Starting phenix.real_space_refine on Mon Mar 11 06:13:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/03_2024/6irs_9721_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/03_2024/6irs_9721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/03_2024/6irs_9721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/03_2024/6irs_9721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/03_2024/6irs_9721_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/03_2024/6irs_9721_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 27 5.16 5 C 4807 2.51 5 N 1172 2.21 5 O 1329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 421": "NH1" <-> "NH2" Residue "B ARG 427": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7337 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3650 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446} Chain: "B" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3479 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 24, 'TRANS': 432} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.56, per 1000 atoms: 0.62 Number of scatterers: 7337 At special positions: 0 Unit cell: (82.916, 84.007, 124.374, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 2 15.00 O 1329 8.00 N 1172 7.00 C 4807 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 164 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.4 seconds 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 5 sheets defined 51.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 179 through 206 removed outlier: 3.677A pdb=" N LEU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 222 removed outlier: 3.863A pdb=" N THR A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 222' Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 252 removed outlier: 3.985A pdb=" N GLY A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TYR A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 300 removed outlier: 3.631A pdb=" N LYS A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 341 removed outlier: 4.212A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.717A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.837A pdb=" N LEU A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 392' Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.530A pdb=" N THR A 427 " --> pdb=" O TYR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 459 removed outlier: 3.921A pdb=" N GLN A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 513 No H-bonds generated for 'chain 'A' and resid 510 through 513' Processing helix chain 'A' and resid 520 through 533 removed outlier: 3.619A pdb=" N ARG A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 539 Processing helix chain 'B' and resid 54 through 63 removed outlier: 3.908A pdb=" N ILE B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 69 removed outlier: 3.554A pdb=" N PHE B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 66 through 69' Processing helix chain 'B' and resid 72 through 79 removed outlier: 3.760A pdb=" N GLU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 109 removed outlier: 3.553A pdb=" N PHE B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER B 96 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.638A pdb=" N TYR B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU B 122 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 136 removed outlier: 3.542A pdb=" N GLU B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 154 removed outlier: 3.860A pdb=" N GLN B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 187 removed outlier: 4.036A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 220 removed outlier: 3.848A pdb=" N ARG B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 removed outlier: 3.721A pdb=" N SER B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 274 through 299 removed outlier: 3.698A pdb=" N ILE B 279 " --> pdb=" O PRO B 275 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Proline residue: B 283 - end of helix removed outlier: 4.205A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 removed outlier: 3.817A pdb=" N LEU B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 327 through 338 removed outlier: 3.855A pdb=" N SER B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 