Starting phenix.real_space_refine on Fri Feb 14 23:07:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qm5_4588/02_2025/6qm5_4588.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qm5_4588/02_2025/6qm5_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/cci-nas-00/data/ceres_data/6qm5_4588/02_2025/6qm5_4588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qm5_4588/02_2025/6qm5_4588.map" model { file = "/net/cci-nas-00/data/ceres_data/6qm5_4588/02_2025/6qm5_4588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qm5_4588/02_2025/6qm5_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-5592/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: 9.14, per 1000 atoms: 0.84 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: 2.62 Conformation dependent library (CDL) restraints added in 1.3 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: 1.06 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: 2.99 Time building geometry restraints manager: 3.01 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: 0.05 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: 0.980 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.100 Find NCS groups from input model: 0.190 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.610 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.197 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: 0.2358 time to fit residues: 55.1821 Evaluate side-chains 107 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.137928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107616 restraints weight = 15459.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109655 restraints weight = 10184.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.110356 restraints weight = 7305.057| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 1.180 Fit side-chains REVERT: A 124 THR cc_start: 0.9323 (m) cc_final: 0.8948 (p) REVERT: A 145 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7134 (tm-30) REVERT: A 290 LEU cc_start: 0.9023 (tp) cc_final: 0.8766 (tt) REVERT: A 312 LEU cc_start: 0.8777 (tt) cc_final: 0.8492 (tt) REVERT: A 318 GLU cc_start: 0.8539 (mp0) cc_final: 0.8271 (mp0) REVERT: A 542 LYS cc_start: 0.8646 (ttpt) cc_final: 0.8302 (ttpp) REVERT: A 692 GLU cc_start: 0.8259 (mp0) cc_final: 0.7973 (mp0) REVERT: B 79 GLN cc_start: 0.8416 (tp40) cc_final: 0.8155 (tp-100) REVERT: B 82 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7508 (ttp80) REVERT: B 145 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7146 (tm-30) REVERT: B 290 LEU cc_start: 0.9078 (tp) cc_final: 0.8856 (tt) REVERT: B 312 LEU cc_start: 0.8802 (tt) cc_final: 0.8572 (tt) REVERT: B 318 GLU cc_start: 0.8546 (mp0) cc_final: 0.8290 (mp0) outliers start: 13 outliers final: 7 residues processed: 148 average time/residue: 0.1967 time to fit residues: 44.0965 Evaluate side-chains 122 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 103 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 412 GLN B 378 ASN B 412 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.091393 restraints weight = 15778.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.092322 restraints weight = 9786.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.092557 restraints weight = 8292.558| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2337 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= 0.190 Angle : 0.519 6.908 15120 Z= 0.271 Chirality : 0.040 0.161 1658 Planarity : 0.004 0.048 1920 Dihedral : 4.440 16.783 1446 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.21 % Allowed : 14.10 % Favored : 84.69 % 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: -2.82 (0.21), residues: 1322 helix: -1.44 (0.16), residues: 902 sheet: -2.62 (0.45), residues: 74 loop : -2.35 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 235 HIS 0.003 0.001 HIS A 479 PHE 0.029 0.001 PHE B 205 TYR 0.013 0.001 TYR B 26 ARG 0.005 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 134 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 1.171 Fit side-chains REVERT: A 124 THR cc_start: 0.9303 (m) cc_final: 0.8875 (p) REVERT: A 145 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7257 (tm-30) REVERT: A 290 LEU cc_start: 0.9032 (tp) cc_final: 