Starting phenix.real_space_refine on Wed Sep 17 19:26:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qm5_4588/09_2025/6qm5_4588.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qm5_4588/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6qm5_4588/09_2025/6qm5_4588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qm5_4588/09_2025/6qm5_4588.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qm5_4588/09_2025/6qm5_4588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qm5_4588/09_2025/6qm5_4588.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.15, per 1000 atoms: 0.38 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: 0.87 Conformation dependent library (CDL) restraints added in 377.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.22 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: 1.48 Time building geometry restraints manager: 1.14 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: 0.02 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.600 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.040 ------------------------------------------------------------------------------- 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= 0.281 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 57 TYR 0.012 0.002 TYR B 195 PHE 0.023 0.002 PHE A 396 TRP 0.016 0.002 TRP A 235 HIS 0.007 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00654 (11150) covalent geometry : angle 0.83050 (15120) hydrogen bonds : bond 0.28989 ( 536) hydrogen bonds : angle 10.76974 ( 1572) *********************** 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 : 0.440 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: 0.1045 time to fit residues: 24.5998 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 : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS A 128 ASN A 143 HIS A 256 GLN A 378 ASN A 510 GLN A 617 GLN A 650 ASN B 25 HIS B 79 GLN B 128 ASN B 256 GLN B 378 ASN B 510 GLN B 650 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.108060 restraints weight = 15499.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.111031 restraints weight = 9065.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112935 restraints weight = 6681.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113977 restraints weight = 5615.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114469 restraints weight = 5113.186| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2062 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= 0.126 Angle : 0.556 7.607 15120 Z= 0.298 Chirality : 0.040 0.168 1658 Planarity : 0.005 0.047 1920 Dihedral : 4.833 15.364 1446 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.12 % Allowed : 12.11 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.30 (0.17), residues: 1322 helix: -2.73 (0.13), residues: 894 sheet: -3.32 (0.48), residues: 54 loop : -2.47 (0.26), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 710 TYR 0.014 0.001 TYR B 26 PHE 0.029 0.001 PHE A 205 TRP 0.010 0.001 TRP B 521 HIS 0.003 0.001 HIS B 479 Details of bonding type rmsd covalent geometry : bond 0.00278 (11150) covalent geometry : angle 0.55622 (15120) hydrogen bonds : bond 0.03822 ( 536) hydrogen bonds : angle 4.80736 ( 1572) *********************** 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 145 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.419 Fit side-chains REVERT: A 124 THR cc_start: 0.9343 (m) cc_final: 0.8895 (p) REVERT: A 145 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 290 LEU cc_start: 0.9037 (tp) cc_final: 0.8783 (tt) REVERT: A 312 LEU cc_start: 0.8760 (tt) cc_final: 0.8533 (tt) REVERT: A 318 GLU cc_start: 0.8588 (mp0) cc_final: 0.8315 (mp0) REVERT: A 542 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8296 (ttpp) REVERT: A 692 GLU cc_start: 0.8272 (mp0) cc_final: 0.7957 (mp0) REVERT: B 79 GLN cc_start: 0.8448 (tp40) cc_final: 0.8173 (tp-100) REVERT: B 82 ARG cc_start: 0.7855 (ttp-170) cc_final: 0.7522 (ttp80) REVERT: B 145 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7208 (tm-30) REVERT: B 290 LEU cc_start: 0.9078 (tp) cc_final: 0.8863 (tt) REVERT: B 312 LEU cc_start: 0.8793 (tt) cc_final: 0.8553 (tt) REVERT: B 318 GLU cc_start: 0.8579 (mp0) cc_final: 0.8321 (mp0) outliers start: 13 outliers final: 9 residues processed: 142 average time/residue: 0.0909 time to fit residues: 19.4711 Evaluate side-chains 122 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 93 optimal weight: 0.0010 chunk 51 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN B 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.122123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.091264 restraints weight = 15824.