Starting phenix.real_space_refine on Wed Sep 25 16:44:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm5_4588/09_2024/6qm5_4588.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm5_4588/09_2024/6qm5_4588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm5_4588/09_2024/6qm5_4588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm5_4588/09_2024/6qm5_4588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm5_4588/09_2024/6qm5_4588.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm5_4588/09_2024/6qm5_4588.cif" } resolution = 3.6 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= 0.008 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 Ca 4 9.91 5 S 40 5.16 5 C 7066 2.51 5 N 1818 2.21 5 O 1946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10874 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5435 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 29, 'TRANS': 643} Chain breaks: 5 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 10.37, per 1000 atoms: 0.95 Number of scatterers: 10874 At special positions: 0 Unit cell: (87.032, 142.692, 108.284, 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) Ca 4 19.99 S 40 16.00 O 1946 8.00 N 1818 7.00 C 7066 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: 2.49 Conformation dependent library (CDL) restraints added in 1.2 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2548 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 69.1% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 33 through 49 removed outlier: 3.882A pdb=" N ALA A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 89 removed outlier: 4.132A pdb=" N LYS A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 111 through 124 removed outlier: 3.520A pdb=" N LEU A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.700A pdb=" N ALA A 139 " --> pdb=" O PRO A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 165 removed outlier: 3.711A pdb=" N LYS A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 187 removed outlier: 3.515A pdb=" N ASN A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLU A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N SER A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 removed outlier: 3.516A pdb=" N SER A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 removed outlier: 3.683A pdb=" N PHE A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 246 removed outlier: 3.771A pdb=" N GLY A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A 228 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.534A pdb=" N ARG A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 319 removed outlier: 3.639A pdb=" N PHE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 330 through 356 removed outlier: 3.542A pdb=" N GLY A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Proline residue: A 341 - end of helix removed outlier: 3.505A pdb=" N SER A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 392 removed outlier: 3.636A pdb=" N THR A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 399 removed outlier: 4.008A pdb=" N ILE A 399 " --> pdb=" O PHE A 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 399' Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.732A pdb=" N ARG A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 442 through 453 removed outlier: 3.772A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 460 removed outlier: 3.521A pdb=" N GLN A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 482 through 493 Processing helix chain 'A' and resid 499 through 516 removed outlier: 3.838A pdb=" N ASP A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 511 " --> pdb=" O MET A 507 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 524 Proline residue: A 522 - end of helix Processing helix chain 'A' and resid 525 through 545 removed outlier: 3.873A pdb=" N VAL A 530 " --> pdb=" O CYS A 526 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN A 531 " --> pdb=" O CYS A 527 