Starting phenix.real_space_refine on Sat Sep 12 23:38:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dmu_7966/09_2026/6dmu_7966_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dmu_7966/09_2026/6dmu_7966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dmu_7966/09_2026/6dmu_7966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dmu_7966/09_2026/6dmu_7966.map" model { file = "/net/cci-nas-00/data/ceres_data/6dmu_7966/09_2026/6dmu_7966_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dmu_7966/09_2026/6dmu_7966_neut.cif" } resolution = 4.0 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= 0.003 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 140 5.16 5 C 12668 2.51 5 N 3292 2.21 5 O 3524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19636 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4862 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 24, 'TRANS': 582} Chain breaks: 1 Chain: "B" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4862 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 24, 'TRANS': 582} Chain breaks: 1 Chain: "C" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4862 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 24, 'TRANS': 582} Chain breaks: 1 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4862 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 24, 'TRANS': 582} Chain breaks: 1 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.05, per 1000 atoms: 0.21 Number of scatterers: 19636 At special positions: 0 Unit cell: (135.3, 135.3, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 12 15.00 O 3524 8.00 N 3292 7.00 C 12668 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: 1.46 Conformation dependent library (CDL) restraints added in 833.8 milliseconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4584 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 8 sheets defined 65.8% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 3.792A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.792A pdb=" N ALA A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.541A pdb=" N LEU A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.656A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 removed outlier: 4.135A pdb=" N LEU A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.654A pdb=" N LEU A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 4.005A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N MET A 126 " --> pdb=" O HIS A 122 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 removed outlier: 3.722A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.715A pdb=" N GLY A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.766A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 4.451A pdb=" N ASN A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 206 removed outlier: 3.592A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 225 removed outlier: 3.529A pdb=" N ALA A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 removed outlier: 3.744A pdb=" N GLY A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.843A pdb=" N PHE A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 298 Processing helix chain 'A' and resid 302 through 309 removed outlier: 4.056A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 removed outlier: 4.392A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 348 removed outlier: 4.048A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 411 removed outlier: 4.461A pdb=" N ARG A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Proline residue: A 405 - end of helix removed outlier: 3.991A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.618A pdb=" N PHE A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 removed outlier: 4.165A pdb=" N ILE A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.912A pdb=" N LEU A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.548A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 493 through 512 removed outlier: 3.998A pdb=" N MET A 497 " --> pdb=" O PHE A 493 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.557A pdb=" N ALA A 529 " --> pdb=" O ASP A 525 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 566 removed outlier: 4.537A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 586 removed outlier: 3.790A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 608 removed outlier: 4.689A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.792A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.792A pdb=" N ALA B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 67 removed outlier: 3.541A pdb=" N LEU B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.656A pdb=" N VAL B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 100 removed outlier: 4.134A pdb=" N LEU B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.655A pdb=" N LEU B 105 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 4.005A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N MET B 126 " --> pdb=" O HIS B 122 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 removed outlier: 3.722A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.714A pdb=" N GLY B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.766A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 removed outlier: 4.451A pdb=" N ASN B 197 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 206 removed outlier: 3.591A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 206 " --> pdb=" O ILE B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 225 removed outlier: 3.529A pdb=" N ALA B 212 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.744A pdb=" N GLY B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.844A pdb=" N PHE B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 298 Processing helix chain 'B' and resid 302 through 309 removed outlier: 4.056A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 removed outlier: 4.392A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 348 removed outlier: 4.047A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 411 removed outlier: 4.461A