0.8829 (tt) REVERT: A 312 LEU cc_start: 0.8811 (tt) cc_final: 0.8540 (tt) REVERT: A 318 GLU cc_start: 0.8532 (mp0) cc_final: 0.8203 (mp0) REVERT: A 542 LYS cc_start: 0.8590 (ttpt) cc_final: 0.8360 (ttpp) REVERT: A 692 GLU cc_start: 0.8545 (mp0) cc_final: 0.8160 (mp0) REVERT: B 79 GLN cc_start: 0.8450 (tp40) cc_final: 0.8185 (tp-100) REVERT: B 82 ARG cc_start: 0.7736 (ttp-170) cc_final: 0.7486 (ttp80) REVERT: B 145 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7256 (tm-30) REVERT: B 312 LEU cc_start: 0.8807 (tt) cc_final: 0.8494 (tt) REVERT: B 318 GLU cc_start: 0.8572 (mp0) cc_final: 0.8257 (mp0) outliers start: 14 outliers final: 11 residues processed: 130 average time/residue: 0.2116 time to fit residues: 41.0227 Evaluate side-chains 117 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 A residue 569 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 62 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 123 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.0070 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110089 restraints weight = 15395.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.112100 restraints weight = 8887.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112567 restraints weight = 6498.140| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11150 Z= 0.145 Angle : 0.494 7.266 15120 Z= 0.254 Chirality : 0.039 0.155 1658 Planarity : 0.004 0.040 1920 Dihedral : 4.142 16.565 1446 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.12 % Allowed : 15.48 % Favored : 83.39 % 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: -1.83 (0.22), residues: 1322 helix: -0.65 (0.17), residues: 902 sheet: -2.35 (0.46), residues: 78 loop : -2.09 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.002 0.000 HIS A 479 PHE 0.027 0.001 PHE B 205 TYR 0.013 0.001 TYR B 26 ARG 0.005 0.000 ARG A 710 *********************** 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 146 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 1.254 Fit side-chains REVERT: A 124 THR cc_start: 0.9264 (m) cc_final: 0.8924 (p) REVERT: A 145 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7214 (tm-30) REVERT: A 318 GLU cc_start: 0.8464 (mp0) cc_final: 0.8095 (mp0) REVERT: A 406 PHE cc_start: 0.8903 (t80) cc_final: 0.8555 (t80) REVERT: A 648 GLN cc_start: 0.7034 (pp30) cc_final: 0.6758 (pp30) REVERT: A 692 GLU cc_start: 0.8396 (mp0) cc_final: 0.8068 (mp0) REVERT: A 711 MET cc_start: 0.7819 (ttm) cc_final: 0.7558 (mtp) REVERT: B 79 GLN cc_start: 0.8453 (tp40) cc_final: 0.8159 (tp-100) REVERT: B 82 ARG cc_start: 0.7673 (ttp-170) cc_final: 0.7445 (ttp80) REVERT: B 145 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7297 (tm-30) REVERT: B 318 GLU cc_start: 0.8438 (mp0) cc_final: 0.8100 (mp0) REVERT: B 406 PHE cc_start: 0.8922 (t80) cc_final: 0.8573 (t80) outliers start: 13 outliers final: 13 residues processed: 142 average time/residue: 0.1995 time to fit residues: 42.8300 Evaluate side-chains 129 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 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 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 616 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 128 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN B 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.121174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.089317 restraints weight = 15696.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.090850 restraints weight = 10318.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.090977 restraints weight = 8619.640| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11150 Z= 0.246 Angle : 0.543 10.585 15120 Z= 0.277 Chirality : 0.041 0.165 1658 Planarity : 0.004 0.039 1920 Dihedral : 4.185 16.637 1446 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.38 % Allowed : 17.13 % Favored : 81.49 % 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: -1.50 (0.23), residues: 1322 helix: -0.37 (0.18), residues: 904 sheet: -2.15 (0.48), residues: 78 loop : -2.10 (0.31), residues: 340 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 0.025 0.001 PHE B 205 TYR 0.012 0.001 TYR B 26 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 132 