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 572 removed outlier: 3.724A pdb=" N PHE A 567 " --> pdb=" O THR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 removed outlier: 4.249A pdb=" N VAL A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A 581 " --> pdb=" O SER A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 587 Processing helix chain 'A' and resid 598 through 627 removed outlier: 4.033A pdb=" N TYR A 613 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 625 " --> pdb=" O ARG A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 651 removed outlier: 3.649A pdb=" N GLU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 640 " --> pdb=" O ARG A 636 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 682 Processing helix chain 'A' and resid 691 through 696 removed outlier: 4.052A pdb=" N TRP A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 717 removed outlier: 3.516A pdb=" N GLU A 706 " --> pdb=" O GLN A 702 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 712 " --> pdb=" O GLY A 708 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN A 715 " --> pdb=" O MET A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 49 removed outlier: 3.883A pdb=" N ALA B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR B 48 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 89 removed outlier: 4.132A pdb=" N LYS B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 111 through 124 removed outlier: 3.520A pdb=" N LEU B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.700A pdb=" N ALA B 139 " --> pdb=" O PRO B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 165 removed outlier: 3.711A pdb=" N LYS B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 187 removed outlier: 3.516A pdb=" N ASN B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLU B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N SER B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL B 185 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 197 removed outlier: 3.515A pdb=" N SER B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.683A pdb=" N PHE B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 246 removed outlier: 3.772A pdb=" N GLY B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER B 228 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.534A pdb=" N ARG B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 319 removed outlier: 3.639A pdb=" N PHE B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 329 No H-bonds generated for 'chain 'B' and resid 327 through 329' Processing helix chain 'B' and resid 330 through 356 removed outlier: 3.542A pdb=" N GLY B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.504A pdb=" N SER B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 392 removed outlier: 3.636A pdb=" N THR B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER B 382 " --> pdb=" O ASN B 378 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 391 " --> pdb=" O PHE B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 399 removed outlier: 4.007A pdb=" N ILE B 399 " --> pdb=" O PHE B 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 399' Processing helix chain 'B' and resid 400 through 413 removed outlier: 3.732A pdb=" N ARG B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 442 Processing helix chain 'B' and resid 442 through 453 removed outlier: 3.771A pdb=" N ASN B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 460 removed outlier: 3.521A pdb=" N GLN B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 482 through 493 Processing helix chain 'B' and resid 499 through 516 removed outlier: 3.839A pdb=" N ASP B 503 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 504 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 511 " --> pdb=" O MET B 507 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 514 " --> pdb=" O GLN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 524 Proline residue: B 522 - end of helix Processing helix chain 'B' and resid 525 