (mmm160) cc_final: 0.6182 (mmm160) REVERT: B 243 VAL cc_start: 0.7259 (m) cc_final: 0.7013 (t) REVERT: B 305 SER cc_start: 0.6882 (m) cc_final: 0.6666 (m) REVERT: B 333 ASN cc_start: 0.7768 (t0) cc_final: 0.7498 (t0) REVERT: B 335 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8321 (tt) REVERT: B 341 GLN cc_start: 0.6759 (pm20) cc_final: 0.6426 (pt0) REVERT: B 362 SER cc_start: 0.7402 (p) cc_final: 0.7175 (p) REVERT: B 373 LYS cc_start: 0.7615 (ttmt) cc_final: 0.6856 (ttmt) REVERT: B 377 LYS cc_start: 0.7915 (mttp) cc_final: 0.7497 (mttp) REVERT: B 392 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7659 (tp) REVERT: B 415 ARG cc_start: 0.7645 (mtt90) cc_final: 0.7195 (mtm-85) REVERT: B 469 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7554 (mm-40) REVERT: B 470 HIS cc_start: 0.7617 (p-80) cc_final: 0.7384 (p-80) REVERT: C 130 GLU cc_start: 0.5837 (pm20) cc_final: 0.5587 (pm20) REVERT: C 206 ARG cc_start: 0.7172 (ttt180) cc_final: 0.6838 (tpp80) REVERT: C 265 LYS cc_start: 0.7587 (mttp) cc_final: 0.7315 (mttp) REVERT: C 389 TYR cc_start: 0.7895 (t80) cc_final: 0.7631 (t80) REVERT: C 484 GLU cc_start: 0.6483 (tt0) cc_final: 0.6250 (tt0) REVERT: D 8 GLN cc_start: 0.6856 (tt0) cc_final: 0.6635 (tt0) REVERT: D 18 PHE cc_start: 0.7304 (m-80) cc_final: 0.6891 (m-80) REVERT: D 35 LYS cc_start: 0.7833 (ttmt) cc_final: 0.7629 (ttmt) REVERT: D 104 ASP cc_start: 0.7486 (p0) cc_final: 0.6877 (p0) REVERT: D 106 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6284 (mt-10) REVERT: D 120 ARG cc_start: 0.6571 (ttt-90) cc_final: 0.6356 (ptt-90) REVERT: D 154 ILE cc_start: 0.7651 (mm) cc_final: 0.7416 (mt) REVERT: D 202 MET cc_start: 0.6542 (mmt) cc_final: 0.6259 (mmt) REVERT: D 207 VAL cc_start: 0.8483 (t) cc_final: 0.7569 (p) REVERT: D 227 ARG cc_start: 0.6351 (mmt180) cc_final: 0.6123 (mmt180) REVERT: D 256 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7515 (mtm110) REVERT: D 267 LEU cc_start: 0.7734 (mm) cc_final: 0.7137 (mt) REVERT: D 294 SER cc_start: 0.7273 (t) cc_final: 0.6687 (p) REVERT: D 308 VAL cc_start: 0.8815 (t) cc_final: 0.8569 (m) REVERT: D 314 THR cc_start: 0.8396 (p) cc_final: 0.8112 (m) REVERT: D 333 ARG cc_start: 0.6673 (ttm110) cc_final: 0.6462 (ttm110) REVERT: D 441 LEU cc_start: 0.8552 (mt) cc_final: 0.8305 (mp) REVERT: D 464 GLU cc_start: 0.7388 (tp30) cc_final: 0.7057 (tp30) REVERT: E 44 ILE cc_start: 0.6756 (tp) cc_final: 0.6453 (tp) REVERT: E 92 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6719 (mt) REVERT: E 101 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: E 188 VAL cc_start: 0.7205 (t) cc_final: 0.7001 (p) REVERT: E 197 ASP cc_start: 0.6381 (t0) cc_final: 0.6030 (t0) REVERT: E 199 TYR cc_start: 0.7950 (t80) cc_final: 0.6906 (t80) REVERT: E 203 LYS cc_start: 0.7879 (tppp) cc_final: 0.7142 (tppp) REVERT: E 207 VAL cc_start: 0.7557 (t) cc_final: 0.7330 (m) REVERT: E 369 LYS cc_start: 0.8141 (mtmm) cc_final: 0.7884 (mttm) REVERT: E 372 GLN cc_start: 0.7595 (mt0) cc_final: 0.7212 (mt0) REVERT: E 380 LEU cc_start: 0.8031 (tp) cc_final: 0.7381 (tp) REVERT: E 384 ILE cc_start: 0.8226 (mt) cc_final: 0.7386 (mt) REVERT: E 410 LEU cc_start: 0.8501 (mt) cc_final: 0.8247 (mt) REVERT: E 450 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6865 (pm20) REVERT: E 453 PHE cc_start: 0.7750 (m-80) cc_final: 0.7282 (m-10) REVERT: E 469 MET cc_start: 0.5739 (OUTLIER) cc_final: 0.5453 (mmm) REVERT: F 202 MET cc_start: 0.6149 (mmp) cc_final: 0.5765 (mmp) REVERT: F 240 ARG cc_start: 0.5515 (OUTLIER) cc_final: 0.5286 (ppt90) REVERT: F 241 ASP cc_start: 0.7053 (m-30) cc_final: 0.6387 (m-30) REVERT: F 285 MET cc_start: 0.6978 (ttp) cc_final: 0.6453 (ttp) REVERT: F 331 LEU cc_start: 0.7678 (mt) cc_final: 0.7211 (mp) REVERT: F 377 TYR cc_start: 0.7926 (t80) cc_final: 0.7662 (t80) REVERT: F 389 MET cc_start: 0.6152 (mmm) cc_final: 0.5859 (mmm) REVERT: G 11 LYS cc_start: 0.8753 (tptt) cc_final: 0.8196 (tppt) REVERT: G 15 ASN cc_start: 0.8422 (m-40) cc_final: 0.8133 (m110) REVERT: G 22 GLN cc_start: 0.7854 (tt0) cc_final: 0.7629 (tm-30) REVERT: G 33 SER cc_start: 0.8339 (t) cc_final: 0.8115 (p) REVERT: G 43 LYS cc_start: 0.8570 (ttpt) cc_final: 0.8309 (ttpt) REVERT: G 48 TYR cc_start: 0.7609 (t80) cc_final: 0.7352 (t80) REVERT: G 70 MET cc_start: 0.7872 (mmp) cc_final: 0.7497 (mmp) REVERT: G 94 TYR cc_start: 0.6977 (t80) cc_final: 0.6681 (t80) REVERT: G 104 GLN cc_start: 0.8188 (mt0) cc_final: 0.7923 (mt0) REVERT: G 132 ARG cc_start: 0.7754 (mmp80) cc_final: 0.7390 (mmm-85) REVERT: G 148 SER cc_start: 0.8765 (m) cc_final: 0.8434 (p) REVERT: G 222 GLN cc_start: 0.7853 (mt0) cc_final: 0.7631 (mt0) REVERT: G 239 GLU cc_start: 0.7556 (tt0) cc_final: 0.7285 (tt0) REVERT: G 269 ARG cc_start: 0.7351 (ttp80) cc_final: 0.6994 (ttp80) REVERT: G 275 GLN cc_start: 0.7662 (tp40) cc_final: 0.6316 (tp40) REVERT: G 278 THR cc_start: 0.7926 (p) cc_final: 0.7412 (p) REVERT: G 279 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6515 (mm-30) outliers start: 140 outliers final: 58 residues processed: 1049 average time/residue: 0.3892 time to fit residues: 606.1497 Evaluate side-chains 1024 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 958 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 397 LYS Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 273 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 234 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 282 optimal weight: 6.9990 chunk 304 optimal weight: 6.9990 chunk 251 optimal weight: 10.0000 chunk 279 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 433 GLN A 469 GLN B 467 ASN B 474 HIS ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN C 469 GLN ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS D 200 HIS D 401 HIS ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 HIS F 174 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN G 253 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 24608 Z= 0.426 Angle : 0.800 17.222 33370 Z= 0.429 Chirality : 0.053 0.355 3840 Planarity : 0.006 0.084 4349 Dihedral : 9.747 87.330 3589 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.43 % Rotamer: Outliers : 6.18 % Allowed : 23.92 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3104 helix: 0.10 (0.14), residues: 1271 sheet: -0.14 (0.23), residues: 493 loop : -1.13 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS E 119 PHE 0.028 0.003 PHE A 463 TYR 0.033 0.003 TYR G 103 ARG 0.011 0.001 ARG C 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1002 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6489 (mm-30) REVERT: A 93 ARG cc_start: 0.7283 (ttm-80) cc_final: 0.6599 (ttm-80) REVERT: A 154 ASP cc_start: 0.7767 (m-30) cc_final: 0.7422 (t0) REVERT: A 156 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7146 (mt) REVERT: A 164 ARG cc_start: 0.6718 (mtm110) cc_final: 0.6462 (mtm-85) REVERT: A 167 ILE cc_start: 0.8243 (mt) cc_final: 0.8040 (mm) REVERT: A 424 LEU cc_start: 0.7615 (tp) cc_final: 0.7159 (tp) REVERT: A 432 LYS cc_start: 0.7931 (mttt) cc_final: 0.7256 (mtpp) REVERT: A 448 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7470 (mm) REVERT: A 456 PHE cc_start: 0.7704 (t80) cc_final: 0.7426 (t80) REVERT: A 476 ARG cc_start: 0.7376 (tpm170) cc_final: 0.7148 (tpm170) REVERT: A 492 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7552 (mm-30) REVERT: B 36 ASP cc_start: 0.4856 (t0) cc_final: 0.4609 (t0) REVERT: B 38 ILE cc_start: 0.7899 (mp) cc_final: 0.7646 (mt) REVERT: B 181 ASP cc_start: 0.6952 (t70) cc_final: 0.6674 (t0) REVERT: B 275 LEU cc_start: 0.8344 (mt) cc_final: 0.8122 (mp) REVERT: B 284 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: B 305 SER cc_start: 0.7274 (m) cc_final: 0.7073 (m) REVERT: B 333 ASN cc_start: 0.7961 (t0) cc_final: 0.7570 (t0) REVERT: B 341 GLN cc_start: 0.6723 (OUTLIER) cc_final: 0.6509 (pt0) REVERT: B 342 ILE cc_start: 0.7797 (mt) cc_final: 0.7580 (mt) REVERT: B 373 LYS cc_start: 0.7659 (ttmt) cc_final: 0.7143 (ttmt) REVERT: B 419 VAL cc_start: 0.8341 (t) cc_final: 0.7932 (m) REVERT: B 423 ASP cc_start: 0.7415 (p0) cc_final: 0.6518 (p0) REVERT: B 463 PHE cc_start: 0.8131 (t80) cc_final: 0.7825 (t80) REVERT: B 469 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7568 (mm-40) REVERT: C 52 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7132 (mt) REVERT: C 206 ARG cc_start: 0.7283 (ttt180) cc_final: 0.6950 (tpp80) REVERT: C 265 LYS cc_start: 0.7630 (mttp) cc_final: 0.7374 (mttp) REVERT: C 377 LYS cc_start: 0.7767 (tttp) cc_final: 0.7536 (tttp) REVERT: C 389 TYR cc_start: 0.8180 (t80) cc_final: 0.7727 (t80) REVERT: C 402 LEU cc_start: 0.7171 (mm) cc_final: 0.6942 (mt) REVERT: C 484 GLU cc_start: 0.6686 (tt0) cc_final: 0.6274 (tt0) REVERT: C 488 ASN cc_start: 0.7379 (m110) cc_final: 0.7011 (m110) REVERT: D 35 LYS cc_start: 0.7928 (ttmt) cc_final: 0.7684 (ttmt) REVERT: D 97 ASN cc_start: 0.7088 (p0) cc_final: 0.6856 (p0) REVERT: D 104 ASP cc_start: 0.7155 (p0) cc_final: 0.6479 (p0) REVERT: D 106 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6359 (mt-10) REVERT: D 202 MET cc_start: 0.6747 (mmt) cc_final: 0.6429 (mmt) REVERT: D 207 VAL cc_start: 0.8595 (t) cc_final: 0.7406 (p) REVERT: D 256 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7579 (mtt90) REVERT: D 294 SER cc_start: 0.7301 (t) cc_final: 0.6712 (p) REVERT: D 333 ARG cc_start: 0.6615 (ttm110) cc_final: 0.6304 (ttm110) REVERT: D 340 ILE cc_start: 0.8590 (pt) cc_final: 0.8306 (mt) REVERT: D 347 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7169 (mt) REVERT: D 381 GLN cc_start: 0.7341 (pm20) cc_final: 0.7066 (pm20) REVERT: D 441 LEU cc_start: 0.8609 (mt) cc_final: 0.8404 (mp) REVERT: D 464 GLU cc_start: 0.7422 (tp30) cc_final: 0.7105 (tp30) REVERT: E 101 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: E 197 ASP cc_start: 0.6586 (t0) cc_final: 0.6168 (t0) REVERT: E 199 TYR cc_start: 0.7977 (t80) cc_final: 0.7764 (t80) REVERT: E 201 GLU cc_start: 0.7206 (tp30) cc_final: 0.6950 (tp30) REVERT: E 203 LYS cc_start: 0.8103 (tppp) cc_final: 0.7815 (tppp) REVERT: E 207 VAL cc_start: 0.7876 (t) cc_final: 0.7597 (m) REVERT: E 291 ARG cc_start: 0.7025 (mtt180) cc_final: 0.6637 (mtt180) REVERT: E 352 ARG cc_start: 0.7668 (tmm-80) cc_final: 0.7134 (ttt-90) REVERT: E 369 LYS cc_start: 0.8255 (mtmm) cc_final: 0.7970 (mttm) REVERT: E 372 GLN cc_start: 0.7576 (mt0) cc_final: 0.7151 (mt0) REVERT: E 378 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7729 (tmmm) REVERT: E 380 LEU cc_start: 0.8091 (tp) cc_final: 0.7745 (pp) REVERT: E 384 ILE cc_start: 0.8217 (mt) cc_final: 0.7646 (mt) REVERT: E 391 GLU cc_start: 0.6015 (OUTLIER) cc_final: 0.5767 (tm-30) REVERT: E 442 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7810 (mt-10) REVERT: E 453 PHE cc_start: 0.7869 (m-80) cc_final: 0.7388 (m-10) REVERT: E 460 GLU cc_start: 0.7511 (mp0) cc_final: 0.7297 (mp0) REVERT: E 469 MET cc_start: 0.5828 (mmm) cc_final: 0.5559 (mmm) REVERT: F 54 LEU cc_start: 0.7476 (mt) cc_final: 0.7255 (mt) REVERT: F 201 GLU cc_start: 0.6844 (tp30) cc_final: 0.6536 (tp30) REVERT: F 202 MET cc_start: 0.6235 (mmp) cc_final: 0.5891 (mmp) REVERT: F 240 ARG cc_start: 0.5754 (OUTLIER) cc_final: 0.5412 (ppt90) REVERT: F 241 ASP cc_start: 0.7154 (m-30) cc_final: 0.6305 (m-30) REVERT: F 285 MET cc_start: 0.6973 (ttp) cc_final: 0.6471 (ttp) REVERT: F 306 ILE cc_start: 0.7683 (mp) cc_final: 0.7438 (mp) REVERT: F 354 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6767 (tp) REVERT: F 389 MET cc_start: 0.6361 (mmm) cc_final: 0.6127 (mmm) REVERT: F 398 LEU cc_start: 0.8579 (mm) cc_final: 0.8373 (mp) REVERT: F 435 ARG cc_start: 0.7102 (mtp-110) cc_final: 0.6723 (mtm110) REVERT: F 442 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6825 (mt-10) REVERT: F 456 VAL cc_start: 0.7431 (p) cc_final: 0.7001 (m) REVERT: G 11 LYS cc_start: 0.8785 (tptt) cc_final: 0.8341 (tppt) REVERT: G 15 ASN cc_start: 0.8454 (m-40) cc_final: 0.8139 (m110) REVERT: G 22 GLN cc_start: 0.7805 (tt0) cc_final: 0.7562 (tm-30) REVERT: G 33 SER cc_start: 0.8331 (t) cc_final: 0.8055 (p) REVERT: G 43 LYS cc_start: 0.8439 (ttpt) cc_final: 0.8147 (ttpt) REVERT: G 48 TYR cc_start: 0.7623 (t80) cc_final: 0.7342 (t80) REVERT: G 103 TYR cc_start: 0.7534 (t80) cc_final: 0.7049 (t80) REVERT: G 104 GLN cc_start: 0.8189 (mt0) cc_final: 0.7947 (mt0) REVERT: G 132 ARG cc_start: 0.7857 (mmp80) cc_final: 0.7155 (mmm-85) REVERT: G 146 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.7140 (pp30) REVERT: G 148 SER cc_start: 0.8561 (m) cc_final: 0.8169 (p) REVERT: G 183 GLN cc_start: 0.7354 (pp30) cc_final: 0.6286 (pp30) REVERT: G 185 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6360 (mm-30) REVERT: G 222 GLN cc_start: 0.7922 (mt0) cc_final: 0.7652 (mt0) REVERT: G 239 GLU cc_start: 0.7656 (tt0) cc_final: 0.7454 (tt0) REVERT: G 267 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7513 (ttm-80) REVERT: G 269 ARG cc_start: 0.7439 (ttp80) cc_final: 0.7051 (ttp80) REVERT: G 279 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6743 (mm-30) outliers start: 158 outliers final: 102 residues processed: 1073 average time/residue: 0.3861 time to fit residues: 616.3221 Evaluate side-chains 1082 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 968 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 273 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 299 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 268 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 215 HIS A 294 HIS A 397 GLN A 433 GLN B 69 ASN B 426 GLN ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 HIS C 185 ASN D 200 HIS D 289 GLN ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN F 119 HIS ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN G 107 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24608 Z= 0.236 Angle : 0.679 18.861 33370 Z= 0.355 Chirality : 0.048 0.365 3840 Planarity : 0.006 0.070 4349 Dihedral : 9.226 88.807 3582 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 6.37 % Allowed : 26.43 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3104 helix: 0.54 (0.14), residues: 1281 sheet: 0.07 (0.23), residues: 490 loop : -1.10 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS F 179 PHE 0.021 0.002 PHE D 255 TYR 0.028 0.002 TYR G 103 ARG 0.007 0.001 ARG E 458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 992 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6537 (mm-30) REVERT: A 154 ASP cc_start: 0.7862 (m-30) cc_final: 0.7517 (t0) REVERT: A 157 VAL cc_start: 0.8157 (t) cc_final: 0.7870 (m) REVERT: A 164 ARG cc_start: 0.6656 (mtm110) cc_final: 0.6456 (mtm110) REVERT: A 176 THR cc_start: 0.7183 (OUTLIER) cc_final: 0.6659 (p) REVERT: A 181 ASP cc_start: 0.6961 (m-30) cc_final: 0.6712 (m-30) REVERT: A 283 ARG cc_start: 0.7105 (ttm110) cc_final: 0.6773 (mtp85) REVERT: A 365 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6833 (mtt-85) REVERT: A 415 ARG cc_start: 0.7792 (mtt90) cc_final: 0.7378 (mtt90) REVERT: A 448 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7299 (mm) REVERT: A 456 PHE cc_start: 0.7632 (t80) cc_final: 0.7335 (t80) REVERT: A 476 ARG cc_start: 0.7244 (tpm170) cc_final: 0.7024 (tpp-160) REVERT: A 492 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7492 (mm-30) REVERT: A 496 LYS cc_start: 0.8490 (mmtt) cc_final: 0.8251 (mmtt) REVERT: B 38 ILE cc_start: 0.7809 (mp) cc_final: 0.7564 (mt) REVERT: B 83 LYS cc_start: 0.7031 (mtmt) cc_final: 0.6741 (mtmt) REVERT: B 96 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6403 (mt-10) REVERT: B 171 ARG cc_start: 0.6777 (mtp-110) cc_final: 0.6558 (mtp85) REVERT: B 181 ASP cc_start: 0.6848 (t70) cc_final: 0.6580 (t0) REVERT: B 333 ASN cc_start: 0.7877 (t0) cc_final: 0.7515 (t0) REVERT: B 362 SER cc_start: 0.7479 (p) cc_final: 0.7249 (p) REVERT: B 373 LYS cc_start: 0.7586 (ttmt) cc_final: 0.7047 (ttmt) REVERT: B 392 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7715 (tp) REVERT: B 415 ARG cc_start: 0.7230 (mtt90) cc_final: 0.6886 (mmt90) REVERT: B 460 PHE cc_start: 0.7075 (t80) cc_final: 0.6861 (t80) REVERT: B 463 PHE cc_start: 0.8212 (t80) cc_final: 0.7869 (t80) REVERT: B 474 HIS cc_start: 0.7205 (t-90) cc_final: 0.6993 (t-170) REVERT: C 52 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6996 (mt) REVERT: C 184 ILE cc_start: 0.8736 (mt) cc_final: 0.8511 (mm) REVERT: C 206 ARG cc_start: 0.7207 (ttt180) cc_final: 0.6948 (tpp80) REVERT: C 377 LYS cc_start: 