344 No H-bonds generated for 'chain 'B' and resid 341 through 344' Processing helix chain 'B' and resid 347 through 355 removed outlier: 3.563A pdb=" N PHE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 389 removed outlier: 3.510A pdb=" N MET B 383 " --> pdb=" O PHE B 379 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 420 removed outlier: 3.619A pdb=" N ASN B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 409 " --> pdb=" O TRP B 405 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 452 removed outlier: 3.841A pdb=" N VAL B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 439 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 441 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 447 " --> pdb=" O CYS B 443 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 449 " --> pdb=" O PHE B 445 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TRP B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 463 Processing helix chain 'B' and resid 467 through 473 removed outlier: 4.007A pdb=" N VAL B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 500 removed outlier: 3.656A pdb=" N GLY B 488 " --> pdb=" O TRP B 484 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 496 " --> pdb=" O THR B 492 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 225 through 227 Processing sheet with id= B, first strand: chain 'A' and resid 259 through 262 removed outlier: 6.928A pdb=" N ARG A 304 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU A 262 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE A 306 " --> pdb=" O LEU A 262 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 346 through 348 Processing sheet with id= D, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.514A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 624 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ARG A 626 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LEU A 596 " --> pdb=" O ARG A 626 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 266 through 268 removed outlier: 6.986A pdb=" N GLN A 280 " --> pdb=" O LYS A 267 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 762 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: 1.82 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1456 1.33 - 1.45: 1777 1.45 - 1.57: 4235 1.57 - 1.69: 4 1.69 - 1.81: 40 Bond restraints: 7512 Sorted by residual: bond pdb=" C31 3PH B 601 " pdb=" O31 3PH B 601 " ideal model delta sigma weight residual 1.325 1.454 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C31 3PH B 602 " pdb=" O31 3PH B 602 " ideal model delta sigma weight residual 1.325 1.452 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C21 3PH B 602 " pdb=" O21 3PH B 602 " ideal model delta sigma weight residual 1.328 1.455 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C21 3PH B 601 " pdb=" O21 3PH B 601 " ideal model delta sigma weight residual 1.328 1.455 -0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C1 NAG D 1 " pdb=" C2 NAG D 1 " ideal model delta sigma weight residual 1.532 1.632 -0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 7507 not shown) Histogram of bond angle deviations from ideal: 95.75 - 103.53: 108 103.53 - 111.31: 3194 111.31 - 119.09: 3000 119.09 - 126.86: 3780 126.86 - 134.64: 128 Bond angle restraints: 10210 Sorted by residual: angle pdb=" C SER A 176 " pdb=" N PRO A 177 " pdb=" CA PRO A 177 " ideal model delta sigma weight residual 119.84 129.79 -9.95 1.25e+00 6.40e-01 6.34e+01 angle pdb=" N MET A 490 " pdb=" CA MET A 490 " pdb=" C MET A 490 " ideal model delta sigma weight residual 109.15 97.87 11.28 1.44e+00 4.82e-01 6.14e+01 angle pdb=" N MET A 508 " pdb=" CA MET A 508 " pdb=" C MET A 508 " ideal model delta sigma weight residual 111.28 118.86 -7.58 1.09e+00 8.42e-01 4.84e+01 angle pdb=" N HIS B 319 " pdb=" CA HIS B 319 " pdb=" C HIS B 319 " ideal model delta sigma weight residual 111.28 117.70 -6.42 1.09e+00 8.42e-01 3.47e+01 angle pdb=" C PHE B 161 " pdb=" N PRO B 162 " pdb=" CA PRO B 162 " ideal model delta sigma weight residual 119.84 127.10 -7.26 1.25e+00 6.40e-01 3.38e+01 ... (remaining 10205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.15: 4267 21.15 - 42.29: 213 42.29 - 63.44: 36 63.44 - 84.59: 13 84.59 - 105.74: 7 Dihedral angle restraints: 4536 