through 545 removed outlier: 3.874A pdb=" N VAL B 530 " --> pdb=" O CYS B 526 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN B 531 " --> pdb=" O CYS B 527 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 572 removed outlier: 3.724A pdb=" N PHE B 567 " --> pdb=" O THR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 583 removed outlier: 4.249A pdb=" N VAL B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 587 Processing helix chain 'B' and resid 598 through 627 removed outlier: 4.033A pdb=" N TYR B 613 " --> pdb=" O ALA B 609 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 625 " --> pdb=" O ARG B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 651 removed outlier: 3.649A pdb=" N GLU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 643 " --> pdb=" O ARG B 639 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 682 Processing helix chain 'B' and resid 691 through 696 removed outlier: 4.052A pdb=" N TRP B 695 " --> pdb=" O GLU B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 717 removed outlier: 3.515A pdb=" N GLU B 706 " --> pdb=" O GLN B 702 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 712 " --> pdb=" O GLY B 708 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 713 " --> pdb=" O ARG B 709 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B 715 " --> pdb=" O MET B 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 268 removed outlier: 3.639A pdb=" N HIS A 265 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 267 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 268 removed outlier: 3.639A pdb=" N HIS B 265 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 267 " --> pdb=" O VAL B 276 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1572 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: 3.16 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3446 1.34 - 1.46: 2110 1.46 - 1.57: 5528 1.57 - 1.69: 0 1.69 - 1.80: 66 Bond restraints: 11150 Sorted by residual: bond pdb=" C ILE B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.21e+00 bond pdb=" CA PHE A 396 " pdb=" CB PHE A 396 " ideal model delta sigma weight residual 1.524 1.564 -0.040 1.62e-02 3.81e+03 6.20e+00 bond pdb=" C ILE A 394 " pdb=" N PRO A 395 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.20e+00 bond pdb=" CA PHE B 396 " pdb=" CB PHE B 396 " ideal model delta sigma weight residual 1.524 1.564 -0.040 1.62e-02 3.81e+03 6.18e+00 bond pdb=" CB PRO B 202 " pdb=" CG PRO B 202 " ideal model delta sigma weight residual 1.492 1.405 0.087 5.00e-02 4.00e+02 3.00e+00 ... (remaining 11145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 14484 1.81 - 3.61: 542 3.61 - 5.42: 58 5.42 - 7.23: 18 7.23 - 9.04: 18 Bond angle restraints: 15120 Sorted by residual: angle pdb=" N VAL B 319 " pdb=" CA VAL B 319 " pdb=" C VAL B 319 " ideal model delta sigma weight residual 106.53 112.19 -5.66 1.41e+00 5.03e-01 1.61e+01 angle pdb=" N VAL A 319 " pdb=" CA VAL A 319 " pdb=" C VAL A 319 " ideal model delta sigma weight residual 106.53 112.17 -5.64 1.41e+00 5.03e-01 1.60e+01 angle pdb=" CA ILE B 394 " pdb=" C ILE B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 118.88 124.70 -5.82 1.54e+00 4.22e-01 1.43e+01 angle pdb=" CA ILE A 394 " pdb=" C ILE A 394 " pdb=" N PRO A 395 " ideal model delta sigma weight residual 118.88 124.69 -5.81 1.54e+00 4.22e-01 1.43e+01 angle pdb=" N VAL A 134 " pdb=" CA VAL A 134 " pdb=" C VAL A 134 " ideal model delta sigma weight residual 109.34 102.14 7.20 2.08e+00 2.31e-01 1.20e+01 ... (remaining 15115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5784 17.89 - 35.77: 630 35.77 - 53.66: 112 53.66 - 71.55: 22 71.55 - 89.43: 20 Dihedral angle restraints: 6568 sinusoidal: 2642 harmonic: 3926 Sorted by residual: dihedral pdb=" CA HIS A 401 " pdb=" C HIS A 401 " pdb=" N PRO A 402 " pdb=" CA PRO A 402 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA HIS B 401 " pdb=" C HIS B 401 " pdb=" N PRO B 402 " pdb=" CA PRO B 402 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ALA