pdb=" N ARG B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU B 402 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU B 403 " --> pdb=" O ILE B 399 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Proline residue: B 405 - end of helix removed outlier: 3.992A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.618A pdb=" N PHE B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 removed outlier: 4.165A pdb=" N ILE B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.912A pdb=" N LEU B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 removed outlier: 3.548A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 Processing helix chain 'B' and resid 493 through 512 removed outlier: 3.998A pdb=" N MET B 497 " --> pdb=" O PHE B 493 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE B 504 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.556A pdb=" N ALA B 529 " --> pdb=" O ASP B 525 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 566 removed outlier: 4.537A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 586 removed outlier: 3.789A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 608 removed outlier: 4.689A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.793A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.792A pdb=" N ALA C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.541A pdb=" N LEU C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.655A pdb=" N VAL C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 removed outlier: 4.135A pdb=" N LEU C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.654A pdb=" N LEU C 105 " --> pdb=" O ALA C 102 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 4.005A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N MET C 126 " --> pdb=" O HIS C 122 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 removed outlier: 3.722A pdb=" N VAL C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.715A pdb=" N GLY C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.765A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 removed outlier: 4.452A pdb=" N ASN C 197 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 206 removed outlier: 3.591A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN C 206 " --> pdb=" O ILE C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 225 removed outlier: 3.529A pdb=" N ALA C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 removed outlier: 3.744A pdb=" N GLY C 251 " --> pdb=" O ALA C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.843A pdb=" N PHE C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 298 Processing helix chain 'C' and resid 302 through 309 removed outlier: 4.056A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 324 removed outlier: 4.392A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 348 removed outlier: 4.047A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 411 removed outlier: 4.462A pdb=" N ARG C 385 " --> pdb=" O GLN C 381 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU C 386 " --> pdb=" O ASP C 382 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL C 387 " --> pdb=" O ASN C 383 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU C 402 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU C 403 " --> pdb=" O ILE C 399 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Proline residue: C 405 - end of helix removed outlier: 3.992A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.618A pdb=" N PHE C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 removed outlier: 4.164A pdb=" N ILE C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.912A pdb=" N LEU C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 470 removed outlier: 3.548A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 Processing helix chain 'C' and resid 493 through 512 removed outlier: 3.999A pdb=" N MET C 497 " --> pdb=" O PHE C 493 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE C 504 " --> pdb=" O VAL C 500 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE C 512 " --> pdb=" O PHE C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.557A pdb=" N ALA C 529 " --> pdb=" O ASP C 525 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 566 removed outlier: 4.538A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 586 removed outlier: 3.790A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 585 " --> pdb=" O THR C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 608 removed outlier: 4.688A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.792A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.792A pdb=" N ALA D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.540A pdb=" N LEU D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.656A pdb=" N VAL D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 100 removed outlier: 4.135A pdb=" N LEU D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.655A pdb=" N LEU D 105 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 4.005A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N MET D 126 " --> pdb=" O HIS D 122 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 removed outlier: 3.723A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.714A pdb=" N GLY D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.766A pdb=" N LEU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 removed outlier: 4.451A pdb=" N ASN D 197 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 206 removed outlier: 3.591A pdb=" N ILE D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN D 206 " --> pdb=" O ILE D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.529A pdb=" N ALA D 212 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS D 225 " --> pdb=" O SER D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.744A pdb=" N GLY D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.843A pdb=" N PHE D 256 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 298 Processing helix chain 'D' and resid 302 through 309 removed outlier: 4.056A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 324 removed outlier: 