sinusoidal: 1883 harmonic: 2653 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sinusoidal sigma weight residual 93.00 -178.35 -88.65 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CA PRO B 360 " pdb=" C PRO B 360 " pdb=" N SER B 361 " pdb=" CA SER B 361 " ideal model delta harmonic sigma weight residual -180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA HIS A 221 " pdb=" C HIS A 221 " pdb=" N THR A 222 " pdb=" CA THR A 222 " ideal model delta harmonic sigma weight residual 180.00 -155.73 -24.27 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 4533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 983 0.081 - 0.162: 184 0.162 - 0.242: 23 0.242 - 0.323: 6 0.323 - 0.404: 4 Chirality restraints: 1200 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.17e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.58e+01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 507 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.07e+00 ... (remaining 1197 not shown) Planarity restraints: 1258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.337 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG D 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.503 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.321 2.00e-02 2.50e+03 2.77e-01 9.60e+02 pdb=" C7 NAG D 1 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.021 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.481 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 507 " -0.090 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" CG ASN A 507 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 507 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 507 " 0.196 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.133 2.00e-02 2.50e+03 ... (remaining 1255 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 403 2.70 - 3.25: 7108 3.25 - 3.80: 11590 3.80 - 4.35: 14642 4.35 - 4.90: 23870 Nonbonded interactions: 57613 Sorted by model distance: nonbonded pdb=" ND1 HIS B 367 " pdb=" CD PRO B 368 " model vdw 2.150 3.520 nonbonded pdb=" O GLY B 107 " pdb=" OG SER B 111 " model vdw 2.199 2.440 nonbonded pdb=" C TRP A 492 " pdb=" CG2 THR A 509 " model vdw 2.221 3.690 nonbonded pdb=" CD1 ILE A 228 " pdb=" CZ PHE A 234 " model vdw 2.250 3.760 nonbonded pdb=" O CYS B 92 " pdb=" OH TYR B 254 " model vdw 2.277 2.440 ... (remaining 57608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.010 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.110 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.011 0.129 7512 Z= 0.710 Angle : 1.357 12.491 10210 Z= 0.743 Chirality : 0.069 0.404 1200 Planarity : 0.014 0.287 1254 Dihedral : 14.191 105.736 2829 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.79 % Favored : 90.35 % Rotamer: Outliers : 3.66 % Allowed : 6.81 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -5.69 (0.19), residues: 922 helix: -4.10 (0.12), residues: 475 sheet: -1.86 (0.67), residues: 51 loop : -3.48 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP A 558 HIS 0.012 0.003 HIS A 221 PHE 0.034 0.004 PHE A 552 TYR 0.050 0.004 TYR A 454 ARG 0.015 0.002 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 221 time to evaluate : 0.888 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 191 TRP cc_start: 0.7934 (m100) cc_final: 0.7555 (m-10) REVERT: A 290 ASP cc_start: 0.8431 (m-30) cc_final: 0.8038 (t0) REVERT: A 332 LYS cc_start: 0.8937 (tttt) cc_final: 0.8619 (tttm) REVERT: A 458 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8452 (mp) REVERT: A 480 LEU cc_start: 0.8759 (tp) cc_final: 0.8544 (tt) REVERT: A 554 TYR cc_start: 0.8030 (p90) cc_final: 0.7266 (p90) REVERT: B 137 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8171 (mt) REVERT: B 145 GLN cc_start: 0.8348 (mt0) cc_final: 0.8015 (mt0) REVERT: B 210 LEU cc_start: 0.8944 (tt) cc_final: 0.8678 (tt) REVERT: B 305 MET cc_start: 0.7393 (mtp) cc_final: 0.6996 (mtp) REVERT: B 452 TRP cc_start: 0.6384 (t60) cc_final: 0.6011 (t60) outliers start: 28 outliers final: 7 residues processed: 238 average time/residue: 0.2134 time to fit residues: 65.7800 Evaluate side-chains 144 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.1980 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 46 optimal weight: 0.0070 chunk 36 