B 139 " pdb=" C ALA B 139 " pdb=" N LYS B 140 " pdb=" CA LYS B 140 " ideal model delta harmonic sigma weight residual 180.00 162.86 17.14 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 6565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1211 0.051 - 0.101: 355 0.101 - 0.152: 75 0.152 - 0.202: 13 0.202 - 0.253: 4 Chirality restraints: 1658 Sorted by residual: chirality pdb=" CA THR B 340 " pdb=" N THR B 340 " pdb=" C THR B 340 " pdb=" CB THR B 340 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA THR A 340 " pdb=" N THR A 340 " pdb=" C THR A 340 " pdb=" CB THR A 340 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL A 229 " pdb=" CA VAL A 229 " pdb=" CG1 VAL A 229 " pdb=" CG2 VAL A 229 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1655 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 401 " 0.050 5.00e-02 4.00e+02 7.46e-02 8.90e+00 pdb=" N PRO A 402 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 402 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 402 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 401 " 0.050 5.00e-02 4.00e+02 7.44e-02 8.87e+00 pdb=" N PRO B 402 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 402 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 402 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 125 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO B 126 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " 0.033 5.00e-02 4.00e+02 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3542 2.83 - 3.35: 9667 3.35 - 3.86: 17289 3.86 - 4.38: 20239 4.38 - 4.90: 34700 Nonbonded interactions: 85437 Sorted by model distance: nonbonded pdb=" OH TYR B 188 " pdb=" OD2 ASP B 539 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR A 188 " pdb=" OD2 ASP A 539 " model vdw 2.311 3.040 nonbonded pdb=" OE1 GLU A 145 " pdb=" OG SER A 146 " model vdw 2.338 3.040 nonbonded pdb=" OE1 GLU B 145 " pdb=" OG SER B 146 " model vdw 2.339 3.040 nonbonded pdb=" OH TYR A 498 " pdb=" OD2 ASP A 503 " model vdw 2.340 3.040 ... (remaining 85432 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.600 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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: 33.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 11150 Z= 0.412 Angle : 0.831 9.037 15120 Z= 0.461 Chirality : 0.052 0.253 1658 Planarity : 0.006 0.075 1920 Dihedral : 15.765 89.434 4020 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -6.65 (0.13), residues: 1322 helix: -4.69 (0.06), residues: 874 sheet: -4.21 (0.36), residues: 54 loop : -2.99 (0.24), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 235 HIS 0.007 0.001 HIS A 479 PHE 0.023 0.002 PHE A 396 TYR 0.012 0.002 TYR B 195 ARG 0.003 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.206 Fit side-chains REVERT: A 124 THR cc_start: 0.9217 (m) cc_final: 0.8934 (p) REVERT: A 145 GLU cc_start: 0.7604 (tm-30) cc_final: 0.6891 (tm-30) REVERT: A 312 LEU cc_start: 0.8876 (tt) cc_final: 0.8577 (tt) REVERT: A 408 ARG cc_start: 0.7766 (mtp85) cc_final: 0.7542 (ttp80) REVERT: A 457 TYR cc_start: 0.7277 (t80) cc_final: 0.6914 (t80) REVERT: A 542 LYS cc_start: 0.8781 (ttpt) cc_final: 0.8429 (ttpp) REVERT: A 692 GLU cc_start: 0.8100 (mp0) cc_final: 0.7619 (mp0) REVERT: B 692 GLU cc_start: 0.8238 (mp0) cc_final: 0.7689 (mp0) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2329 time to fit residues: 54.6547 Evaluate side-chains 107 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 54 optimal weight: 0.5980 chunk 105 optimal weight: 0.0270 chunk 40 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 121 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS A 256 GLN A 378 ASN A 510 GLN A 617 GLN A 650 ASN B 25 HIS B 79 GLN B 256 GLN B 510 GLN B 650 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11150 Z= 0.152 Angle : 0.545 7.548 15120 Z= 0.291 Chirality : 0.040 0.172 1658 Planarity : 0.005 0.047 1920 Dihedral : 4.790 15.355 1446 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.12 % Allowed : 11.42 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.26 (0.17), residues: 1322 helix: -2.70 (0.13), residues: 894 sheet: -3.34 (0.48), residues: 54 loop : -2.44 (0.27), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 141 HIS 0.002 0.001 HIS B 479 PHE 0.031 0.001 PHE A 205 TYR 0.014 0.001 TYR B 26 ARG 0.005 0.000 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 1.265 Fit side-chains REVERT: A 124 THR cc_start: 0.9333 (m) cc_final: 0.8959 (p) REVERT: A 145 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7104 (tm-30) REVERT: A 290 LEU cc_start: 0.9030 (tp) cc_final: 0.8777 (tt) REVERT: A 312 LEU cc_start: 0.8785 (tt) cc_final: 0.8502 (tt) REVERT: A 318 GLU cc_start: 0.8540 (mp0) cc_final: 0.8269 (mp0) REVERT: A 542 LYS cc_start: 0.8648 (ttpt) cc_final: 0.8302 (ttpp) REVERT: A 692 GLU cc_start: 0.8405 (mp0) cc_final: 0.8044 (mp0) REVERT: B 79 GLN cc_start: 0.8405 (tp40) cc_final: 0.8146 (tp-100) REVERT: B 82 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7505 (ttp80) REVERT: B 145 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7108 (tm-30) REVERT: B 290 LEU cc_start: 0.9084 (tp) cc_final: 0.8864 (tt) REVERT: B 312 LEU cc_start: 0.8802 (tt) cc_final: 0.8577 (tt) REVERT: B 318 GLU cc_start: 0.8558 (mp0) cc_final: 0.8298 (mp0) outliers start: 13 outliers final: 7 residues processed: 148 average time/residue: 0.1910 time to fit residues: 42.6504 Evaluate side-chains 122 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 523 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.0030 chunk 37 optimal weight: 0.6980 chunk 101 optimal weight: 0.0980 chunk 82 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 41 optimal weight: 0.0060 chunk 97 optimal weight: 1.9990 overall best weight: 0.3006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN B 378 ASN B 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11150 Z= 0.126 Angle : 0.491 7.294 15120 Z= 0.255 Chirality : 0.038 0.154 1658 Planarity : 0.004 0.047 1920 Dihedral : 4.258 17.938 1446 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.87 % Allowed : 13.84 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.62 (0.21), residues: 1322 helix: -1.28 (0.16), residues: 902 sheet: -2.61 (0.45), residues: 74 loop : -2.29 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.002 0.000 HIS A 479 PHE 0.031 0.001 PHE B 205 TYR 0.013 0.001 TYR B 26 ARG 0.004 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 137 time to evaluate : 1.231 Fit side-chains REVERT: A 124 THR cc_start: 0.9260 (m) cc_final: 0.8984 (p) REVERT: A 145 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7167 (tm-30) REVERT: A 312 LEU cc_start: 0.8772 (tt) cc_final: 0.8474 (tt) REVERT: A 318 GLU cc_start: 0.8482 (mp0) cc_final: 0.8144 (mp0) REVERT: A 406 PHE cc_start: 0.8894 (t80) cc_final: 0.8579 (t80) REVERT: A 692 GLU cc_start: 0.8400 (mp0) cc_final: 0.8120 (mp0) REVERT: B 79 GLN cc_start: 0.8386 (tp40) cc_final: 0.8117 (tp-100) REVERT: B 145 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7158 (tm-30) REVERT: B 195 TYR cc_start: 0.9244 (t80) cc_final: 0.8990 (t80) REVERT: B 290 LEU cc_start: 0.9045 (tp) cc_final: 0.8844 (tt) REVERT: B 312 LEU cc_start: 0.8794 (tt) cc_final: 0.8526 (tt) REVERT: B 318 GLU cc_start: 0.8504 (mp0) cc_final: 0.8207 (mp0) outliers start: 10 outliers final: 8 residues processed: 143 average time/residue: 0.1931 time to fit residues: 41.7197 Evaluate side-chains 127 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 523 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 265 HIS A 412 GLN B 378 ASN B 412 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11150 Z= 0.199 Angle : 0.515 6.360 15120 Z= 0.266 Chirality : 0.040 0.163 1658 Planarity : 0.004 0.040 1920 Dihedral : 4.147 18.200 1446 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.04 % Allowed : 15.48 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.76 (0.22), residues: 1322 helix: -0.58 (0.17), residues: 902 sheet: -2.24 (0.47), residues: 78 loop : -2.12 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.006 0.001 HIS A 265 PHE 0.026 0.001 PHE B 205 TYR 0.012 0.001 TYR A 195 ARG 0.002 0.000 ARG B 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 1.213 Fit side-chains REVERT: A 124 THR cc_start: 0.9306 (m) cc_final: 0.8912 (p) REVERT: A 318 GLU cc_start: 0.8478 (mp0) cc_final: 0.8078 (mp0) REVERT: A 406 PHE cc_start: 0.8957 (t80) cc_final: 0.8585 (t80) REVERT: A 648 GLN cc_start: 0.7047 (pp30) cc_final: 0.6751 (pp30) REVERT: A 692 GLU cc_start: 0.8526 (mp0) cc_final: 0.8184 (mp0) REVERT: B 79 GLN cc_start: 0.8509 (tp40) cc_final: 0.8165 (tp-100) REVERT: B 145 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7219 (tm-30) REVERT: B 183 GLU cc_start: 0.7542 (mp0) cc_final: 0.7341 (mp0) REVERT: B 318 GLU cc_start: 0.8469 (mp0) cc_final: 0.8111 (mp0) REVERT: B 406 PHE cc_start: 0.8974 (t80) cc_final: 0.8606 (t80) REVERT: B 516 MET cc_start: 0.8502 (mtm) cc_final: 0.8256 (mtp) outliers start: 12 outliers final: 10 residues processed: 135 average time/residue: 0.1906 time to fit residues: 39.7563 Evaluate side-chains 125 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 616 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 412 GLN B 378 ASN B 412 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11150 Z= 0.315 Angle : 0.578 11.084 15120 Z= 0.296 Chirality : 0.042 0.170 1658 Planarity : 0.004 0.040 1920 Dihedral : 4.354 19.118 1446 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.73 % Allowed : 17.47 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.61 (0.23), residues: 1322 helix: -0.45 (0.18), residues: 906 sheet: -2.09 (0.49), residues: 78 loop : -2.16 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.005 0.001 HIS B 479 PHE 0.025 0.001 PHE B 205 TYR 0.015 0.001 TYR A 195 ARG 0.005 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.298 Fit side-chains REVERT: A 145 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7370 (tm-30) REVERT: A 183 GLU cc_start: 0.7466 (mp0) cc_final: 0.7237 (mp0) REVERT: A 318 GLU cc_start: 0.8512 (mp0) cc_final: 0.8128 (mp0) REVERT: A 406 PHE cc_start: 0.9014 (t80) cc_final: 0.8676 (t80) REVERT: A 648 GLN cc_start: 0.7095 (pp30) cc_final: 0.6800 (pp30) REVERT: A 692 GLU cc_start: 0.8543 (mp0) cc_final: 0.8141 (mp0) REVERT: B 79 GLN cc_start: 0.8548 (tp40) cc_final: 0.8292 (tp-100) REVERT: B 145 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7340 (tm-30) REVERT: B 183 GLU cc_start: 0.7634 (mp0) cc_final: 0.7269 (mp0) REVERT: B 318 GLU cc_start: 0.8520 (mp0) cc_final: 0.8149 (mp0) REVERT: B 406 PHE cc_start: 0.9029 (t80) cc_final: 0.8670 (t80) REVERT: B 516 MET cc_start: 0.8609 (mtm) cc_final: 0.8358 (mtp) outliers start: 20 outliers final: 15 residues processed: 135 average time/residue: 0.2015 time to fit residues: 41.3203 Evaluate side-chains 124 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 616 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.0970 chunk 25 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 129 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 0.0170 chunk 124 optimal weight: 0.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11150 Z= 0.156 Angle : 0.517 11.461 15120 Z= 0.260 Chirality : 0.039 0.157 1658 Planarity : 0.004 0.041 1920 Dihedral : 4.058 16.571 1446 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.73 % Allowed : 17.73 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.23), residues: 1322 helix: 0.01 (0.18), residues: 906 sheet: -1.91 (0.50), residues: 78 loop : -2.01 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 235 HIS 0.003 0.000 HIS B 479 PHE 0.026 0.001 PHE B 205 TYR 0.014 0.001 TYR B 26 ARG 0.006 0.000 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 1.244 Fit side-chains REVERT: A 183 GLU cc_start: 0.7420 (mp0) cc_final: 0.7162 (mp0) REVERT: A 318 GLU cc_start: 0.8468 (mp0) cc_final: 0.8125 (mp0) REVERT: A 406 PHE cc_start: 0.8941 (t80) cc_final: 0.8614 (t80) REVERT: A 437 MET