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.091337 restraints weight = 9782.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.091859 restraints weight = 8902.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.092017 restraints weight = 8132.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.092315 restraints weight = 7672.944| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2310 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= 0.139 Angle : 0.522 7.216 15120 Z= 0.274 Chirality : 0.040 0.163 1658 Planarity : 0.004 0.046 1920 Dihedral : 4.498 16.381 1446 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.38 % Allowed : 14.36 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.87 (0.21), residues: 1322 helix: -1.48 (0.16), residues: 902 sheet: -2.66 (0.45), residues: 74 loop : -2.35 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 33 TYR 0.014 0.001 TYR B 26 PHE 0.028 0.001 PHE A 205 TRP 0.010 0.001 TRP A 235 HIS 0.003 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00325 (11150) covalent geometry : angle 0.52208 (15120) hydrogen bonds : bond 0.03403 ( 536) hydrogen bonds : angle 4.26672 ( 1572) *********************** 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 138 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.265 Fit side-chains REVERT: A 145 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7266 (tm-30) REVERT: A 290 LEU cc_start: 0.9045 (tp) cc_final: 0.8836 (tt) REVERT: A 312 LEU cc_start: 0.8790 (tt) cc_final: 0.8483 (tt) REVERT: A 318 GLU cc_start: 0.8552 (mp0) cc_final: 0.8220 (mp0) REVERT: A 406 PHE cc_start: 0.8972 (t80) cc_final: 0.8637 (t80) REVERT: A 542 LYS cc_start: 0.8623 (ttpt) cc_final: 0.8391 (ttpp) REVERT: A 692 GLU cc_start: 0.8531 (mp0) cc_final: 0.8162 (mp0) REVERT: B 79 GLN cc_start: 0.8447 (tp40) cc_final: 0.8178 (tp-100) REVERT: B 82 ARG cc_start: 0.7740 (ttp-170) cc_final: 0.7475 (ttp80) REVERT: B 145 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7345 (tm-30) REVERT: B 318 GLU cc_start: 0.8558 (mp0) cc_final: 0.8230 (mp0) outliers start: 16 outliers final: 12 residues processed: 133 average time/residue: 0.0864 time to fit residues: 17.3997 Evaluate side-chains 115 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 78 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3355 r_free = 0.3355 target = 0.120842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.089911 restraints weight = 15959.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.089734 restraints weight = 9985.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.090126 restraints weight = 9127.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.090427 restraints weight = 8399.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.090556 restraints weight = 7867.031| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2511 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= 0.149 Angle : 0.525 7.082 15120 Z= 0.273 Chirality : 0.040 0.162 1658 Planarity : 0.004 0.041 1920 Dihedral : 4.321 13.751 1446 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.47 % Allowed : 16.52 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.22), residues: 1322 helix: -0.80 (0.17), residues: 902 sheet: -2.37 (0.46), residues: 78 loop : -2.14 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 710 TYR 0.013 0.001 TYR B 26 PHE 0.026 0.001 PHE B 205 TRP 0.011 0.001 TRP A 235 HIS 0.003 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00353 (11150) covalent geometry : angle 0.52503 (15120) hydrogen bonds : bond 0.03176 ( 536) hydrogen bonds : angle 4.06286 ( 1572) *********************** 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 to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.443 Fit side-chains REVERT: A 318 GLU cc_start: 0.8513 (mp0) cc_final: 0.8154 (mp0) REVERT: A 406 PHE cc_start: 0.9004 (t80) cc_final: 