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.0070 chunk 82 optimal weight: 0.9990 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS B 145 GLN B 186 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7512 Z= 0.193 Angle : 0.784 9.791 10210 Z= 0.377 Chirality : 0.046 0.220 1200 Planarity : 0.006 0.058 1254 Dihedral : 12.388 88.906 1254 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.29 % Favored : 93.49 % Rotamer: Outliers : 3.53 % Allowed : 15.18 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -4.06 (0.22), residues: 922 helix: -2.49 (0.18), residues: 501 sheet: -1.11 (0.71), residues: 50 loop : -3.07 (0.28), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 558 HIS 0.007 0.002 HIS A 539 PHE 0.023 0.002 PHE B 474 TYR 0.014 0.002 TYR B 259 ARG 0.008 0.001 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7906 (m100) cc_final: 0.7448 (m-10) REVERT: A 192 LEU cc_start: 0.8724 (mm) cc_final: 0.8494 (mm) REVERT: A 278 LEU cc_start: 0.8234 (mt) cc_final: 0.7987 (mt) REVERT: A 290 ASP cc_start: 0.8235 (m-30) cc_final: 0.7759 (t0) REVERT: A 300 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8157 (mmtt) REVERT: A 332 LYS cc_start: 0.8881 (tttt) cc_final: 0.8569 (tttm) REVERT: A 454 TYR cc_start: 0.8395 (m-80) cc_final: 0.8137 (m-80) REVERT: A 458 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8417 (mp) REVERT: A 511 LYS cc_start: 0.8376 (mmtt) cc_final: 0.8125 (mmtt) REVERT: A 593 LYS cc_start: 0.7972 (mttp) cc_final: 0.7736 (ttpt) REVERT: B 137 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7929 (mt) REVERT: B 145 GLN cc_start: 0.8139 (mt0) cc_final: 0.7844 (mt0) REVERT: B 188 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.6212 (t80) REVERT: B 210 LEU cc_start: 0.8733 (tt) cc_final: 0.8417 (tt) REVERT: B 320 LEU cc_start: 0.7085 (tp) cc_final: 0.6585 (tp) REVERT: B 421 ARG cc_start: 0.7156 (mmp80) cc_final: 0.6889 (mmp80) REVERT: B 493 THR cc_start: 0.9055 (m) cc_final: 0.8817 (m) outliers start: 27 outliers final: 12 residues processed: 179 average time/residue: 0.1988 time to fit residues: 47.5587 Evaluate side-chains 137 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 444 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 89 optimal weight: 0.0170 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7512 Z= 0.190 Angle : 0.714 9.739 10210 Z= 0.341 Chirality : 0.044 0.206 1200 Planarity : 0.005 0.043 1254 Dihedral : 11.369 87.005 1241 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.16 % Favored : 92.62 % Rotamer: Outliers : 3.66 % Allowed : 18.46 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -3.00 (0.25), residues: 922 helix: -1.46 (0.20), residues: 506 sheet: -0.63 (0.73), residues: 51 loop : -2.89 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 405 HIS 0.008 0.001 HIS B 319 PHE 0.019 0.002 PHE B 474 TYR 0.020 0.002 TYR A 629 ARG 0.006 0.001 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7882 (m100) cc_final: 0.7376 (m-10) REVERT: A 192 LEU cc_start: 0.8678 (mm) cc_final: 0.8451 (mm) REVERT: A 290 ASP cc_start: 0.8172 (m-30) cc_final: 0.7761 (t0) REVERT: A 300 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8288 (mmtt) REVERT: A 454 TYR cc_start: 0.8418 (m-80) cc_final: 0.8090 (m-80) REVERT: A 458 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8580 (mp) REVERT: A 511 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7866 (mmtt) REVERT: A 593 LYS cc_start: 0.7967 (mttp) cc_final: 0.7749 (ttpt) REVERT: B 145 GLN cc_start: 0.8146 (mt0) cc_final: 0.7825 (mt0) REVERT: B 188 TYR cc_start: 0.7236 (OUTLIER) cc_final: 0.6266 (t80) REVERT: B 195 ARG cc_start: 0.7775 (mtp85) cc_final: 0.7098 (ttt90) REVERT: B 210 LEU cc_start: 0.8647 (tt) cc_final: 0.8397 (tt) REVERT: B 320 LEU cc_start: 0.6970 (tp) cc_final: 0.6529 (tp) REVERT: B 444 LEU cc_start: 0.9219 (tp) cc_final: 0.8958 (tp) outliers start: 28 outliers final: 15 residues processed: 151 average time/residue: 0.2031 time to fit residues: 40.7574 Evaluate side-chains 135 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 440 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 0.0170 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7512 Z= 0.186 Angle : 0.679 10.393 10210 Z= 0.322 Chirality : 0.044 0.214 1200 Planarity : 0.005 0.066 