0.7735 (tttp) cc_final: 0.7510 (tttp) REVERT: C 389 TYR cc_start: 0.8072 (t80) cc_final: 0.7765 (t80) REVERT: C 433 GLN cc_start: 0.7853 (mt0) cc_final: 0.7615 (mt0) REVERT: C 484 GLU cc_start: 0.6598 (tt0) cc_final: 0.6103 (tt0) REVERT: C 488 ASN cc_start: 0.7278 (m110) cc_final: 0.6889 (m110) REVERT: D 35 LYS cc_start: 0.7922 (ttmt) cc_final: 0.7567 (ttmt) REVERT: D 97 ASN cc_start: 0.7093 (p0) cc_final: 0.6865 (p0) REVERT: D 120 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6306 (ptt-90) REVERT: D 202 MET cc_start: 0.6677 (mmt) cc_final: 0.6363 (mmt) REVERT: D 203 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7682 (ttmm) REVERT: D 207 VAL cc_start: 0.8631 (t) cc_final: 0.7264 (p) REVERT: D 256 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.7534 (mtt90) REVERT: D 267 LEU cc_start: 0.7655 (mm) cc_final: 0.7095 (mt) REVERT: D 294 SER cc_start: 0.7196 (t) cc_final: 0.6595 (p) REVERT: D 333 ARG cc_start: 0.6573 (ttm110) cc_final: 0.6279 (ttm110) REVERT: D 340 ILE cc_start: 0.8537 (pt) cc_final: 0.8177 (mm) REVERT: D 378 LYS cc_start: 0.8079 (tttt) cc_final: 0.7345 (mtpp) REVERT: D 381 GLN cc_start: 0.7287 (pm20) cc_final: 0.7000 (pm20) REVERT: D 394 ASP cc_start: 0.7603 (m-30) cc_final: 0.7368 (m-30) REVERT: D 439 GLU cc_start: 0.5970 (mm-30) cc_final: 0.5764 (mm-30) REVERT: D 441 LEU cc_start: 0.8541 (mt) cc_final: 0.8334 (mp) REVERT: D 464 GLU cc_start: 0.7373 (tp30) cc_final: 0.7056 (tp30) REVERT: E 26 ILE cc_start: 0.8581 (mt) cc_final: 0.8320 (tt) REVERT: E 101 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: E 201 GLU cc_start: 0.7174 (tp30) cc_final: 0.6970 (tp30) REVERT: E 203 LYS cc_start: 0.8024 (tppp) cc_final: 0.7568 (tppp) REVERT: E 207 VAL cc_start: 0.7647 (t) cc_final: 0.7327 (m) REVERT: E 248 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6560 (tp) REVERT: E 291 ARG cc_start: 0.6947 (mtt180) cc_final: 0.6723 (mtt180) REVERT: E 378 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7703 (tmmm) REVERT: E 380 LEU cc_start: 0.8122 (tp) cc_final: 0.7709 (pp) REVERT: E 384 ILE cc_start: 0.8061 (mt) cc_final: 0.7846 (mt) REVERT: E 391 GLU cc_start: 0.5833 (OUTLIER) cc_final: 0.5596 (tm-30) REVERT: E 450 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6852 (pm20) REVERT: E 453 PHE cc_start: 0.7713 (m-80) cc_final: 0.7280 (m-10) REVERT: E 469 MET cc_start: 0.5763 (mmm) cc_final: 0.5496 (mmm) REVERT: F 85 VAL cc_start: 0.7771 (t) cc_final: 0.7404 (p) REVERT: F 234 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.6882 (t) REVERT: F 240 ARG cc_start: 0.5577 (OUTLIER) cc_final: 0.5330 (ppt90) REVERT: F 241 ASP cc_start: 0.7074 (m-30) cc_final: 0.6284 (m-30) REVERT: F 285 MET cc_start: 0.6862 (ttp) cc_final: 0.6385 (ttp) REVERT: F 389 MET cc_start: 0.6404 (mmm) cc_final: 0.6033 (mmm) REVERT: F 398 LEU cc_start: 0.8573 (mm) cc_final: 0.8336 (mp) REVERT: F 435 ARG cc_start: 0.6992 (mtp-110) cc_final: 0.6631 (mtm110) REVERT: F 442 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6784 (mt-10) REVERT: G 15 ASN cc_start: 0.8379 (m-40) cc_final: 0.8084 (m110) REVERT: G 37 ARG cc_start: 0.7519 (ttp80) cc_final: 0.6986 (ttp80) REVERT: G 43 LYS cc_start: 0.8341 (ttpt) cc_final: 0.8013 (ttpt) REVERT: G 48 TYR cc_start: 0.7579 (t80) cc_final: 0.7276 (t80) REVERT: G 103 TYR cc_start: 0.7438 (t80) cc_final: 0.6868 (t80) REVERT: G 105 THR cc_start: 0.8324 (m) cc_final: 0.8101 (t) REVERT: G 132 ARG cc_start: 0.7788 (mmp80) cc_final: 0.7506 (mmm-85) REVERT: G 146 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.7101 (pp30) REVERT: G 148 SER cc_start: 0.8716 (m) cc_final: 0.8327 (p) REVERT: G 153 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7343 (tttm) REVERT: G 183 GLN cc_start: 0.7363 (pp30) cc_final: 0.6925 (pp30) REVERT: G 222 GLN cc_start: 0.7879 (mt0) cc_final: 0.7598 (mt0) REVERT: G 239 GLU cc_start: 0.7596 (tt0) cc_final: 0.7395 (tt0) REVERT: G 267 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7459 (ttm-80) REVERT: G 269 ARG cc_start: 0.7439 (ttp80) cc_final: 0.7025 (ttp80) REVERT: G 279 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6577 (mm-30) outliers start: 163 outliers final: 95 residues processed: 1062 average time/residue: 0.3976 time to fit residues: 631.7492 Evaluate side-chains 1088 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 977 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 200 HIS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 267 ARG Chi-restraints excluded: chain G residue 273 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 223 optimal weight: 0.0980 chunk 123 optimal weight: 7.9990 chunk 255 optimal weight: 0.4980 chunk 207 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 268 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN A 433 GLN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS C 185 ASN C 407 GLN D 200 HIS ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN F 8 GLN F 22 HIS F 40 ASN ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS G 285 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24608 Z= 0.246 Angle : 0.675 18.611 33370 Z= 0.351 Chirality : 0.048 0.325 3840 Planarity : 0.005 0.070 4349 Dihedral : 9.016 86.836 3582 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.78 % Rotamer: Outliers : 6.80 % Allowed : 27.56 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3104 helix: 0.63 (0.14), residues: 1276 sheet: 0.01 (0.23), residues: 492 loop : -1.04 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS F 179 PHE 0.027 0.002 PHE A 398 TYR 0.028 0.002 TYR G 229 ARG 0.009 0.001 ARG B 476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 964 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7361 (mp) REVERT: A 87 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6563 (mm-30) REVERT: A 154 ASP cc_start: 0.7838 (m-30) cc_final: 0.7543 (t0) REVERT: A 164 ARG cc_start: 0.6658 (mtm110) cc_final: 0.6439 (mtm110) REVERT: A 215 HIS cc_start: 0.7057 (OUTLIER) cc_final: 0.6053 (t-90) REVERT: A 283 ARG cc_start: 0.7122 (ttm110) cc_final: 0.6756 (mtp85) REVERT: A 349 PHE cc_start: 0.7913 (t80) cc_final: 0.7708 (t80) REVERT: A 365 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6833 (mtt-85) REVERT: A 420 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7666 (mm) REVERT: A 424 LEU cc_start: 0.7295 (tp) cc_final: 0.6867 (tp) REVERT: A 448 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7486 (mm) REVERT: A 456 PHE cc_start: 0.7665 (t80) cc_final: 0.7366 (t80) REVERT: A 476 ARG cc_start: 0.7212 (tpm170) cc_final: 0.6996 (tpp-160) REVERT: A 492 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7578 (mm-30) REVERT: A 496 LYS cc_start: 0.8563 (mmtt) cc_final: 0.8325 (mmtt) REVERT: B 38 ILE cc_start: 0.7872 (mp) cc_final: 0.7648 (mt) REVERT: B 83 LYS cc_start: 0.6943 (mtmt) cc_final: 0.6688 (mtmt) REVERT: B 181 ASP cc_start: 0.6918 (t70) cc_final: 0.6650 (t0) REVERT: B 275 LEU cc_start: 0.8362 (mt) cc_final: 0.8092 (mp) REVERT: B 333 ASN cc_start: 0.7908 (t0) cc_final: 0.7529 (t0) REVERT: B 341 GLN cc_start: 0.6649 (pt0) cc_final: 0.6388 (pt0) REVERT: B 362 SER cc_start: 0.7389 (p) cc_final: 0.7185 (p) REVERT: B 364 SER cc_start: 0.8054 (p) cc_final: 0.7826 (t) REVERT: B 373 LYS cc_start: 0.7543 (ttmt) cc_final: 0.6960 (ttmt) REVERT: B 377 LYS cc_start: 0.7968 (mttp) cc_final: 0.7597 (mttp) REVERT: B 392 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7706 (tp) REVERT: B 461 TYR cc_start: 0.7157 (m-10) cc_final: 0.6936 (m-10) REVERT: B 463 PHE cc_start: 0.8252 (t80) cc_final: 0.7981 (t80) REVERT: C 52 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6996 (mt) REVERT: C 206 ARG cc_start: 0.7229 (ttt180) cc_final: 0.6983 (tpp-160) REVERT: C 376 LYS cc_start: 0.7430 (mmmt) cc_final: 0.7216 (mmmm) REVERT: C 377 LYS cc_start: 0.7830 (tttp) cc_final: 0.7610 (tttp) REVERT: C 389 TYR cc_start: 0.8079 (t80) cc_final: 0.7793 (t80) REVERT: C 404 LYS cc_start: 0.7695 (mmtt) cc_final: 0.7354 (mmtt) REVERT: C 407 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7256 (mt0) REVERT: C 484 GLU cc_start: 0.6616 (tt0) cc_final: 0.6143 (tt0) REVERT: C 488 ASN cc_start: 0.7293 (m110) cc_final: 0.6928 (m110) REVERT: D 35 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7608 (ttmt) REVERT: D 97 ASN cc_start: 0.7068 (p0) cc_final: 0.6845 (p0) REVERT: D 120 ARG cc_start: 0.6632 (OUTLIER) cc_final: 0.6390 (ptt-90) REVERT: D 202 MET cc_start: 0.6741 (mmt) cc_final: 0.6394 (mmt) REVERT: D 203 LYS cc_start: 0.7908 (ttmt) cc_final: 0.7666 (ttmm) REVERT: D 207 VAL cc_start: 0.8650 (t) cc_final: 0.7221 (p) REVERT: D 233 LEU cc_start: 0.7531 (tp) cc_final: 0.7302 (tp) REVERT: D 256 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7535 (mtt90) REVERT: D 267 LEU cc_start: 0.7677 (mm) cc_final: 0.7087 (mt) REVERT: D 294 SER cc_start: 0.7200 (t) cc_final: 0.6586 (p) REVERT: D 333 ARG cc_start: 0.6516 (ttm110) cc_final: 0.6278 (ttm110) REVERT: D 378 LYS cc_start: 0.8132 (tttt) cc_final: 0.7398 (mtpp) REVERT: D 428 VAL cc_start: 0.6193 (OUTLIER) cc_final: 0.5227 (p) REVERT: D 439 GLU cc_start: 0.6139 (mm-30) cc_final: 0.5917 (mm-30) REVERT: D 441 LEU cc_start: 0.8581 (mt) cc_final: 0.8359 (mp) REVERT: D 464 GLU cc_start: 0.7385 (tp30) cc_final: 0.7058 (tp30) REVERT: D 465 LYS cc_start: 0.8226 (tttt) cc_final: 0.7997 (tttt) REVERT: E 26 ILE cc_start: 0.8595 (mt) cc_final: 0.8334 (tt) REVERT: E 112 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6803 (m-30) REVERT: E 207 VAL cc_start: 0.7772 (t) cc_final: 0.6855 (m) REVERT: E 248 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6576 (tp) REVERT: E 291 ARG cc_start: 0.7048 (mtt180) cc_final: 0.6739 (mtt180) REVERT: E 369 LYS cc_start: 0.8073 (mttt) cc_final: 0.7791 (mtmm) REVERT: E 378 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7708 (tmmm) REVERT: E 380 LEU cc_start: 0.8142 (tp) cc_final: 0.7652 (pp) REVERT: E 453 PHE cc_start: 0.7684 (m-80) cc_final: 0.7230 (m-10) REVERT: E 458 ARG cc_start: 0.6777 (mtm110) cc_final: 0.6277 (ptm-80) REVERT: E 469 MET cc_start: 0.5784 (mmm) cc_final: 0.5472 (mmm) REVERT: F 85 VAL cc_start: 0.7769 (t) cc_final: 0.7389 (p) REVERT: F 234 THR cc_start: 0.7578 (OUTLIER) cc_final: 0.6909 (t) REVERT: F 240 ARG cc_start: 0.5626 (OUTLIER) cc_final: 0.5360 (ppt90) REVERT: F 241 ASP cc_start: 0.7070 (m-30) cc_final: 0.6238 (m-30) REVERT: F 278 GLN cc_start: 0.7528 (pm20) cc_final: 0.7303 (pm20) REVERT: F 285 MET cc_start: 0.6923 (ttp) cc_final: 0.6447 (ttp) REVERT: F 330 ASN cc_start: 0.6008 (m-40) cc_final: 0.5718 (m-40) REVERT: F 354 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6413 (tp) REVERT: F 435 ARG cc_start: 0.6970 (mtp-110) cc_final: 0.6660 (mtm110) REVERT: F 442 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6864 (mt-10) REVERT: G 15 ASN cc_start: 0.8388 (m-40) cc_final: 0.8149 (m110) REVERT: G 29 MET cc_start: 0.7363 (mmm) cc_final: 0.7135 (mmm) REVERT: G 37 ARG cc_start: 0.7507 (ttp80) cc_final: 0.7092 (ttp80) REVERT: G 43 LYS cc_start: 0.8302 (ttpt) cc_final: 0.8010 (ttpt) REVERT: G 48 TYR cc_start: 0.7583 (t80) cc_final: 0.7281 (t80) REVERT: G 97 ASN cc_start: 0.7731 (m-40) cc_final: 0.7511 (m-40) REVERT: G 103 TYR cc_start: 0.7381 (t80) cc_final: 0.6794 (t80) REVERT: G 132 ARG cc_start: 0.7731 (mmp80) cc_final: 0.7159 (mmm-85) REVERT: G 146 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7079 (pp30) REVERT: G 148 SER cc_start: 0.8710 (m) cc_final: 0.8393 (p) REVERT: G 153 LYS cc_start: 0.7740 (tttm) cc_final: 0.7399 (tttm) REVERT: G 183 GLN cc_start: 0.7280 (pp30) cc_final: 0.6553 (pp30) REVERT: G 222 GLN cc_start: 0.7901 (mt0) cc_final: 0.7600 (mt0) REVERT: G 269 ARG cc_start: 0.7449 (ttp80) cc_final: 0.7022 (ttp80) outliers start: 174 outliers final: 119 residues processed: 1044 average time/residue: 0.3567 time to fit residues: 555.4734 Evaluate side-chains 1073 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 937 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 324 HIS Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 267 ARG Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 285 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 6.9990 chunk 269 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 299 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 157 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 397 GLN A 425 HIS A 433 GLN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 GLN D 304 GLN ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS G 285 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 24608 Z= 0.370 Angle : 0.743 18.492 33370 Z= 0.392 Chirality : 0.050 0.329 3840 Planarity : 0.006 0.073 4349 Dihedral : 9.143 84.709 3579 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.19 % Favored : 94.78 % Rotamer: Outliers : 7.31 % Allowed : 28.77 % Favored : 63.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3104 helix: 0.26 (0.14), residues: 1287 sheet: -0.12 (0.23), residues: 497 loop : -1.16 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.002 HIS F 324 PHE 0.028 0.002 PHE A 463 TYR 0.028 0.002 TYR F 199 ARG 0.012 0.001 ARG E 333 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 959 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7513 (mp) REVERT: A 67 GLU cc_start: 0.6518 (mm-30) cc_final: 0.6316 (mm-30) REVERT: A 87 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6560 (mm-30) REVERT: A 154 ASP cc_start: 0.7897 (m-30) cc_final: 0.7608 (t0) REVERT: A 157 VAL cc_start: 0.8257 (OUTLIER) cc_final: 0.7816 (p) REVERT: A 164 ARG cc_start: 0.6719 (mtm110) cc_final: 0.6479 (mtm110) REVERT: A 190 ASN cc_start: 0.7376 (m-40) cc_final: 0.7138 (m-40) REVERT: A 215 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6189 (t-90) REVERT: A 317 PRO cc_start: 0.8363 (Cg_endo) cc_final: 0.8106 (Cg_exo) REVERT: A 349 PHE cc_start: 0.7951 (t80) cc_final: 0.7740 (t80) REVERT: A 365 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6882 (mmm-85) REVERT: A 383 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6687 (tpt170) REVERT: A 391 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6565 (pt0) REVERT: A 420 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7720 (mm) REVERT: A 424 LEU cc_start: 0.7295 (tp) cc_final: 0.6949 (tp) REVERT: A 456 PHE cc_start: 0.7666 (t80) cc_final: 0.7399 (t80) REVERT: A 476 ARG cc_start: 0.7334 (tpm170) cc_final: 0.7094 (tpp-160) REVERT: A 492 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7539 (mm-30) REVERT: B 38 ILE cc_start: 0.7967 (mp) cc_final: 0.7725 (mt) REVERT: B 181 ASP cc_start: 0.6899 (t70) cc_final: 0.6673 (t0) REVERT: B 333 ASN cc_start: 0.7953 (t0) cc_final: 0.7523 (t0) REVERT: B 341 GLN cc_start: 0.6620 (pt0) cc_final: 0.6391 (pt0) REVERT: B 373 LYS cc_start: 0.7563 (ttmt) cc_final: 0.6981 (ttmt) REVERT: B 377 LYS cc_start: 0.7873 (mttp) cc_final: 0.7552 (mttp) REVERT: B 452 ASP cc_start: 0.7516 (m-30) cc_final: 0.6973 (m-30) REVERT: B 458 LYS cc_start: 0.7349 (tmmt) cc_final: 0.7013 (mttp) REVERT: B 460 PHE cc_start: 0.7166 (t80) cc_final: 0.6895 (t80) REVERT: B 463 PHE cc_start: 0.8279 (t80) cc_final: 0.7958 (t80) REVERT: C 52 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6982 (mt) REVERT: C 184 ILE cc_start: 0.8705 (mt) cc_final: 0.8487 (mm) REVERT: C 206 ARG cc_start: 0.7271 (ttt180) cc_final: 0.7031 (tpp80) REVERT: C 377 LYS cc_start: 0.7846 (tttp) cc_final: 0.7604 (tttp) REVERT: C 389 TYR cc_start: 0.8129 (t80) cc_final: 0.7747 (t80) REVERT: C 407 GLN cc_start: 0.7735 (mt0) cc_final: 0.7462 (mt0) REVERT: C 470 HIS cc_start: 0.7556 (p-80) cc_final: 0.7323 (p90) REVERT: C 484 GLU cc_start: 0.6825 (tt0) cc_final: 0.6359 (tt0) REVERT: C 488 ASN cc_start: 0.7399 (m110) cc_final: 0.7057 (m110) REVERT: D 35 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7583 (ttmt) REVERT: D 97 ASN cc_start: 0.7078 (p0) cc_final: 0.6852 (p0) REVERT: D 120 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.6388 (ptt-90) REVERT: D 185 PHE cc_start: 0.8139 (t80) cc_final: 0.7919 (t80) REVERT: D 202 MET cc_start: 0.6750 (mmt) cc_final: 0.6509 (mmt) REVERT: D 203 LYS cc_start: 0.7930 (ttmt) cc_final: 0.7696 (ttmm) REVERT: D 207 VAL cc_start: 0.8664 (t) cc_final: 0.7925 (p) REVERT: D 227 ARG cc_start: 0.6607 (mmt90) cc_final: 0.6099 (mmt-90) REVERT: D 233 LEU cc_start: 0.7583 (tp) cc_final: 0.7370 (tp) REVERT: D 242 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6577 (mm-30) REVERT: D 256 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7576 (mtt90) REVERT: D 267 LEU cc_start: 0.7783 (mm) cc_final: 0.7220 (mt) REVERT: D 294 SER cc_start: 0.7143 (t) cc_final: 0.6638 (p) REVERT: D 333 ARG cc_start: 0.6560 (ttm110) cc_final: 0.6304 (ttm110) REVERT: D 340 ILE cc_start: 0.8582 (pt) cc_final: 0.8184 (mm) REVERT: D 378 LYS cc_start: 0.8044 (tttt) cc_final: 0.7764 (mtpp) REVERT: D 439 GLU cc_start: 0.6164 (mm-30) cc_final: 0.5932 (mm-30) REVERT: D 441 LEU cc_start: 0.8598 (mt) cc_final: 0.8391 (mp) REVERT: D 464 GLU cc_start: 0.7402 (tp30) cc_final: 0.7056 (tp30) REVERT: D 465 LYS cc_start: 0.8215 (tttt) cc_final: 0.7928 (tttt) REVERT: E 5 ARG cc_start: 0.6512 (ptm-80) cc_final: 0.6259 (ptm-80) REVERT: E 112 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6787 (m-30) REVERT: E 199 TYR cc_start: 0.8023 (t80) cc_final: 0.7675 (t80) REVERT: E 202 MET cc_start: 0.6865 (ttt) cc_final: 0.6567 (ttt) REVERT: E 207 VAL cc_start: 0.7866 (t) cc_final: 0.7102 (m) REVERT: E 248 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6618 (tp) REVERT: E 291 ARG cc_start: 0.7137 (mtt180) cc_final: 0.6850 (mtt180) REVERT: E 314 THR cc_start: 0.7648 (OUTLIER) cc_final: 0.7400 (p) REVERT: E 375 GLN cc_start: 0.7671 (tp40) cc_final: 0.7346 (tp40) REVERT: E 378 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7739 (tmmm) REVERT: E 380 LEU cc_start: 0.8127 (tp) cc_final: 0.7910 (pp) REVERT: E 391 GLU cc_start: 0.5736 (OUTLIER) cc_final: 0.5375 (tm-30) REVERT: E 450 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6989 (pm20) REVERT: E 453 PHE cc_start: 0.7739 (m-80) cc_final: 0.7268 (m-10) REVERT: E 458 ARG cc_start: 0.6847 (mtm110) cc_final: 0.6370 (ptm-80) REVERT: E 469 MET cc_start: 0.5719 (mmm) cc_final: 0.5437 (mmm) REVERT: F 234 THR cc_start: 0.7557 (OUTLIER) cc_final: 0.6910 (t) REVERT: F 240 ARG cc_start: 0.5714 (OUTLIER) cc_final: 0.5408 (ppt90) REVERT: F 241 ASP cc_start: 0.7118 (m-30) cc_final: 0.5979 (m-30) REVERT: F 285 MET cc_start: 0.7071 (ttp) cc_final: 0.6580 (ttp) REVERT: F 330 ASN cc_start: 0.6031 (m-40) cc_final: 0.5731 (m-40) REVERT: F 354 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6482 (tp) REVERT: G 33 SER cc_start: 0.8404 (t) cc_final: 0.8152 (p) REVERT: G 37 ARG cc_start: 0.7577 (ttp80) cc_final: 0.7268 (ttp80) REVERT: G 43 LYS cc_start: 0.8338 (ttpt) cc_final: 0.8055 (ttpt) REVERT: G 48 TYR cc_start: 0.7610 (t80) cc_final: 0.7322 (t80) REVERT: G 70 MET cc_start: 0.7851 (mmp) cc_final: 0.7363 (mmp) REVERT: G 146 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7178 (pp30) REVERT: G 148 SER cc_start: 0.8722 (m) cc_final: 0.8380 (p) REVERT: G 153 LYS cc_start: 0.7795 (tttm) cc_final: 0.7449 (tttm) REVERT: G 183 GLN cc_start: 0.7466 (pp30) cc_final: 0.7226 (pp30) REVERT: G 188 GLU cc_start: 0.6685 (tt0) cc_final: 0.6315 (tt0) REVERT: G 222 GLN cc_start: 0.7960 (mt0) cc_final: 0.7667 (mt0) REVERT: G 269 ARG cc_start: 0.7450 (ttp80) cc_final: 0.7069 (ttp80) outliers start: 187 outliers final: 130 residues processed: 1045 average time/residue: 0.3941 time to fit residues: 613.2149 Evaluate side-chains 1096 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 947 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 215 HIS Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 153 LYS Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 179 HIS Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 381 GLN Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 285 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 252 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 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 230 GLN A 397 GLN A 433 GLN B 215 HIS C 407 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN F 119 HIS F 324 HIS ** G 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24608 Z= 0.212 Angle : 0.682 19.105 33370 Z= 0.351 Chirality : 0.047 0.287 3840 Planarity : 0.005 0.072 4349 Dihedral : 8.766 83.251 3577 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 6.29 % Allowed : 30.53 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3104 helix: 0.68 (0.14), residues: 1272 sheet: -0.00 (0.24), residues: 481 loop : -0.98 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 179 PHE 0.023 0.002 PHE B 236 TYR 0.027 0.001 TYR G 103 ARG 0.012 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 939 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 VAL cc_start: 0.7733 (OUTLIER) cc_final: 0.7427 (p) REVERT: A 87 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6532 (mm-30) REVERT: A 154 ASP cc_start: 0.7874 (m-30) cc_final: 0.7573 (t0) REVERT: A 157 VAL cc_start: 0.8191 (OUTLIER) cc_final: 0.7739 (p) REVERT: A 164 ARG cc_start: 0.6664 (mtm110) cc_final: 0.6455 (mtm110) REVERT: A 190 ASN cc_start: 0.7303 (m-40) cc_final: 0.7015 (m-40) REVERT: A 215 HIS cc_start: 0.7134 (OUTLIER) cc_final: 0.6185 (t-90) REVERT: A 220 TYR cc_start: 0.7294 (p90) cc_final: 0.6967 (p90) REVERT: A 266 GLN cc_start: 0.7407 (tp40) cc_final: 0.6946 (tp40) REVERT: A 283 ARG cc_start: 0.7183 (ttm110) cc_final: 0.6974 (mtp85) REVERT: A 349 PHE cc_start: 0.7900 (t80) cc_final: 0.7693 (t80) REVERT: A 365 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6729 (mmt-90) REVERT: A 391 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6487 (pt0) REVERT: A 420 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7654 (mm) REVERT: A 424 LEU cc_start: 0.7242 (tp) cc_final: 0.6948 (tp) REVERT: A 456 PHE cc_start: 0.7659 (t80) cc_final: 0.7389 (t80) REVERT: A 476 ARG cc_start: 0.7352 (tpm170) cc_final: 0.6898 (tpp-160) REVERT: A 479 LYS cc_start: 0.7621 (mppt) cc_final: 0.6963 (mppt) REVERT: A 492 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7475 (mm-30) REVERT: B 181 ASP cc_start: 0.6853 (t70) cc_final: 0.6593 (t0) REVERT: B 299 GLU cc_start: 0.6188 (OUTLIER) cc_final: 0.5495 (mt-10) REVERT: B 333 ASN cc_start: 0.7891 (t0) cc_final: 0.7495 (t0) REVERT: B 341 GLN cc_start: 0.6554 (pt0) cc_final: 0.6338 (pt0) REVERT: B 373 LYS cc_start: 0.7555 (ttmt) cc_final: 0.6960 (ttmt) REVERT: B 377 LYS cc_start: 0.7827 (mttp) cc_final: 0.7493 (mttp) REVERT: B 432 LYS cc_start: 0.8538 (mttt) cc_final: 0.8165 (mttt) REVERT: B 458 LYS cc_start: 0.7312 (tmmt) cc_final: 0.7009 (mttp) REVERT: B 460 PHE cc_start: 0.7065 (t80) cc_final: 0.6790 (t80) REVERT: B 463 PHE cc_start: 0.8234 (t80) cc_final: 0.7780 (t80) REVERT: C 52 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6923 (mt) REVERT: C 358 ASN cc_start: 0.7753 (t0) cc_final: 0.7479 (p0) REVERT: C 377 LYS cc_start: 0.7817 (tttp) cc_final: 0.7554 (tttp) REVERT: C 389 TYR cc_start: 0.8023 (t80) cc_final: 0.7736 (t80) REVERT: C 435 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7776 (mm) REVERT: C 484 GLU cc_start: 0.6649 (tt0) cc_final: 0.6116 (tt0) REVERT: C 488 ASN cc_start: 0.7333 (m110) cc_final: 0.6962 (m110) REVERT: D 8 GLN cc_start: 0.6694 (tt0) cc_final: 0.6036 (tt0) REVERT: D 35 LYS cc_start: 0.7846 (ttmt) cc_final: 0.7589 (ttmt) REVERT: D 115 ARG cc_start: 0.6257 (mtt-85) cc_final: 0.6032 (mtt-85) REVERT: D 120 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.6370 (ptt-90) REVERT: D 185 PHE cc_start: 0.8065 (t80) cc_final: 0.7800 (t80) REVERT: D 207 VAL cc_start: 0.8668 (t) cc_final: 0.7996 (p) REVERT: D 256 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7493 (mtt90) REVERT: D 267 LEU cc_start: 0.7610 (mm) cc_final: 0.7051 (mt) REVERT: D 294 SER cc_start: 0.7016 (t) cc_final: 0.6514 (p) REVERT: D 333 ARG cc_start: 0.6444 (ttm110) cc_final: 0.6207 (ttm110) REVERT: D 340 ILE cc_start: 0.8551 (pt) cc_final: 0.8198 (mm) REVERT: D 396 ASP cc_start: 0.7324 (m-30) cc_final: 0.7098 (m-30) REVERT: D 405 ARG cc_start: 0.7085 (mpt90) cc_final: 0.6804 (mpt90) REVERT: D 428 VAL cc_start: 0.6192 (OUTLIER) cc_final: 0.5253 (p) REVERT: D 439 GLU cc_start: 0.6021 (mm-30) cc_final: 0.5788 (mm-30) REVERT: D 441 LEU cc_start: 0.8564 (mt) cc_final: 0.8352 (mp) REVERT: D 464 GLU cc_start: 0.7339 (tp30) cc_final: 0.7001 (tp30) REVERT: D 465 LYS cc_start: 0.8201 (tttt) cc_final: 0.7924 (tttt) REVERT: E 112 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6818 (m-30) REVERT: E 207 VAL cc_start: 0.7701 (t) cc_final: 0.6817 (m) REVERT: E 248 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6572 (tp) REVERT: E 291 ARG cc_start: 0.7062 (mtt180) cc_final: 0.6832 (mtt180) REVERT: E 330 ASN cc_start: 0.6674 (m-40) cc_final: 0.6465 (t0) REVERT: E 369 LYS cc_start: 0.7993 (mtmm) cc_final: 0.7699 (mppt) REVERT: E 375 GLN cc_start: 0.7626 (tp40) cc_final: 0.7403 (tp40) REVERT: E 378 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7715 (tmmm) REVERT: E 380 LEU cc_start: 0.8098 (tp) cc_final: 0.7887 (pp) REVERT: E 391 GLU cc_start: 0.5708 (OUTLIER) cc_final: 0.5323 (tm-30) REVERT: E 450 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6996 (pm20) REVERT: E 458 ARG cc_start: 0.6655 (mtm110) cc_final: 0.6211 (ptm-80) REVERT: E 469 MET cc_start: 0.5732 (mmm) cc_final: 0.5399 (mmm) REVERT: F 126 GLU cc_start: 0.7154 (pm20) cc_final: 0.6877 (pm20) REVERT: F 234 THR cc_start: 0.7533 (OUTLIER) cc_final: 0.6931 (t) REVERT: F 240 ARG cc_start: 0.5568 (OUTLIER) cc_final: 0.5339 (ppt90) REVERT: F 241 ASP cc_start: 0.7072 (m-30) cc_final: 0.6262 (m-30) REVERT: F 278 GLN cc_start: 0.7590 (pm20) cc_final: 0.7351 (pm20) REVERT: F 285 MET cc_start: 0.6971 (ttp) cc_final: 0.6545 (ttp) REVERT: F 330 ASN cc_start: 0.5939 (m-40) cc_final: 0.5725 (m-40) REVERT: F 354 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6462 (tp) REVERT: G 37 ARG cc_start: 0.7478 (ttp80) cc_final: 0.7067 (ttp80) REVERT: G 48 TYR cc_start: 0.7575 (t80) cc_final: 0.7249 (t80) REVERT: G 70 MET cc_start: 0.7796 (mmp) cc_final: 0.7270 (mmp) REVERT: G 134 MET cc_start: 0.5498 (mtt) cc_final: 0.5252 (mtt) REVERT: G 146 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.7098 (pp30) REVERT: G 148 SER cc_start: 0.8715 (m) cc_final: 0.8350 (p) REVERT: G 153 LYS cc_start: 0.7731 (tttm) cc_final: 0.7390 (tttm) REVERT: G 183 GLN cc_start: 0.7252 (pp30) cc_final: 0.7006 (pp30) REVERT: G 222 GLN cc_start: 0.7918 (mt0) cc_final: 0.7663 (mt0) REVERT: G 244 MET cc_start: 0.7172 (ttp) cc_final: 0.6886 (ttp) REVERT: G 267 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7470 (ttm-80) REVERT: G 269 ARG cc_start: 0.7437 (ttp80) cc_final: 0.7030 (ttp80) outliers start: 161 outliers final: 107 residues processed: 1019 average time/residue: 0.4010 time to fit residues: 611.2989 Evaluate side-chains 1054 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 926 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 200 HIS Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 153 LYS Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 267 ARG Chi-restraints excluded: chain G residue 273 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 147 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 chunk 234 optimal weight: 7.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 433 GLN C 189 GLN C 407 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 GLN E 174 ASN F 179 HIS F 324 HIS ** G 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 24608 Z= 0.340 Angle : 0.750 18.167 33370 Z= 0.392 Chirality : 0.051 0.341 3840 Planarity : 0.006 0.072 4349 Dihedral : 8.874 89.552 3577 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.39 % Rotamer: Outliers : 6.84 % Allowed : 30.92 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 3104 helix: 0.39 (0.14), residues: 1289 sheet: -0.15 (0.23), residues: 499 loop : -1.13 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS F 401 PHE 0.029 0.002 PHE D 255 TYR 0.022 0.002 TYR G 103 ARG 0.012 0.001 ARG G 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 961 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7535 (mp) REVERT: A 154 ASP cc_start: 0.7889 (m-30) cc_final: 0.7601 (t0) REVERT: A 157 VAL cc_start: 0.8255 (OUTLIER) cc_final: 0.7811 (p) REVERT: A 164 ARG cc_start: 0.6716 (mtm110) cc_final: 0.6414 (mtm110) REVERT: A 190 ASN cc_start: 0.7302 (m-40) cc_final: 0.7062 (m-40) REVERT: A 215 HIS cc_start: 0.7251 (OUTLIER) cc_final: 0.6336 (t-90) REVERT: A 266 GLN cc_start: 0.7491 (tp40) cc_final: 0.6828 (tp40) REVERT: A 300 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6805 (mtt180) REVERT: A 317 PRO cc_start: 0.8328 (Cg_endo) cc_final: 0.8075 (Cg_exo) REVERT: A 349 PHE cc_start: 0.7969 (t80) cc_final: 0.7757 (t80) REVERT: A 365 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6832 (mtt-85) REVERT: A 383 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6748 (tpt170) REVERT: A 391 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6526 (pt0) REVERT: A 420 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7680 (mm) REVERT: A 456 PHE cc_start: 0.7657 (t80) cc_final: 0.7415 (t80) REVERT: A 476 ARG cc_start: 0.7428 (tpm170) cc_final: 0.7147 (tpm170) REVERT: B 76 LEU cc_start: 0.5702 (mp) cc_final: 0.5353 (mp) REVERT: B 136 VAL cc_start: 0.5893 (t) cc_final: 0.4826 (m) REVERT: B 181 ASP cc_start: 0.6904 (t70) cc_final: 0.6679 (t0) REVERT: B 333 ASN cc_start: 0.7990 (t0) cc_final: 0.7543 (t0) REVERT: B 341 GLN cc_start: 0.6535 (pt0) cc_final: 0.6308 (pt0) REVERT: B 373 LYS cc_start: 0.7523 (ttmt) cc_final: 0.6917 (ttmt) REVERT: B 377 LYS cc_start: 0.7894 (mttp) cc_final: 0.7580 (mttp) REVERT: B 422 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: B 432 LYS cc_start: 0.8546 (mttt) cc_final: 0.8128 (mttt) REVERT: B 458 LYS cc_start: 0.7346 (tmmt) cc_final: 0.7056 (mttp) REVERT: B 460 PHE cc_start: 0.7100 (t80) cc_final: 0.6895 (t80) REVERT: B 463 PHE cc_start: 0.8169 (t80) cc_final: 0.7923 (t80) REVERT: C 299 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6516 (tt0) REVERT: C 389 TYR cc_start: 0.8104 (t80) cc_final: 0.7795 (t80) REVERT: C 484 GLU cc_start: 0.6777 (tt0) cc_final: 0.6279 (tt0) REVERT: C 488 ASN cc_start: 0.7415 (m110) cc_final: 0.7071 (m110) REVERT: D 35 LYS cc_start: 0.7864 (ttmt) cc_final: 0.7601 (ttmt) REVERT: D 72 ARG cc_start: 0.7406 (mtm-85) cc_final: 0.7184 (mtm110) REVERT: D 115 ARG cc_start: 0.6405 (mtt-85) cc_final: 0.6164 (mtt-85) REVERT: D 153 LYS cc_start: 0.6525 (OUTLIER) cc_final: 0.6311 (mtmm) REVERT: D 202 MET cc_start: 0.6890 (mmt) cc_final: 0.6418 (mmp) REVERT: D 207 VAL cc_start: 0.8601 (t) cc_final: 0.8170 (p) REVERT: D 256 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7566 (mtt90) REVERT: D 267 LEU cc_start: 0.7756 (mm) cc_final: 0.7170 (mt) REVERT: D 294 SER cc_start: 0.7080 (t) cc_final: 0.6577 (p) REVERT: D 333 ARG cc_start: 0.6519 (ttm110) cc_final: 0.6301 (ttm110) REVERT: D 340 ILE cc_start: 0.8587 (pt) cc_final: 0.8240 (mm) REVERT: D 381 GLN cc_start: 0.7341 (pm20) cc_final: 0.7019 (pm20) REVERT: D 382 ASP cc_start: 0.7758 (p0) cc_final: 0.7497 (p0) REVERT: D 396 ASP cc_start: 0.7415 (m-30) cc_final: 0.7151 (m-30) REVERT: D 405 ARG cc_start: 0.7211 (mpt90) cc_final: 0.6958 (mpt90) REVERT: D 439 GLU cc_start: 0.6154 (mm-30) cc_final: 0.5894 (mm-30) REVERT: D 441 LEU cc_start: 0.8593 (mt) cc_final: 0.8380 (mp) REVERT: D 464 GLU cc_start: 0.7369 (tp30) cc_final: 0.7019 (tp30) REVERT: D 465 LYS cc_start: 0.8268 (tttt) cc_final: 0.7987 (tttt) REVERT: E 112 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6795 (m-30) REVERT: E 202 MET cc_start: 0.6682 (ttt) cc_final: 0.6481 (tmt) REVERT: E 248 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6674 (tp) REVERT: E 314 THR cc_start: 0.7658 (p) cc_final: 0.7452 (p) REVERT: E 369 LYS cc_start: 0.8097 (mtmm) cc_final: 0.7775 (mtmm) REVERT: E 378 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7717 (tmmm) REVERT: E 391 GLU cc_start: 0.5720 (OUTLIER) cc_final: 0.5358 (tm-30) REVERT: E 450 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7026 (pm20) REVERT: E 469 MET cc_start: 0.5709 (mmm) cc_final: 0.5379 (mmm) REVERT: F 85 VAL cc_start: 0.7637 (t) cc_final: 0.7327 (p) REVERT: F 126 GLU cc_start: 0.7157 (pm20) cc_final: 0.6830 (pm20) REVERT: F 234 THR cc_start: 0.7553 (OUTLIER) cc_final: 0.6910 (t) REVERT: F 240 ARG cc_start: 0.5718 (OUTLIER) cc_final: 0.5441 (ppt90) REVERT: F 241 ASP cc_start: 0.7133 (m-30) cc_final: 0.6061 (m-30) REVERT: F 285 MET cc_start: 0.7039 (ttp) cc_final: 0.6596 (ttp) REVERT: F 330 ASN cc_start: 0.5974 (m-40) cc_final: 0.5730 (m-40) REVERT: F 354 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6566 (tp) REVERT: F 389 MET cc_start: 0.6771 (mmm) cc_final: 0.6424 (mmm) REVERT: G 37 ARG cc_start: 0.7540 (ttp80) cc_final: 0.7224 (ttp80) REVERT: G 48 TYR cc_start: 0.7606 (t80) cc_final: 0.7248 (t80) REVERT: G 70 MET cc_start: 0.7877 (mmp) cc_final: 0.7252 (mmp) REVERT: G 134 MET cc_start: 0.5473 (mtt) cc_final: 0.5246 (mtt) REVERT: G 146 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7201 (pp30) REVERT: G 148 SER cc_start: 0.8762 (m) cc_final: 0.8405 (p) REVERT: G 153 LYS cc_start: 0.7760 (tttm) cc_final: 0.7419 (tttm) REVERT: G 155 ILE cc_start: 0.8222 (mp) cc_final: 0.7970 (mt) REVERT: G 183 GLN cc_start: 0.7393 (pp30) cc_final: 0.6642 (pp30) REVERT: G 222 GLN cc_start: 0.8003 (mt0) cc_final: 0.7732 (mt0) REVERT: G 244 MET cc_start: 0.7232 (ttp) cc_final: 0.6979 (ttp) REVERT: G 265 TYR cc_start: 0.7939 (t80) cc_final: 0.7685 (t80) REVERT: G 269 ARG cc_start: 0.7442 (ttp80) cc_final: 0.7111 (ttp80) outliers start: 175 outliers final: 129 residues processed: 1038 average time/residue: 0.3984 time to fit residues: 616.8604 Evaluate side-chains 1093 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 945 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 215 HIS Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 245 GLN Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 435 ARG Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 179 HIS Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 324 HIS Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 239 GLU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 285 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 1.9990 chunk 286 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 278 optimal weight: 0.7980 chunk 167 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 218 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 chunk 263 optimal weight: 5.9990 chunk 277 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 433 GLN C 407 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 GLN E 174 ASN F 174 ASN F 324 HIS G 104 GLN ** G 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24608 Z= 0.252 Angle : 0.732 18.422 33370 Z= 0.377 Chirality : 0.049 0.329 3840 Planarity : 0.006 0.072 4349 Dihedral : 8.649 85.229 3577 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.48 % Favored : 95.49 % Rotamer: Outliers : 5.82 % Allowed : 32.33 % Favored : 61.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3104 helix: 0.57 (0.14), residues: 1285 sheet: -0.10 (0.24), residues: 467 loop : -1.04 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS F 401 PHE 0.038 0.002 PHE D 255 TYR 0.022 0.002 TYR G 103 ARG 0.011 0.001 ARG C 383 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 949 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7477 (mp) REVERT: A 154 ASP cc_start: 0.7871 (m-30) cc_final: 0.7578 (t0) REVERT: A 157 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7768 (p) REVERT: A 190 ASN cc_start: 0.7253 (m-40) cc_final: 0.7014 (m-40) REVERT: A 215 HIS cc_start: 0.7224 (OUTLIER) cc_final: 0.6313 (t-90) REVERT: A 266 GLN cc_start: 0.7425 (tp40) cc_final: 0.6826 (tp40) REVERT: A 365 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6836 (mtt-85) REVERT: A 383 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6714 (tpt170) REVERT: A 391 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6443 (pt0) REVERT: A 420 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7663 (mm) REVERT: A 424 LEU cc_start: 0.6973 (tp) cc_final: 0.6619 (tp) REVERT: A 456 PHE cc_start: 0.7667 (t80) cc_final: 0.7418 (t80) REVERT: A 476 ARG cc_start: 0.7231 (tpm170) cc_final: 0.6987 (tpm170) REVERT: A 492 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7179 (mm-30) REVERT: B 181 ASP cc_start: 0.6868 (t70) cc_final: 0.6612 (t0) REVERT: B 333 ASN cc_start: 0.7966 (t0) cc_final: 0.7561 (t0) REVERT: B 373 LYS cc_start: 0.7545 (ttmt) cc_final: 0.6930 (ttmt) REVERT: B 377 LYS cc_start: 0.7832 (mttp) cc_final: 0.7516 (mttp) REVERT: B 423 ASP cc_start: 0.7856 (p0) cc_final: 0.7164 (p0) REVERT: B 432 LYS cc_start: 0.8531 (mttt) cc_final: 0.8134 (mttt) REVERT: B 458 LYS cc_start: 0.7328 (tmmt) cc_final: 0.7042 (mttp) REVERT: B 463 PHE cc_start: 0.8146 (t80) cc_final: 0.7905 (t80) REVERT: C 358 ASN cc_start: 0.7756 (t0) cc_final: 0.7465 (p0) REVERT: C 389 TYR cc_start: 0.8064 (t80) cc_final: 0.7774 (t80) REVERT: C 435 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7859 (mm) REVERT: C 484 GLU cc_start: 0.6735 (tt0) cc_final: 0.6213 (tt0) REVERT: C 488 ASN cc_start: 0.7364 (m110) cc_final: 0.7003 (m110) REVERT: D 35 LYS cc_start: 0.7862 (ttmt) cc_final: 0.7601 (ttmt) REVERT: D 154 ILE cc_start: 0.7701 (mp) cc_final: 0.7383 (mt) REVERT: D 202 MET cc_start: 0.6882 (mmt) cc_final: 0.6377 (mmp) REVERT: D 207 VAL cc_start: 0.8622 (t) cc_final: 0.8141 (p) REVERT: D 227 ARG cc_start: 0.6575 (mmt90) cc_final: 0.6323 (mmt90) REVERT: D 233 LEU cc_start: 0.7457 (tp) cc_final: 0.7138 (tp) REVERT: D 256 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7529 (mtt90) REVERT: D 267 LEU cc_start: 0.7673 (mm) cc_final: 0.7057 (mt) REVERT: D 294 SER cc_start: 0.7056 (t) cc_final: 0.6559 (p) REVERT: D 333 ARG cc_start: 0.6467 (ttm110) cc_final: 0.6247 (ttm110) REVERT: D 340 ILE cc_start: 0.8558 (pt) cc_final: 0.8211 (mm) REVERT: D 365 GLN cc_start: 0.6902 (mp10) cc_final: 0.6649 (mp10) REVERT: D 375 GLN cc_start: 0.7385 (tp40) cc_final: 0.7158 (tp40) REVERT: D 381 GLN cc_start: 0.7292 (pm20) cc_final: 0.7031 (pm20) REVERT: D 396 ASP cc_start: 0.7412 (m-30) cc_final: 0.7144 (m-30) REVERT: D 405 ARG cc_start: 0.7086 (mpt90) cc_final: 0.6861 (mpt90) REVERT: D 441 LEU cc_start: 0.8561 (mt) cc_final: 0.8351 (mp) REVERT: D 464 GLU cc_start: 0.7337 (tp30) cc_final: 0.6984 (tp30) REVERT: D 465 LYS cc_start: 0.8276 (tttt) cc_final: 0.7996 (tttt) REVERT: E 112 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6728 (m-30) REVERT: E 168 ILE cc_start: 0.8579 (mm) cc_final: 0.8224 (tt) REVERT: E 248 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6654 (tp) REVERT: E 378 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7729 (tmmm) REVERT: E 391 GLU cc_start: 0.5701 (OUTLIER) cc_final: 0.5359 (tm-30) REVERT: E 405 ARG cc_start: 0.7367 (mpt180) cc_final: 0.7163 (mpt180) REVERT: E 450 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6022 (pm20) REVERT: E 469 MET cc_start: 0.5681 (mmm) cc_final: 0.5354 (mmm) REVERT: F 85 VAL cc_start: 0.7579 (t) cc_final: 0.7232 (p) REVERT: F 234 THR cc_start: 0.7531 (OUTLIER) cc_final: 0.6881 (t) REVERT: F 240 ARG cc_start: 0.5620 (OUTLIER) cc_final: 0.5374 (ppt90) REVERT: F 241 ASP cc_start: 0.7084 (m-30) cc_final: 0.6017 (m-30) REVERT: F 278 GLN cc_start: 0.7508 (pm20) cc_final: 0.7297 (pm20) REVERT: F 285 MET cc_start: 0.7059 (ttp) cc_final: 0.6634 (ttp) REVERT: F 330 ASN cc_start: 0.5898 (m-40) cc_final: 0.5677 (m-40) REVERT: F 389 MET cc_start: 0.6764 (mmm) cc_final: 0.6433 (mmm) REVERT: G 15 ASN cc_start: 0.8364 (m-40) cc_final: 0.8062 (m-40) REVERT: G 32 THR cc_start: 0.7175 (p) cc_final: 0.6941 (t) REVERT: G 37 ARG cc_start: 0.7498 (ttp80) cc_final: 0.7161 (ttp80) REVERT: G 48 TYR cc_start: 0.7594 (t80) cc_final: 0.7228 (t80) REVERT: G 70 MET cc_start: 0.7844 (mmp) cc_final: 0.7217 (mmp) REVERT: G 134 MET cc_start: 0.5507 (mtt) cc_final: 0.5272 (mtt) REVERT: G 146 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7153 (pp30) REVERT: G 148 SER cc_start: 0.8723 (m) cc_final: 0.8353 (p) REVERT: G 153 LYS cc_start: 0.7711 (tttm) cc_final: 0.7377 (tttm) REVERT: G 155 ILE cc_start: 0.8229 (mp) cc_final: 0.8014 (mt) REVERT: G 183 GLN cc_start: 0.7373 (pp30) cc_final: 0.6605 (pp30) REVERT: G 222 GLN cc_start: 0.7964 (mt0) cc_final: 0.7731 (mt0) REVERT: G 265 TYR cc_start: 0.7924 (t80) cc_final: 0.7652 (t80) REVERT: G 269 ARG cc_start: 0.7446 (ttp80) cc_final: 0.7123 (ttp80) outliers start: 149 outliers final: 106 residues processed: 1016 average time/residue: 0.4001 time to fit residues: 606.2865 Evaluate side-chains 1057 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 935 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 153 LYS Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 179 HIS Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 285 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 6.9990 chunk 294 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 204 optimal weight: 0.9980 chunk 308 optimal weight: 1.9990 chunk 284 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 143 HIS A 230 GLN A 433 GLN C 407 GLN C 433 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** F 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24608 Z= 0.297 Angle : 0.762 18.310 33370 Z= 0.393 Chirality : 0.050 0.287 3840 Planarity : 0.006 0.087 4349 Dihedral : 8.603 87.378 3577 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.67 % Favored : 94.30 % Rotamer: Outliers : 5.51 % Allowed : 32.72 % Favored : 61.