0.8615 (t80) REVERT: A 648 GLN cc_start: 0.7102 (pp30) cc_final: 0.6791 (pp30) REVERT: A 692 GLU cc_start: 0.8511 (mp0) cc_final: 0.8144 (mp0) REVERT: B 79 GLN cc_start: 0.8507 (tp40) cc_final: 0.8195 (tp-100) REVERT: B 82 ARG cc_start: 0.7728 (ttp-170) cc_final: 0.7451 (ttp80) REVERT: B 145 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7376 (tm-30) REVERT: B 318 GLU cc_start: 0.8521 (mp0) cc_final: 0.8175 (mp0) REVERT: B 406 PHE cc_start: 0.8999 (t80) cc_final: 0.8656 (t80) outliers start: 17 outliers final: 15 residues processed: 132 average time/residue: 0.0989 time to fit residues: 19.2820 Evaluate side-chains 125 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 569 SER 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 378 ASN Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 523 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 20 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 120 optimal weight: 0.0770 chunk 101 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110445 restraints weight = 15429.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112904 restraints weight = 8756.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113448 restraints weight = 6118.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113739 restraints weight = 6032.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113935 restraints weight = 5484.161| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2746 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= 0.100 Angle : 0.509 11.914 15120 Z= 0.256 Chirality : 0.039 0.155 1658 Planarity : 0.004 0.041 1920 Dihedral : 4.077 15.963 1446 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.30 % Allowed : 17.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.23), residues: 1322 helix: -0.26 (0.18), residues: 904 sheet: -2.12 (0.48), residues: 78 loop : -2.06 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 710 TYR 0.013 0.001 TYR B 26 PHE 0.027 0.001 PHE B 205 TRP 0.010 0.001 TRP A 235 HIS 0.002 0.000 HIS B 479 Details of bonding type rmsd covalent geometry : bond 0.00231 (11150) covalent geometry : angle 0.50852 (15120) hydrogen bonds : bond 0.02804 ( 536) hydrogen bonds : angle 3.80409 ( 1572) *********************** 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 144 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.412 Fit side-chains REVERT: A 145 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7308 (tm-30) REVERT: A 318 GLU cc_start: 0.8462 (mp0) cc_final: 0.8128 (mp0) REVERT: A 406 PHE cc_start: 0.8904 (t80) cc_final: 0.8595 (t80) REVERT: A 648 GLN cc_start: 0.7026 (pp30) cc_final: 0.6752 (pp30) REVERT: A 692 GLU cc_start: 0.8340 (mp0) cc_final: 0.8093 (mp0) REVERT: B 79 GLN cc_start: 0.8467 (tp40) cc_final: 0.8175 (tp-100) REVERT: B 82 ARG cc_start: 0.7683 (ttp-170) cc_final: 0.7434 (ttp80) REVERT: B 145 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7343 (tm-30) REVERT: B 318 GLU cc_start: 0.8455 (mp0) cc_final: 0.8140 (mp0) outliers start: 15 outliers final: 14 residues processed: 138 average time/residue: 0.0906 time to fit residues: 18.7766 Evaluate side-chains 131 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 131 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 115 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN B 378 ASN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.140673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110548 restraints weight = 15402.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.113017 restraints weight = 8808.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113343 restraints weight = 6117.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113755 restraints weight = 6258.