1254 Dihedral : 10.764 84.846 1238 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.94 % Favored : 92.84 % Rotamer: Outliers : 3.27 % Allowed : 20.03 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.36 (0.25), residues: 922 helix: -0.88 (0.21), residues: 498 sheet: -0.21 (0.75), residues: 52 loop : -2.69 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 405 HIS 0.007 0.001 HIS B 319 PHE 0.015 0.001 PHE B 451 TYR 0.015 0.002 TYR A 469 ARG 0.011 0.001 ARG B 272 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7939 (m100) cc_final: 0.7419 (m-10) REVERT: A 192 LEU cc_start: 0.8729 (mm) cc_final: 0.8510 (mm) REVERT: A 290 ASP cc_start: 0.8226 (m-30) cc_final: 0.7771 (t0) REVERT: A 300 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8332 (mmtt) REVERT: A 404 SER cc_start: 0.8900 (m) cc_final: 0.8546 (p) REVERT: A 440 ARG cc_start: 0.8581 (tpp80) cc_final: 0.8316 (mtp85) REVERT: A 511 LYS cc_start: 0.8276 (mmtt) cc_final: 0.8075 (mmtt) REVERT: A 593 LYS cc_start: 0.7974 (mttp) cc_final: 0.7751 (ttpt) REVERT: B 145 GLN cc_start: 0.8204 (mt0) cc_final: 0.7984 (mt0) REVERT: B 188 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.6199 (t80) REVERT: B 210 LEU cc_start: 0.8678 (tt) cc_final: 0.8295 (tt) REVERT: B 320 LEU cc_start: 0.6937 (tp) cc_final: 0.6515 (tp) REVERT: B 444 LEU cc_start: 0.9145 (tp) cc_final: 0.8933 (tp) outliers start: 25 outliers final: 13 residues processed: 139 average time/residue: 0.2048 time to fit residues: 38.2938 Evaluate side-chains 131 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 440 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7512 Z= 0.221 Angle : 0.679 10.238 10210 Z= 0.322 Chirality : 0.044 0.221 1200 Planarity : 0.004 0.041 1254 Dihedral : 10.185 83.204 1236 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.05 % Favored : 92.73 % Rotamer: Outliers : 3.27 % Allowed : 21.20 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.89 (0.26), residues: 922 helix: -0.41 (0.22), residues: 493 sheet: -0.07 (0.75), residues: 52 loop : -2.58 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 405 HIS 0.008 0.001 HIS B 319 PHE 0.015 0.002 PHE B 451 TYR 0.019 0.002 TYR A 629 ARG 0.004 0.001 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7939 (m100) cc_final: 0.7434 (m-10) REVERT: A 192 LEU cc_start: 0.8741 (mm) cc_final: 0.8521 (mm) REVERT: A 290 ASP cc_start: 0.8292 (m-30) cc_final: 0.7796 (t0) REVERT: A 300 LYS cc_start: 0.8644 (mmtt) cc_final: 0.8353 (mmtt) REVERT: A 381 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8549 (m) REVERT: A 404 SER cc_start: 0.8896 (m) cc_final: 0.8636 (p) REVERT: A 511 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8238 (mmtt) REVERT: A 539 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7598 (p90) REVERT: A 559 ASP cc_start: 0.8007 (t0) cc_final: 0.7712 (m-30) REVERT: A 593 LYS cc_start: 0.7916 (mttp) cc_final: 0.7682 (ttpt) REVERT: B 145 GLN cc_start: 0.8226 (mt0) cc_final: 0.8021 (mt0) REVERT: B 188 TYR cc_start: 0.7199 (OUTLIER) cc_final: 0.6225 (t80) REVERT: B 210 LEU cc_start: 0.8718 (tt) cc_final: 0.8415 (tt) outliers start: 25 outliers final: 15 residues processed: 139 average time/residue: 0.2107 time to fit residues: 38.9250 Evaluate side-chains 129 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7512 Z= 0.171 Angle : 0.653 11.369 10210 Z= 0.306 Chirality : 0.043 0.241 1200 Planarity : 0.004 0.041 1254 Dihedral : 9.741 79.894 1236 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.83 % Favored : 93.06 % Rotamer: Outliers : 3.40 % Allowed : 21.73 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.48 (0.27), residues: 922 helix: 0.04 (0.23), residues: 488 sheet: 0.02 (0.74), residues: 52 loop : -2.54 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 405 HIS 0.006 0.001 HIS B 319 PHE 0.014 0.001 PHE B 451 TYR 0.015 0.001 TYR A 469 ARG 0.004 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7905 (m100) cc_final: 0.7392 (m-10) REVERT: A 192 LEU cc_start: 0.8772 (mm) cc_final: 0.8568 (mm) REVERT: A 290 ASP cc_start: 0.8270 (m-30) cc_final: 0.7772 (t0) REVERT: A 300 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8325 (mmtt) REVERT: A 404 SER cc_start: 0.8872 (m) cc_final: 0.8632 (p) REVERT: A 415 HIS cc_start: 0.7530 (OUTLIER) cc_final: 0.7237 (t-170) REVERT: A 454 TYR cc_start: 0.8337 (m-80) cc_final: 0.8093 (m-80) REVERT: A 511 LYS cc_start: 0.8591 (mmtt) cc_final: 0.8351 (mmtt) REVERT: A 559 ASP cc_start: 0.7917 (t0) cc_final: 0.7662 (t0) REVERT: A 593 LYS cc_start: 0.7838 (mttp) cc_final: 0.7616 (ttpt) REVERT: B 188 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6204 (t80) REVERT: B 210 LEU cc_start: 0.8707 (tt) cc_final: 0.8370 (tt) REVERT: B 291 LEU cc_start: 0.8244 (mp) cc_final: 0.7946 (mp) outliers start: 26 outliers final: 18 residues processed: 132 average time/residue: 0.2183 time to fit residues: 38.0740 Evaluate side-chains 132 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7512 Z= 0.184 Angle : 0.651 10.201 10210 Z= 0.306 Chirality : 0.043 0.255 1200 Planarity : 0.004 0.042 1254 Dihedral : 9.474 77.956 1236 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.83 % Favored : 93.06 % Rotamer: Outliers : 3.66 % Allowed : 22.77 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.28 (0.27), residues: 922 helix: 0.25 (0.23), residues: 488 sheet: 0.00 (0.73), residues: 52 loop : -2.50 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 405 HIS 0.005 0.001 HIS B 319 PHE 0.015 0.001 PHE B 451 TYR 0.016 0.001 TYR B 103 ARG 0.005 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6774 (pp) REVERT: A 191 TRP cc_start: 0.7870 (m100) cc_final: 0.7355 (m-10) REVERT: A 192 LEU cc_start: 0.8764 (mm) cc_final: 0.8540 (mm) REVERT: A 290 ASP cc_start: 0.8278 (m-30) cc_final: 0.7775 (t0) REVERT: A 300 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8309 (mmtt) REVERT: A 404 SER cc_start: 0.8846 (m) cc_final: 0.8636 (p) REVERT: A 415 HIS cc_start: 0.7494 (OUTLIER) cc_final: 0.7229 (t-170) REVERT: A 454 TYR cc_start: 0.8363 (m-80) cc_final: 0.8147 (m-80) REVERT: A 511 LYS cc_start: 0.8594 (mmtt) cc_final: 0.8376 (mmtt) REVERT: A 559 ASP cc_start: 0.7861 (t0) cc_final: 0.7649 (t0) REVERT: B 145 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7787 (mt0) REVERT: B 188 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6223 (t80) REVERT: B 210 LEU cc_start: 0.8711 (tt) cc_final: 0.8377 (tt) outliers start: 28 outliers final: 20 residues processed: 137 average time/residue: 0.2105 time to fit residues: 38.0584 Evaluate side-chains 136 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 76 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7512 Z= 0.170 Angle : 0.656 9.973 10210 Z= 0.308 Chirality : 0.042 0.269 1200 Planarity : 0.004 0.040 1254 Dihedral : 9.290 75.608 1236 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.62 % Favored : 93.28 % Rotamer: Outliers : 3.53 % Allowed : 22.51 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.10 (0.27), residues: 922 helix: 0.45 (0.24), residues: 487 sheet: 0.15 (0.73), residues: 52 loop : -2.50 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 405 HIS 0.005 0.001 HIS B 319 PHE 0.024 0.001 PHE B 474 TYR 0.016 0.001 TYR B 103 ARG 0.004 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6791 (pp) REVERT: A 191 TRP cc_start: 0.7828 (m100) cc_final: 0.7379 (m-10) REVERT: A 192 LEU cc_start: 0.8787 (mm) cc_final: 0.8567 (mm) REVERT: A 290 ASP cc_start: 0.8211 (m-30) cc_final: 0.7723 (t0) REVERT: A 300 LYS cc_start: 0.8556 (mmtt) cc_final: 0.8292 (mmtt) REVERT: A 415 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.7151 (t-170) REVERT: A 511 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8368 (mmtt) REVERT: A 559 ASP cc_start: 0.7865 (t0) cc_final: 0.7652 (t0) REVERT: B 145 GLN cc_start: 0.8177 (mt0) cc_final: 0.7656 (mp10) REVERT: B 188 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6175 (t80) REVERT: B 210 LEU cc_start: 0.8701 (tt) cc_final: 0.8367 (tt) REVERT: B 291 LEU cc_start: 0.8253 (mp) cc_final: 0.7945 (mp) outliers start: 27 outliers final: 19 residues processed: 136 average time/residue: 0.1919 time to fit residues: 35.2067 Evaluate side-chains 133 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 440 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 0.8980 chunk 84 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 0.0970 chunk 25 optimal weight: 0.7980 chunk 73 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 52 optimal weight: 0.0970 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 269 