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.156 Fit side-chains REVERT: A 145 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7359 (tm-30) REVERT: A 318 GLU cc_start: 0.8479 (mp0) cc_final: 0.8099 (mp0) REVERT: A 406 PHE cc_start: 0.8996 (t80) cc_final: 0.8652 (t80) REVERT: A 648 GLN cc_start: 0.7160 (pp30) cc_final: 0.6842 (pp30) REVERT: A 692 GLU cc_start: 0.8553 (mp0) cc_final: 0.8124 (mp0) REVERT: B 79 GLN cc_start: 0.8514 (tp40) cc_final: 0.8195 (tp-100) REVERT: B 82 ARG cc_start: 0.7721 (ttp-170) cc_final: 0.7448 (ttp80) REVERT: B 145 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7388 (tm-30) REVERT: B 318 GLU cc_start: 0.8489 (mp0) cc_final: 0.8147 (mp0) REVERT: B 406 PHE cc_start: 0.9010 (t80) cc_final: 0.8625 (t80) REVERT: B 516 MET cc_start: 0.8574 (mtm) cc_final: 0.8300 (mtp) outliers start: 16 outliers final: 15 residues processed: 128 average time/residue: 0.2195 time to fit residues: 41.7380 Evaluate side-chains 123 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 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 378 ASN Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 701 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 58 HIS B 378 ASN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.143885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.111795 restraints weight = 15633.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114699 restraints weight = 9172.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116463 restraints weight = 6773.803| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11150 Z= 0.156 Angle : 0.523 11.514 15120 Z= 0.260 Chirality : 0.039 0.157 1658 Planarity : 0.004 0.040 1920 Dihedral : 3.999 16.582 1446 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.73 % Allowed : 17.21 % Favored : 81.06 % 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: -1.11 (0.23), residues: 1322 helix: -0.03 (0.18), residues: 914 sheet: -1.95 (0.50), residues: 78 loop : -2.15 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 235 HIS 0.002 0.000 HIS B 479 PHE 0.027 0.001 PHE B 205 TYR 0.013 0.001 TYR A 26 ARG 0.006 0.000 ARG A 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 143 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.248 Fit side-chains REVERT: A 58 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7974 (m-70) REVERT: A 124 THR cc_start: 0.9296 (m) cc_final: 0.8906 (p) REVERT: A 318 GLU cc_start: 0.8433 (mp0) cc_final: 0.8100 (mp0) REVERT: A 406 PHE cc_start: 0.8926 (t80) cc_final: 0.8610 (t80) REVERT: A 648 GLN cc_start: 0.7002 (pp30) cc_final: 0.6718 (pp30) REVERT: A 692 GLU cc_start: 0.8473 (mp0) cc_final: 0.8091 (mp0) REVERT: B 58 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7145 (m90) REVERT: B 79 GLN cc_start: 0.8491 (tp40) cc_final: 0.8179 (tp-100) REVERT: B 82 ARG cc_start: 0.7689 (ttp-170) cc_final: 0.7443 (ttp80) REVERT: B 145 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7342 (tm-30) REVERT: B 318 GLU cc_start: 0.8435 (mp0) cc_final: 0.8110 (mp0) REVERT: B 406 PHE cc_start: 0.8933 (t80) cc_final: 0.8608 (t80) REVERT: B 408 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8246 (ttp80) outliers start: 20 outliers final: 14 residues processed: 139 average time/residue: 0.2002 time to fit residues: 42.2936 Evaluate side-chains 129 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 HIS 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 B residue 58 HIS 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 580 VAL Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 701 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 20 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 71 optimal weight: 0.1980 chunk 119 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109462 restraints weight = 15544.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112455 restraints weight = 8947.