4.393A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 348 removed outlier: 4.048A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 411 removed outlier: 4.461A pdb=" N ARG D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU D 402 " --> pdb=" O ILE D 398 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) Proline residue: D 405 - end of helix removed outlier: 3.992A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 removed outlier: 3.618A pdb=" N PHE D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 445 removed outlier: 4.165A pdb=" N ILE D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N MET D 440 " --> pdb=" O VAL D 436 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR D 445 " --> pdb=" O VAL D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.912A pdb=" N LEU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 470 removed outlier: 3.548A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 Processing helix chain 'D' and resid 493 through 512 removed outlier: 3.999A pdb=" N MET D 497 " --> pdb=" O PHE D 493 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE D 504 " --> pdb=" O VAL D 500 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE D 512 " --> pdb=" O PHE D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.557A pdb=" N ALA D 529 " --> pdb=" O ASP D 525 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 566 removed outlier: 4.537A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 586 removed outlier: 3.790A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 585 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 608 removed outlier: 4.689A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 269 removed outlier: 3.527A pdb=" N HIS A 265 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 269 removed outlier: 3.527A pdb=" N HIS B 265 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 269 removed outlier: 3.527A pdb=" N HIS C 265 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.528A pdb=" N HIS D 265 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 893 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3124 1.31 - 1.44: 5444 1.44 - 1.57: 11268 1.57 - 1.69: 20 1.69 - 1.82: 228 Bond restraints: 20084 Sorted by residual: bond pdb=" C1A PIO B1001 " pdb=" O2C PIO B1001 " ideal model delta sigma weight residual 1.332 1.404 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C1A PIO C1001 " pdb=" O2C PIO C1001 " ideal model delta sigma weight residual 1.332 1.403 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C1A PIO D1001 " pdb=" O2C PIO D1001 " ideal model delta sigma weight residual 1.332 1.403 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C1A PIO A1001 " pdb=" O2C PIO A1001 " ideal model delta sigma weight residual 1.332 1.403 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C1B PIO A1001 " pdb=" O3C PIO A1001 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.13e+01 ... (remaining 20079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 26393 2.65 - 5.30: 736 5.30 - 7.95: 111 7.95 - 10.60: 24 10.60 - 13.25: 8 Bond angle restraints: 27272 Sorted by residual: angle pdb=" C VAL D 451 " pdb=" N VAL D 452 " pdb=" CA VAL D 452 " ideal model delta sigma weight residual 120.33 124.53 -4.20 8.00e-01 1.56e+00 2.75e+01 angle pdb=" C VAL A 451 " pdb=" N VAL A 452 " pdb=" CA VAL A 452 " ideal model delta sigma weight residual 120.33 124.46 -4.13 8.00e-01 1.56e+00 2.66e+01 angle pdb=" C VAL B 451 " pdb=" N VAL B 452 " pdb=" CA VAL B 452 " ideal model delta sigma weight residual 120.33 124.45 -4.12 8.00e-01 1.56e+00 2.65e+01 angle pdb=" C VAL C 451 " pdb=" N VAL C 452 " pdb=" CA VAL C 452 " ideal model delta sigma weight residual 120.33 124.41 -4.08 8.00e-01 1.56e+00 2.61e+01 angle pdb=" O11 PIO C1001 " pdb=" P1 PIO C1001 " pdb=" O12 PIO C1001 " ideal model delta sigma weight residual 121.09 107.84 13.25 3.00e+00 1.11e-01 1.95e+01 ... (remaining 27267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.52: 11066 15.52 - 31.05: 653 31.05 - 46.57: 157 46.57 - 62.10: 4 62.10 - 77.62: 24 Dihedral angle restraints: 11904 sinusoidal: 4812 harmonic: 7092 Sorted by residual: dihedral pdb=" CA GLY C 626 " pdb=" C GLY C 626 " pdb=" N ASP C 627 " pdb=" CA ASP C 627 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLY A 626 " pdb=" C GLY A 626 " pdb=" N ASP A 627 " pdb=" CA ASP A 627 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLY D 626 " pdb=" C GLY D 626 " pdb=" N ASP D 627 " pdb=" CA ASP D 627 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 11901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2238 0.056 - 0.112: 689 0.112 - 0.168: 160 0.168 - 0.224: 9 0.224 - 0.280: 8 Chirality restraints: 3104 Sorted by residual: chirality pdb=" CA THR B 311 " pdb=" N THR B 311 " pdb=" C THR B 311 " pdb=" CB THR B 311 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA THR C 311 " pdb=" N THR C 311 " pdb=" C THR C 311 " pdb=" CB THR C 311 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA THR A 311 " pdb=" N THR A 311 " pdb=" C THR A 311 " pdb=" CB THR A 311 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 3101 not shown) Planarity restraints: 3432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 206 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.37e+00 pdb=" N PRO B 207 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 206 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO A 207 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 206 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO D 207 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 207 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 207 " 0.032 5.00e-02 4.00e+02 ... (remaining 3429 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 6316 2.86 - 3.37: 18279 3.37 - 3.88: 28777 3.88 - 4.39: 29848 4.39 - 4.90: 52840 Nonbonded interactions: 136060 Sorted by model distance: nonbonded pdb=" O GLY D 422 " pdb=" ND1 HIS D 426 " model vdw 2.348 3.120 nonbonded pdb=" O GLY C 422 " pdb=" ND1 HIS C 426 " model vdw 2.348 3.120 nonbonded pdb=" O GLY A 422 " pdb=" ND1 HIS A 426 " model vdw 2.349 