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113895 restraints weight = 5564.029| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 0.034 11150 Z= 0.104 Angle : 0.514 11.332 15120 Z= 0.257 Chirality : 0.039 0.158 1658 Planarity : 0.004 0.039 1920 Dihedral : 3.960 13.911 1446 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.64 % Allowed : 18.60 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.24), residues: 1322 helix: 0.06 (0.18), residues: 904 sheet: -2.02 (0.49), residues: 78 loop : -1.96 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 710 TYR 0.012 0.001 TYR A 26 PHE 0.027 0.001 PHE B 205 TRP 0.010 0.001 TRP A 235 HIS 0.002 0.000 HIS B 479 Details of bonding type rmsd covalent geometry : bond 0.00243 (11150) covalent geometry : angle 0.51375 (15120) hydrogen bonds : bond 0.02731 ( 536) hydrogen bonds : angle 3.70845 ( 1572) *********************** 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 to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.445 Fit side-chains REVERT: A 318 GLU cc_start: 0.8470 (mp0) cc_final: 0.8118 (mp0) REVERT: A 406 PHE cc_start: 0.8925 (t80) cc_final: 0.8599 (t80) REVERT: A 648 GLN cc_start: 0.7114 (pp30) cc_final: 0.6757 (pp30) REVERT: A 692 GLU cc_start: 0.8480 (mp0) cc_final: 0.8111 (mp0) REVERT: B 79 GLN cc_start: 0.8482 (tp40) cc_final: 0.8175 (tp-100) REVERT: B 82 ARG cc_start: 0.7688 (ttp-170) cc_final: 0.7435 (ttp80) REVERT: B 145 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7337 (tm-30) REVERT: B 318 GLU cc_start: 0.8400 (mp0) cc_final: 0.8058 (mp0) REVERT: B 408 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8229 (ttp80) outliers start: 19 outliers final: 14 residues processed: 141 average time/residue: 0.0909 time to fit residues: 19.3733 Evaluate side-chains 135 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 362 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 414 LEU 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 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 39 optimal weight: 7.9990 chunk 120 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.140004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.109464 restraints weight = 15559.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.111155 restraints weight = 9055.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.111723 restraints weight = 7026.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112264 restraints weight = 6638.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.112325 restraints weight = 5924.322| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2862 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= 0.141 Angle : 0.535 10.562 15120 Z= 0.268 Chirality : 0.040 0.163 1658 Planarity : 0.004 0.039 1920 Dihedral : 4.005 14.149 1446 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.56 % Allowed : 18.94 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.23), residues: 1322 helix: 0.10 (0.18), residues: 916 sheet: -1.89 (0.50), residues: 78 loop : -2.13 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 710 TYR 0.012 0.001 TYR A 26 PHE 0.031 0.001 PHE B 406 TRP 0.009 0.001 TRP A 235 HIS 0.003 0.001 HIS B 479 Details of bonding type rmsd covalent geometry : bond 0.00336 (11150) covalent geometry : angle 0.53548 (15120) hydrogen bonds : bond 0.02878 ( 536) hydrogen bonds : angle 3.75341 ( 1572) *********************** 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 to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.442 Fit side-chains REVERT: A 318 GLU cc_start: 0.8445 (mp0) cc_final: 0.8080 (mp0) REVERT: A 408 ARG cc_start: 0.8494 (ttp80) cc_final: 0.8279 (ttp80) REVERT: A 648 GLN cc_start: 0.7158 (pp30) cc_final: 0.6773 (pp30) REVERT: A 692 GLU cc_start: 0.8550 (mp0) cc_final: 0.8119 (mp0) REVERT: B 79 GLN cc_start: 0.8522 (tp40) cc_final: 0.8199 (tp-100) REVERT: B 82 ARG cc_start: 0.7710 (ttp-170) cc_final: 0.7439 (ttp80) REVERT: B 145 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7383 (tm-30) REVERT: B 318 GLU cc_start: 0.8409 (mp0) cc_final: 0.8052 (mp0) REVERT: B 408 ARG cc_start: 0.8526 (ttp80) cc_final: 0.8312 (ttp80) outliers start: 18 outliers final: 18 residues processed: 133 average time/residue: 0.0868 time to fit residues: 17.5825 Evaluate side-chains 130 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 51 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 87 optimal weight: 0.7980 chunk 128 optimal weight: 8.9990 chunk 47 optimal weight: 0.0000 chunk 17 optimal weight: 0.6980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 378 ASN B 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.144637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.112714 restraints weight = 15563.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.115593 restraints weight = 9111.