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114336 restraints weight = 6522.700| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2919 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 10.840 15120 Z= 0.257 Chirality : 0.039 0.160 1658 Planarity : 0.004 0.039 1920 Dihedral : 3.903 12.509 1446 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.56 % Allowed : 17.91 % 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: -0.79 (0.24), residues: 1322 helix: 0.22 (0.18), residues: 916 sheet: -1.91 (0.50), residues: 78 loop : -2.07 (0.31), residues: 328 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 0.027 0.001 PHE B 205 TYR 0.012 0.001 TYR B 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 139 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.277 Fit side-chains REVERT: A 124 THR cc_start: 0.9290 (m) cc_final: 0.8944 (p) REVERT: A 318 GLU cc_start: 0.8397 (mp0) cc_final: 0.8047 (mp0) REVERT: A 406 PHE cc_start: 0.8905 (t80) cc_final: 0.8615 (t80) REVERT: A 437 MET cc_start: 0.9099 (tpp) cc_final: 0.8853 (mmm) REVERT: A 648 GLN cc_start: 0.7011 (pp30) cc_final: 0.6683 (pp30) REVERT: A 692 GLU cc_start: 0.8395 (mp0) cc_final: 0.8066 (mp0) REVERT: B 79 GLN cc_start: 0.8475 (tp40) cc_final: 0.8170 (tp-100) REVERT: B 82 ARG cc_start: 0.7687 (ttp-170) cc_final: 0.7449 (ttp80) REVERT: B 318 GLU cc_start: 0.8407 (mp0) cc_final: 0.8067 (mp0) REVERT: B 406 PHE cc_start: 0.8919 (t80) cc_final: 0.8607 (t80) REVERT: B 408 ARG cc_start: 0.8418 (ttp80) cc_final: 0.8202 (ttp80) REVERT: B 437 MET cc_start: 0.9109 (tpp) cc_final: 0.8847 (mmm) outliers start: 18 outliers final: 17 residues processed: 135 average time/residue: 0.2060 time to fit residues: 42.6138 Evaluate side-chains 127 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 701 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 126 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 86 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS B 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.137598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.106677 restraints weight = 15437.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.107796 restraints weight = 8994.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.108314 restraints weight = 7597.894| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11150 Z= 0.237 Angle : 0.555 10.610 15120 Z= 0.277 Chirality : 0.041 0.166 1658 Planarity : 0.004 0.038 1920 Dihedral : 4.009 12.819 1446 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % 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: -0.79 (0.24), residues: 1322 helix: 0.22 (0.18), residues: 916 sheet: -1.87 (0.51), residues: 78 loop : -2.07 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 195 ARG 0.006 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 133 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 1.269 Fit side-chains REVERT: A 145 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7364 (tm-30) REVERT: A 318 GLU cc_start: 0.8407 (mp0) cc_final: 0.8028 (mp0) REVERT: A 406 PHE cc_start: 0.9008 (t80) cc_final: 0.8650 (t80) REVERT: A 648 GLN cc_start: 0.7117 (pp30) cc_final: 0.6771 (pp30) REVERT: A 692 GLU cc_start: 0.8564 (mp0) cc_final: 0.8109 (mp0) REVERT: B 79 GLN cc_start: 0.8528 (tp40) cc_final: 0.8151 (tp-100) REVERT: B 318 GLU cc_start: 0.8417 (mp0) cc_final: 0.8059 (mp0) REVERT: B 648 GLN cc_start: 0.7003 (pp30) cc_final: 0.6753 (pp30) outliers start: 20 outliers final: 17 residues processed: 129 average time/residue: 0.2002 time to fit residues: 39.4667 Evaluate side-chains 125 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain B residue 701 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 25 optimal weight: 10.0000 chunk 76 optimal weight: 0.0870 chunk 63 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.119620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.088535 restraints weight = 16133.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.088628 restraints weight = 10204.