cc_start: 0.9132 (tpp) cc_final: 0.8897 (mmm) REVERT: A 648 GLN cc_start: 0.7068 (pp30) cc_final: 0.6715 (pp30) REVERT: A 692 GLU cc_start: 0.8524 (mp0) cc_final: 0.8111 (mp0) REVERT: B 79 GLN cc_start: 0.8485 (tp40) cc_final: 0.8174 (tp-100) REVERT: B 145 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7310 (tm-30) REVERT: B 183 GLU cc_start: 0.7520 (mp0) cc_final: 0.7269 (mp0) REVERT: B 318 GLU cc_start: 0.8429 (mp0) cc_final: 0.8099 (mp0) REVERT: B 408 ARG cc_start: 0.8488 (ttp80) cc_final: 0.8268 (ttp80) outliers start: 20 outliers final: 13 residues processed: 140 average time/residue: 0.1924 time to fit residues: 41.6953 Evaluate side-chains 130 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11150 Z= 0.272 Angle : 0.561 10.469 15120 Z= 0.283 Chirality : 0.041 0.167 1658 Planarity : 0.004 0.039 1920 Dihedral : 4.155 13.429 1446 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.73 % Allowed : 18.17 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.01 (0.23), residues: 1322 helix: 0.02 (0.18), residues: 908 sheet: -1.84 (0.51), residues: 78 loop : -2.01 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 235 HIS 0.004 0.001 HIS B 479 PHE 0.024 0.001 PHE B 205 TYR 0.013 0.001 TYR A 26 ARG 0.007 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.173 Fit side-chains REVERT: A 318 GLU cc_start: 0.8468 (mp0) cc_final: 0.8085 (mp0) REVERT: A 406 PHE cc_start: 0.9028 (t80) cc_final: 0.8673 (t80) REVERT: A 408 ARG cc_start: 0.8502 (ttp80) cc_final: 0.8285 (ttp80) REVERT: A 648 GLN cc_start: 0.6994 (pp30) cc_final: 0.6713 (pp30) REVERT: A 692 GLU cc_start: 0.8548 (mp0) cc_final: 0.8074 (mp0) REVERT: B 79 GLN cc_start: 0.8528 (tp40) cc_final: 0.8186 (tp-100) REVERT: B 145 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7341 (tm-30) REVERT: B 183 GLU cc_start: 0.7661 (mp0) cc_final: 0.7376 (mp0) REVERT: B 318 GLU cc_start: 0.8482 (mp0) cc_final: 0.8132 (mp0) outliers start: 20 outliers final: 20 residues processed: 132 average time/residue: 0.1906 time to fit residues: 38.3624 Evaluate side-chains 131 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 12 optimal weight: 0.3980 chunk 101 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11150 Z= 0.176 Angle : 0.535 10.294 15120 Z= 0.267 Chirality : 0.039 0.158 1658 Planarity : 0.004 0.042 1920 Dihedral : 3.987 12.987 1446 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.99 % Allowed : 18.17 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.24), residues: 1322 helix: 0.25 (0.18), residues: 912 sheet: -1.73 (0.52), residues: 78 loop : -1.96 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 235 HIS 0.003 0.001 HIS B 479 PHE 0.031 0.001 PHE B 406 TYR 0.013 0.001 TYR B 26 ARG 0.007 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.266 Fit side-chains revert: symmetry clash REVERT: A 145 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7301 (tm-30) REVERT: A 318 GLU cc_start: 0.8417 (mp0) cc_final: 0.8057 (mp0) REVERT: A 406 PHE cc_start: 0.8966 (t80) cc_final: 0.8634 (t80) REVERT: A 437 MET cc_start: 0.9107 (tpp) cc_final: 0.8873 (mmm) REVERT: A 648 GLN cc_start: 0.7048 (pp30) cc_final: 0.6714 (pp30) REVERT: A 692 GLU cc_start: 0.8529 (mp0) cc_final: 0.8095 (mp0) REVERT: B 79 GLN cc_start: 0.8495 (tp40) cc_final: 0.8177 (tp-100) REVERT: B 145 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7304 (tm-30) REVERT: B 183 GLU cc_start: 0.7580 (mp0) cc_final: 0.7268 (mp0) REVERT: B 318 GLU cc_start: 0.8436 (mp0) cc_final: 0.8095 (mp0) REVERT: B 408 ARG cc_start: 0.8510 (ttp80) cc_final: 0.8304 (ttp80) REVERT: B 437 MET cc_start: 0.9131 (tpp) cc_final: 0.8856 (mmm) REVERT: B 648 GLN cc_start: 0.6917 (pp30) cc_final: 0.6702 (pp30) outliers start: 23 outliers final: 19 residues processed: 139 average time/residue: 0.1945 time to fit residues: 41.6694 Evaluate side-chains 137 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.5980 chunk 123 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 0.1980 chunk 79 optimal weight: 0.0370 chunk 127 optimal weight: 1.