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.117363 restraints weight = 6733.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118360 restraints weight = 5710.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118847 restraints weight = 5216.386| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3029 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= 0.095 Angle : 0.516 10.330 15120 Z= 0.257 Chirality : 0.038 0.158 1658 Planarity : 0.004 0.039 1920 Dihedral : 3.858 14.346 1446 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.82 % Allowed : 19.20 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.24), residues: 1322 helix: 0.35 (0.18), residues: 922 sheet: -1.76 (0.52), residues: 78 loop : -2.01 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 710 TYR 0.012 0.001 TYR A 26 PHE 0.028 0.001 PHE B 205 TRP 0.011 0.001 TRP A 235 HIS 0.002 0.000 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00222 (11150) covalent geometry : angle 0.51598 (15120) hydrogen bonds : bond 0.02606 ( 536) hydrogen bonds : angle 3.59332 ( 1572) *********************** 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 149 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.430 Fit side-chains REVERT: A 145 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7307 (tm-30) REVERT: A 318 GLU cc_start: 0.8393 (mp0) cc_final: 0.8029 (mp0) REVERT: A 408 ARG cc_start: 0.8402 (ttp80) cc_final: 0.8188 (ttp80) REVERT: A 437 MET cc_start: 0.9074 (tpp) cc_final: 0.8854 (mmm) REVERT: A 648 GLN cc_start: 0.6958 (pp30) cc_final: 0.6654 (pp30) REVERT: A 692 GLU cc_start: 0.8376 (mp0) cc_final: 0.8044 (mp0) REVERT: B 79 GLN cc_start: 0.8471 (tp40) cc_final: 0.8172 (tp-100) REVERT: B 82 ARG cc_start: 0.7717 (ttp-170) cc_final: 0.7467 (ttp80) REVERT: B 318 GLU cc_start: 0.8375 (mp0) cc_final: 0.8024 (mp0) REVERT: B 408 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8230 (ttp80) REVERT: B 437 MET cc_start: 0.9090 (tpp) cc_final: 0.8849 (mmm) REVERT: B 648 GLN cc_start: 0.6838 (pp30) cc_final: 0.6620 (pp30) outliers start: 21 outliers final: 16 residues processed: 143 average time/residue: 0.0838 time to fit residues: 18.6209 Evaluate side-chains 133 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 127 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.141343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110848 restraints weight = 15350.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112695 restraints weight = 10126.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113211 restraints weight = 7998.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113604 restraints weight = 6670.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113747 restraints weight = 6243.157| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3101 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= 0.101 Angle : 0.524 10.238 15120 Z= 0.260 Chirality : 0.039 0.160 1658 Planarity : 0.004 0.039 1920 Dihedral : 3.808 13.299 1446 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.30 % Allowed : 19.46 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.24), residues: 1322 helix: 0.52 (0.18), residues: 924 sheet: -1.74 (0.52), residues: 78 loop : -1.97 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 710 TYR 0.012 0.001 TYR B 26 PHE 0.027 0.001 PHE B 205 TRP 0.014 0.001 TRP A 553 HIS 0.002 0.000 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00238 (11150) covalent geometry : angle 0.52368 (15120) hydrogen bonds : bond 0.02588 ( 536) hydrogen bonds : angle 3.54111 ( 1572) *********************** 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 140 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.310 Fit side-chains REVERT: A 145 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7349 (tm-30) REVERT: A 318 GLU cc_start: 0.8393 (mp0) cc_final: 0.8028 (mp0) REVERT: A 408 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8253 (ttp80) REVERT: A 437 MET cc_start: 0.9083 (tpp) cc_final: 0.8846 (mmm) REVERT: A 648 GLN cc_start: 0.6982 (pp30) cc_final: 0.6656 (pp30) REVERT: A 692 GLU cc_start: 0.8476 (mp0) cc_final: 0.8068 (mp0) REVERT: B 79 GLN cc_start: 0.8474 (tp40) cc_final: 0.8167 (tp-100) REVERT: B 82 ARG cc_start: 0.7739 (ttp-170) cc_final: 0.7484 (ttp80) REVERT: B 145 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7291 (tm-30) REVERT: B 146 SER cc_start: 0.8790 (m) cc_final: 0.8483 (p) REVERT: B 318 GLU cc_start: 0.8289 (mp0) cc_final: 0.7949 (mp0) REVERT: B 437 MET cc_start: 0.9093 (tpp) cc_final: 0.8837 (mmm) REVERT: B 648 GLN cc_start: 0.6900 (pp30) cc_final: 0.6656 (pp30) outliers start: 15 outliers final: 15 residues processed: 137 average time/residue: 0.0850 time to fit residues: 17.7639 Evaluate side-chains 127 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 53 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.141990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110508 restraints weight = 15453.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113541 restraints weight = 8935.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115456 restraints weight = 6504.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116353 restraints weight = 5443.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.117064 restraints weight = 4960.096| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11150 Z= 0.102 Angle : 0.537 10.164 15120 Z= 0.264 Chirality : 0.039 0.159 1658 Planarity : 0.004 0.039 1920 Dihedral : 3.765 13.292 1446 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.38 % Allowed : 19.38 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.24), residues: 1322 helix: 0.62 (0.18), residues: 926 sheet: -1.70 (0.53), residues: 78 loop : -1.92 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 710 TYR 0.012 0.001 TYR A 26 PHE 0.027 0.001 PHE B 205 TRP 0.012 0.001 TRP A 553 HIS 0.003 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00244 (11150) covalent geometry : angle 0.53678 (15120) hydrogen bonds : bond 0.02533 ( 536) hydrogen bonds : angle 3.49901 ( 1572) ********************** 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 140 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.429 Fit side-chains REVERT: A 145 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 318 GLU cc_start: 0.8356 (mp0) cc_final: 0.8008 (mp0) REVERT: A 408 ARG cc_start: 0.8427 (ttp80) cc_final: 0.8188 (ttp80) REVERT: A 437 MET cc_start: 0.9077 (tpp) cc_final: 0.8867 (mmm) REVERT: A 648 GLN cc_start: 0.6851 (pp30) cc_final: 0.6593 (pp30) REVERT: A 692 GLU cc_start: 0.8358 (mp0) cc_final: 0.8023 (mp0) REVERT: B 79 GLN cc_start: 0.8503 (tp40) cc_final: 0.8203 (tp-100) REVERT: B 82 ARG cc_start: 0.7751 (ttp-170) cc_final: 0.7498 (ttp80) REVERT: B 145 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7305 (tm-30) REVERT: B 146 SER cc_start: 0.8732 (m) cc_final: 0.8430 (p) REVERT: B 318 GLU cc_start: 0.8334 (mp0) cc_final: 0.7997 (mp0) REVERT: B 437 MET cc_start: 0.9090 (tpp) cc_final: 0.8879 (mmm) outliers start: 16 outliers final: 16 residues processed: 136 average time/residue: 0.0815 time to fit residues: 17.1926 Evaluate side-chains 139 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 531 ASN B 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110598 restraints weight = 15400.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112504 restraints weight = 10504.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.113163 restraints weight = 7776.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113448 restraints weight = 6413.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113635 restraints weight = 6034.206| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11150 Z= 0.138 Angle : 0.549 9.958 15120 Z= 0.273 Chirality : 0.040 0.161 1658 Planarity : 0.004 0.039 1920 Dihedral : 3.824 13.392 1446 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.30 % Allowed : 19.55 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.24), residues: 1322 helix: 0.60 (0.18), residues: 924 sheet: -1.73 (0.52), residues: 78 loop : -1.97 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 710 TYR 0.012 0.001 TYR B 195 PHE 0.038 0.001 PHE A 406 TRP 0.011 0.001 TRP A 553 HIS 0.003 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00334 (11150) covalent geometry : angle 0.54877 (15120) hydrogen bonds : bond 0.02713 ( 536) hydrogen bonds : angle 3.57094 ( 1572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1597.84 seconds wall clock time: 28 minutes 21.97 seconds (1701.97 seconds total)