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3104 helix: 0.50 (0.14), residues: 1281 sheet: -0.18 (0.23), residues: 483 loop : -1.09 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS F 401 PHE 0.040 0.002 PHE D 255 TYR 0.022 0.002 TYR A 461 ARG 0.020 0.001 ARG B 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 939 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7520 (mp) REVERT: A 154 ASP cc_start: 0.7863 (m-30) cc_final: 0.7564 (t0) REVERT: A 157 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.7783 (p) REVERT: A 164 ARG cc_start: 0.6753 (mtm110) cc_final: 0.6449 (mtm110) REVERT: A 190 ASN cc_start: 0.7241 (m-40) cc_final: 0.7004 (m-40) REVERT: A 215 HIS cc_start: 0.7245 (OUTLIER) cc_final: 0.6359 (t-90) REVERT: A 266 GLN cc_start: 0.7484 (tp40) cc_final: 0.6883 (tp40) REVERT: A 317 PRO cc_start: 0.8366 (Cg_endo) cc_final: 0.8087 (Cg_exo) REVERT: A 365 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6807 (mtt-85) REVERT: A 383 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6697 (tpt170) REVERT: A 391 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6444 (pt0) REVERT: A 420 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7643 (mm) REVERT: A 424 LEU cc_start: 0.6951 (tp) cc_final: 0.6604 (tp) REVERT: A 456 PHE cc_start: 0.7688 (t80) cc_final: 0.7460 (t80) REVERT: A 476 ARG cc_start: 0.7299 (tpm170) cc_final: 0.6868 (tpm170) REVERT: A 479 LYS cc_start: 0.7531 (mppt) cc_final: 0.6843 (mppt) REVERT: A 492 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7178 (mm-30) REVERT: B 181 ASP cc_start: 0.6838 (t70) cc_final: 0.6581 (t0) REVERT: B 333 ASN cc_start: 0.7989 (t0) cc_final: 0.7573 (t0) REVERT: B 373 LYS cc_start: 0.7509 (ttmt) cc_final: 0.6882 (ttmt) REVERT: B 377 LYS cc_start: 0.7877 (mttp) cc_final: 0.7558 (mttp) REVERT: B 422 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: B 423 ASP cc_start: 0.7838 (p0) cc_final: 0.7405 (p0) REVERT: B 432 LYS cc_start: 0.8562 (mttt) cc_final: 0.8114 (mttt) REVERT: B 458 LYS cc_start: 0.7295 (tmmt) cc_final: 0.6990 (mttp) REVERT: B 494 PHE cc_start: 0.7642 (t80) cc_final: 0.7346 (t80) REVERT: C 358 ASN cc_start: 0.7767 (t0) cc_final: 0.7465 (p0) REVERT: C 377 LYS cc_start: 0.7880 (tttp) cc_final: 0.7621 (ttpp) REVERT: C 389 TYR cc_start: 0.8065 (t80) cc_final: 0.7759 (t80) REVERT: C 435 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7829 (mm) REVERT: C 484 GLU cc_start: 0.6752 (tt0) cc_final: 0.6236 (tt0) REVERT: C 488 ASN cc_start: 0.7391 (m110) cc_final: 0.7015 (m110) REVERT: D 35 LYS cc_start: 0.7868 (ttmt) cc_final: 0.7593 (ttmt) REVERT: D 154 ILE cc_start: 0.7670 (mp) cc_final: 0.7350 (mt) REVERT: D 202 MET cc_start: 0.6871 (mmt) cc_final: 0.6355 (mmp) REVERT: D 207 VAL cc_start: 0.8635 (t) cc_final: 0.8145 (p) REVERT: D 233 LEU cc_start: 0.7453 (tp) cc_final: 0.7126 (tp) REVERT: D 256 ARG cc_start: 0.7847 (mtm-85) cc_final: 0.7518 (mtt90) REVERT: D 267 LEU cc_start: 0.7720 (mm) cc_final: 0.7125 (mt) REVERT: D 294 SER cc_start: 0.7067 (t) cc_final: 0.6569 (p) REVERT: D 333 ARG cc_start: 0.6499 (ttm110) cc_final: 0.6284 (ttm110) REVERT: D 340 ILE cc_start: 0.8539 (pt) cc_final: 0.8232 (mm) REVERT: D 365 GLN cc_start: 0.6920 (mp10) cc_final: 0.6664 (mp10) REVERT: D 375 GLN cc_start: 0.7395 (tp40) cc_final: 0.7170 (tp40) REVERT: D 378 LYS cc_start: 0.8023 (tttt) cc_final: 0.7796 (tttm) REVERT: D 381 GLN cc_start: 0.7362 (pm20) cc_final: 0.7074 (pm20) REVERT: D 405 ARG cc_start: 0.7146 (mpt90) cc_final: 0.6906 (mpt90) REVERT: D 441 LEU cc_start: 0.8574 (mt) cc_final: 0.8371 (mp) REVERT: D 464 GLU cc_start: 0.7360 (tp30) cc_final: 0.6998 (tp30) REVERT: D 465 LYS cc_start: 0.8287 (tttt) cc_final: 0.8002 (tttt) REVERT: E 168 ILE cc_start: 0.8577 (mm) cc_final: 0.8251 (tt) REVERT: E 248 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6674 (tp) REVERT: E 314 THR cc_start: 0.7658 (p) cc_final: 0.7452 (p) REVERT: E 330 ASN cc_start: 0.6751 (t0) cc_final: 0.6463 (t0) REVERT: E 369 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7731 (mtmm) REVERT: E 378 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7708 (tmmm) REVERT: E 391 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.5377 (tm-30) REVERT: E 450 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6033 (pm20) REVERT: E 465 LYS cc_start: 0.8569 (tttp) cc_final: 0.7853 (tttp) REVERT: E 469 MET cc_start: 0.5659 (mmm) cc_final: 0.5264 (mmm) REVERT: F 85 VAL cc_start: 0.7527 (t) cc_final: 0.7194 (p) REVERT: F 234 THR cc_start: 0.7570 (OUTLIER) cc_final: 0.6943 (t) REVERT: F 240 ARG cc_start: 0.5687 (OUTLIER) cc_final: 0.5430 (ppt90) REVERT: F 241 ASP cc_start: 0.7117 (m-30) cc_final: 0.6045 (m-30) REVERT: F 278 GLN cc_start: 0.7492 (pm20) cc_final: 0.7241 (pm20) REVERT: F 285 MET cc_start: 0.7094 (ttp) cc_final: 0.6613 (ttp) REVERT: F 389 MET cc_start: 0.6781 (mmm) cc_final: 0.6445 (mmm) REVERT: G 37 ARG cc_start: 0.7536 (ttp80) cc_final: 0.7253 (ttp80) REVERT: G 48 TYR cc_start: 0.7617 (t80) cc_final: 0.7070 (t80) REVERT: G 49 MET cc_start: 0.7434 (mmt) cc_final: 0.6532 (mmt) REVERT: G 70 MET cc_start: 0.7882 (mmp) cc_final: 0.7265 (mmp) REVERT: G 134 MET cc_start: 0.5510 (mtt) cc_final: 0.5237 (mtt) REVERT: G 146 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7176 (pp30) REVERT: G 148 SER cc_start: 0.8736 (m) cc_final: 0.8340 (p) REVERT: G 153 LYS cc_start: 0.7711 (tttm) cc_final: 0.7392 (tttm) REVERT: G 183 GLN cc_start: 0.7407 (pp30) cc_final: 0.6692 (pp30) REVERT: G 222 GLN cc_start: 0.7986 (mt0) cc_final: 0.7763 (mt0) REVERT: G 244 MET cc_start: 0.7360 (ttp) cc_final: 0.7124 (ttp) REVERT: G 265 TYR cc_start: 0.7939 (t80) cc_final: 0.7678 (t80) REVERT: G 269 ARG cc_start: 0.7430 (ttp80) cc_final: 0.7122 (ttp80) outliers start: 141 outliers final: 111 residues processed: 1003 average time/residue: 0.4116 time to fit residues: 624.2189 Evaluate side-chains 1058 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 931 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 179 HIS Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 324 HIS Chi-restraints excluded: chain F residue 381 GLN Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 448 LEU Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 285 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 0.3980 chunk 261 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 252 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.0470 overall best weight: 2.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 433 GLN C 189 GLN C 230 GLN C 433 GLN D 289 GLN D 304 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** F 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS ** G 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.142329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.123940 restraints weight = 39755.304| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 3.07 r_work: 0.3580 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 24608 Z= 0.293 Angle : 0.760 18.205 33370 Z= 0.394 Chirality : 0.050 0.291 3840 Planarity : 0.006 0.073 4349 Dihedral : 8.559 88.133 3577 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.25 % Favored : 94.72 % Rotamer: Outliers : 5.47 % Allowed : 33.19 % Favored : 61.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3104 helix: 0.50 (0.14), residues: 1281 sheet: -0.19 (0.24), residues: 478 loop : -1.15 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS F 401 PHE 0.042 0.002 PHE B 463 TYR 0.026 0.002 TYR G 94 ARG 0.013 0.001 ARG B 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9150.15 seconds wall clock time: 162 minutes 50.74 seconds (9770.74 seconds total)