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN B 358 HIS ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7512 Z= 0.149 Angle : 0.665 10.199 10210 Z= 0.309 Chirality : 0.042 0.286 1200 Planarity : 0.004 0.039 1254 Dihedral : 9.015 71.870 1236 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.94 % Favored : 92.95 % Rotamer: Outliers : 3.27 % Allowed : 23.17 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.86 (0.28), residues: 922 helix: 0.69 (0.24), residues: 487 sheet: 0.30 (0.73), residues: 52 loop : -2.45 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 405 HIS 0.004 0.001 HIS B 319 PHE 0.025 0.001 PHE B 474 TYR 0.015 0.001 TYR B 103 ARG 0.007 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7805 (m100) cc_final: 0.7354 (m-10) REVERT: A 192 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8543 (mm) REVERT: A 300 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8293 (mmtt) REVERT: A 490 MET cc_start: 0.5791 (tpt) cc_final: 0.5484 (tpt) REVERT: B 188 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.6169 (t80) REVERT: B 210 LEU cc_start: 0.8693 (tt) cc_final: 0.8358 (tt) outliers start: 25 outliers final: 18 residues processed: 139 average time/residue: 0.1799 time to fit residues: 34.4950 Evaluate side-chains 136 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 440 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 55 optimal weight: 0.0980 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7512 Z= 0.169 Angle : 0.702 12.061 10210 Z= 0.324 Chirality : 0.043 0.293 1200 Planarity : 0.004 0.039 1254 Dihedral : 8.996 70.460 1236 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.83 % Favored : 93.06 % Rotamer: Outliers : 2.75 % Allowed : 23.82 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.27), residues: 922 helix: 0.73 (0.24), residues: 487 sheet: 0.38 (0.73), residues: 52 loop : -2.42 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 405 HIS 0.004 0.001 HIS B 319 PHE 0.017 0.001 PHE B 439 TYR 0.021 0.001 TYR B 103 ARG 0.007 0.001 ARG B 421 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8646 (tppt) cc_final: 0.8283 (ttpp) REVERT: A 191 TRP cc_start: 0.7817 (m100) cc_final: 0.7345 (m-10) REVERT: A 192 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8567 (mm) REVERT: A 300 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8325 (mmtt) REVERT: A 415 HIS cc_start: 0.7426 (OUTLIER) cc_final: 0.6974 (t-170) REVERT: A 490 MET cc_start: 0.5824 (tpt) cc_final: 0.5394 (tpt) REVERT: B 145 GLN cc_start: 0.8096 (mt0) cc_final: 0.7682 (mt0) REVERT: B 188 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.6169 (t80) REVERT: B 210 LEU cc_start: 0.8716 (tt) cc_final: 0.8388 (tt) REVERT: B 291 LEU cc_start: 0.8263 (mp) cc_final: 0.8014 (mp) outliers start: 21 outliers final: 16 residues processed: 132 average time/residue: 0.1918 time to fit residues: 34.1581 Evaluate side-chains 134 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 440 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.0570 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 72 optimal weight: 0.0980 chunk 30 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 0.0770 chunk 13 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 4 optimal weight: 0.4980 chunk 52 optimal weight: 0.0670 overall best weight: 0.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.137270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108378 restraints weight = 11898.725| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.94 r_work: 0.3338 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7512 Z= 0.146 Angle : 0.692 10.777 10210 Z= 0.319 Chirality : 0.043 0.309 1200 Planarity : 0.004 0.041 1254 Dihedral : 8.714 66.297 1236 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.72 % Favored : 93.17 % Rotamer: Outliers : 2.49 % Allowed : 23.95 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.28), residues: 922 helix: 0.94 (0.24), residues: 487 sheet: 0.46 (0.78), residues: 47 loop : -2.40 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 134 HIS 0.004 0.001 HIS B 319 PHE 0.018 0.001 PHE B 439 TYR 0.018 0.001 TYR B 103 ARG 0.008 0.001 ARG A 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1971.13 seconds wall clock time: 36 minutes 17.38 seconds (2177.38 seconds total)