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.088974 restraints weight = 9480.530| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.005 0.052 11150 Z= 0.336 Angle : 0.601 10.261 15120 Z= 0.304 Chirality : 0.043 0.172 1658 Planarity : 0.004 0.039 1920 Dihedral : 4.256 17.580 1446 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.64 % Allowed : 18.43 % Favored : 79.93 % 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: -0.99 (0.23), residues: 1322 helix: 0.05 (0.18), residues: 916 sheet: -1.91 (0.51), residues: 78 loop : -2.07 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 521 HIS 0.005 0.001 HIS B 479 PHE 0.023 0.001 PHE B 205 TYR 0.014 0.001 TYR B 195 ARG 0.005 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 132 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.307 Fit side-chains REVERT: A 318 GLU cc_start: 0.8467 (mp0) cc_final: 0.8063 (mp0) REVERT: A 406 PHE cc_start: 0.9038 (t80) cc_final: 0.8700 (t80) REVERT: A 437 MET cc_start: 0.9161 (tpp) cc_final: 0.8909 (mmm) REVERT: A 546 SER cc_start: 0.9172 (m) cc_final: 0.8861 (t) REVERT: A 648 GLN cc_start: 0.7086 (pp30) cc_final: 0.6721 (pp30) REVERT: A 692 GLU cc_start: 0.8627 (mp0) cc_final: 0.8134 (mp0) REVERT: B 79 GLN cc_start: 0.8557 (tp40) cc_final: 0.8274 (tp-100) REVERT: B 318 GLU cc_start: 0.8456 (mp0) cc_final: 0.8080 (mp0) REVERT: B 437 MET cc_start: 0.9185 (tpp) cc_final: 0.8927 (mmm) REVERT: B 526 CYS cc_start: 0.8464 (t) cc_final: 0.8166 (m) REVERT: B 648 GLN cc_start: 0.7033 (pp30) cc_final: 0.6646 (pp30) outliers start: 19 outliers final: 17 residues processed: 127 average time/residue: 0.2168 time to fit residues: 41.0696 Evaluate side-chains 123 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 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 6 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 7 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.140619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110786 restraints weight = 15389.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112573 restraints weight = 10120.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113309 restraints weight = 7197.997| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11150 Z= 0.152 Angle : 0.536 10.545 15120 Z= 0.267 Chirality : 0.039 0.156 1658 Planarity : 0.004 0.041 1920 Dihedral : 3.924 14.122 1446 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.38 % Allowed : 18.51 % 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: -0.55 (0.24), residues: 1322 helix: 0.37 (0.18), residues: 922 sheet: -1.75 (0.52), residues: 78 loop : -1.94 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 235 HIS 0.003 0.001 HIS B 58 PHE 0.027 0.001 PHE B 205 TYR 0.014 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 132 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.208 Fit side-chains REVERT: A 318 GLU cc_start: 0.8385 (mp0) cc_final: 0.8035 (mp0) REVERT: A 437 MET cc_start: 0.9080 (tpp) cc_final: 0.8845 (mmm) REVERT: A 648 GLN cc_start: 0.7023 (pp30) cc_final: 0.6710 (pp30) REVERT: A 692 GLU cc_start: 0.8407 (mp0) cc_final: 0.8035 (mp0) REVERT: B 79 GLN cc_start: 0.8470 (tp40) cc_final: 0.8146 (tp-100) REVERT: B 82 ARG cc_start: 0.7754 (ttp-170) cc_final: 0.7497 (ttp80) REVERT: B 145 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7395 (tm-30) REVERT: B 318 GLU cc_start: 0.8390 (mp0) cc_final: 0.8042 (mp0) REVERT: B 437 MET cc_start: 0.9123 (tpp) cc_final: 0.8854 (mmm) outliers start: 16 outliers final: 16 residues processed: 128 average time/residue: 0.2123 time to fit residues: 40.7135 Evaluate side-chains 124 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 0.0000 chunk 48 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 92 optimal weight: 0.1980 chunk 25 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.140722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110678 restraints weight = 15358.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112232 restraints weight = 9999.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113154 restraints weight = 7710.328| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11150 Z= 0.149 Angle : 0.530 10.397 15120 Z= 0.263 Chirality : 0.039 0.158 1658 Planarity : 0.004 0.040 1920 Dihedral : 3.842 12.081 1446 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.47 % Allowed : 18.60 % Favored : 79.93 % 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: -0.35 (0.24), residues: 1322 helix: 0.53 (0.18), residues: 924 sheet: -1.74 (0.53), residues: 78 loop : -1.89 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 235 HIS 0.003 0.001 HIS B 58 PHE 0.042 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: 2852.15 seconds wall clock time: 52 minutes 6.46 seconds (3126.46 seconds total)