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11150 Z= 0.156 Angle : 0.528 10.172 15120 Z= 0.263 Chirality : 0.039 0.158 1658 Planarity : 0.004 0.042 1920 Dihedral : 3.894 14.103 1446 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.47 % Allowed : 18.86 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.24), residues: 1322 helix: 0.47 (0.18), residues: 908 sheet: -1.70 (0.52), residues: 78 loop : -1.82 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 235 HIS 0.003 0.000 HIS B 479 PHE 0.027 0.001 PHE B 205 TYR 0.013 0.001 TYR B 26 ARG 0.008 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 145 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7306 (tm-30) REVERT: A 183 GLU cc_start: 0.7434 (mp0) cc_final: 0.7221 (mp0) REVERT: A 318 GLU cc_start: 0.8394 (mp0) cc_final: 0.8030 (mp0) REVERT: A 437 MET cc_start: 0.9116 (tpp) cc_final: 0.8903 (mmm) REVERT: A 648 GLN cc_start: 0.6985 (pp30) cc_final: 0.6673 (pp30) REVERT: A 692 GLU cc_start: 0.8524 (mp0) cc_final: 0.8089 (mp0) REVERT: B 79 GLN cc_start: 0.8466 (tp40) cc_final: 0.8158 (tp-100) REVERT: B 183 GLU cc_start: 0.7574 (mp0) cc_final: 0.7326 (mp0) REVERT: B 318 GLU cc_start: 0.8401 (mp0) cc_final: 0.8050 (mp0) REVERT: B 437 MET cc_start: 0.9132 (tpp) cc_final: 0.8888 (mmm) REVERT: B 648 GLN cc_start: 0.6885 (pp30) cc_final: 0.6643 (pp30) outliers start: 17 outliers final: 17 residues processed: 139 average time/residue: 0.1870 time to fit residues: 39.8769 Evaluate side-chains 136 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 11 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11150 Z= 0.229 Angle : 0.562 9.986 15120 Z= 0.281 Chirality : 0.040 0.164 1658 Planarity : 0.004 0.041 1920 Dihedral : 3.975 14.122 1446 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.64 % Allowed : 18.77 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.50 (0.24), residues: 1322 helix: 0.42 (0.18), residues: 908 sheet: -1.69 (0.53), residues: 78 loop : -1.87 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 235 HIS 0.003 0.001 HIS B 479 PHE 0.025 0.001 PHE B 205 TYR 0.012 0.001 TYR B 26 ARG 0.008 0.000 ARG A 710 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: A 145 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7321 (tm-30) REVERT: A 183 GLU cc_start: 0.7516 (mp0) cc_final: 0.7171 (mp0) REVERT: A 318 GLU cc_start: 0.8427 (mp0) cc_final: 0.8058 (mp0) REVERT: A 648 GLN cc_start: 0.6998 (pp30) cc_final: 0.6692 (pp30) REVERT: A 692 GLU cc_start: 0.8533 (mp0) cc_final: 0.8089 (mp0) REVERT: B 79 GLN cc_start: 0.8515 (tp40) cc_final: 0.8180 (tp-100) REVERT: B 183 GLU cc_start: 0.7614 (mp0) cc_final: 0.7331 (mp0) REVERT: B 318 GLU cc_start: 0.8434 (mp0) cc_final: 0.8078 (mp0) REVERT: B 648 GLN cc_start: 0.6919 (pp30) cc_final: 0.6692 (pp30) outliers start: 19 outliers final: 18 residues processed: 131 average time/residue: 0.2010 time to fit residues: 39.9946 Evaluate side-chains 132 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.140442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110325 restraints weight = 15466.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.111683 restraints weight = 9869.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.112446 restraints weight = 7856.263| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11150 Z= 0.198 Angle : 0.545 9.887 15120 Z= 0.272 Chirality : 0.040 0.160 1658 Planarity : 0.004 0.042 1920 Dihedral : 3.933 13.923 1446 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.73 % Allowed : 18.94 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.24), residues: 1322 helix: 0.50 (0.18), residues: 908 sheet: -1.64 (0.53), residues: 78 loop : -1.85 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 235 HIS 0.003 0.001 HIS B 479 PHE 0.025 0.001 PHE B 205 TYR 0.013 0.001 TYR B 26 ARG 0.008 0.000 ARG A 710 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1962.48 seconds wall clock time: 35 minutes 51.16 seconds (2151.16 seconds total)