3.120 nonbonded pdb=" O GLY B 422 " pdb=" ND1 HIS B 426 " model vdw 2.349 3.120 nonbonded pdb=" OE1 GLU C 403 " pdb=" OH TYR C 415 " model vdw 2.465 3.040 ... (remaining 136055 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.000 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 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 : 0.006 0.072 20084 Z= 0.277 Angle : 1.077 13.246 27272 Z= 0.548 Chirality : 0.056 0.280 3104 Planarity : 0.007 0.058 3432 Dihedral : 11.300 77.622 7320 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.19 % Allowed : 5.14 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.30 (0.13), residues: 2412 helix: -2.49 (0.10), residues: 1380 sheet: -2.69 (0.37), residues: 88 loop : -3.28 (0.15), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 154 TYR 0.016 0.002 TYR B 162 PHE 0.014 0.002 PHE B 468 TRP 0.020 0.002 TRP B 613 HIS 0.007 0.001 HIS B 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.28 (20084) covalent geometry : angle 1.07704 / 0.55 (27272) hydrogen bonds : bond 0.14301 / 9.45 ( 893) hydrogen bonds : angle 5.64695 / 3.85 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 412 time to evaluate : 0.759 Fit side-chains REVERT: A 255 MET cc_start: 0.7701 (ppp) cc_final: 0.7475 (ppp) REVERT: A 340 MET cc_start: 0.8802 (tpp) cc_final: 0.8477 (tpp) REVERT: A 591 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7989 (tp30) REVERT: B 255 MET cc_start: 0.7620 (ppp) cc_final: 0.7246 (ppp) REVERT: B 482 ILE cc_start: 0.8902 (pp) cc_final: 0.8684 (mt) REVERT: B 591 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7820 (tp30) REVERT: C 255 MET cc_start: 0.7593 (ppp) cc_final: 0.7252 (ppp) REVERT: C 340 MET cc_start: 0.8841 (tpp) cc_final: 0.8448 (tpp) REVERT: C 591 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7797 (tp30) REVERT: D 255 MET cc_start: 0.7678 (ppp) cc_final: 0.7341 (ppp) REVERT: D 340 MET cc_start: 0.8865 (tpp) cc_final: 0.8540 (tpp) REVERT: D 591 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7942 (tp30) outliers start: 4 outliers final: 4 residues processed: 416 average time/residue: 0.1473 time to fit residues: 92.7759 Evaluate side-chains 230 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 226 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 277 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.083343 restraints weight = 43387.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.085485 restraints weight = 24881.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.086852 restraints weight = 17170.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.087804 restraints weight = 13559.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.088322 restraints weight = 11588.149| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 20084 Z= 0.169 Angle : 0.697 15.367 27272 Z= 0.353 Chirality : 0.043 0.309 3104 Planarity : 0.005 0.044 3432 Dihedral : 6.400 52.546 2724 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.05 % Allowed : 12.14 % Favored : 84.81 % 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 are not related in a simple way. whole: -2.66 (0.15), residues: 2412 helix: -0.85 (0.13), residues: 1360 sheet: -2.35 (0.40), residues: 88 loop : -3.04 (0.16), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 470 TYR 0.014 0.001 TYR B 621 PHE 0.013 0.001 PHE A 478 TRP 0.009 0.001 TRP D 593 HIS 0.005 0.001 HIS B 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (20084) covalent geometry : angle 0.69737 / 0.35 (27272) hydrogen bonds : bond 0.06595 / 4.35 ( 893) hydrogen bonds : angle 4.30697 / 2.94 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 240 time to evaluate : 0.714 Fit side-chains REVERT: A 255 MET cc_start: 0.7710 (ppp) cc_final: 0.7368 (tmm) REVERT: A 340 MET cc_start: 0.8905 (tpp) cc_final: 0.8657 (tpp) REVERT: A 539 THR cc_start: 0.9568 (OUTLIER) cc_final: 0.9304 (p) REVERT: A 591 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7996 (tp30) REVERT: B 539 THR cc_start: 0.9533 (OUTLIER) cc_final: 0.9224 (p) REVERT: B 591 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7873 (tp30) REVERT: B 631 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7884 (tm) REVERT: C 340 MET cc_start: 0.8914 (tpp) cc_final: 0.8620 (tpp) REVERT: C 539 THR cc_start: 0.9572 (OUTLIER) cc_final: 0.9316 (p) REVERT: C 591 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7869 (tp30) REVERT: C 631 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7923 (tm) REVERT: D 340 MET cc_start: 0.8931 (tpp) cc_final: 0.8680 (tpp) REVERT: D 539 THR cc_start: 0.9559 (OUTLIER) cc_final: 0.9327 (p) REVERT: D 591 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7952 (tp30) outliers start: 64 outliers final: 23 residues processed: 287 average time/residue: 0.1088 time to fit residues: 52.3722 Evaluate side-chains 243 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 564 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 15 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 85 optimal weight: 0.4980 chunk 45 optimal weight: 6.9990 chunk 168 optimal weight: 8.9990 chunk 79 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.083508 restraints weight = 43780.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.085638 restraints weight = 24829.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.087060 restraints weight = 17112.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.087920 restraints weight = 13477.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.088552 restraints weight = 11596.395| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20084 Z= 0.145 Angle : 0.665 15.696 27272 Z= 0.326 Chirality : 0.040 0.253 3104 Planarity : 0.004 0.038 3432 Dihedral : 5.483 46.496 2716 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.67 % Allowed : 13.19 % Favored : 84.14 % 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 are not related in a simple way. whole: -1.91 (0.16), residues: 2412 helix: -0.19 (0.14), residues: 1372 sheet: -1.49 (0.46), residues: 68 loop : -2.88 (0.16), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 470 TYR 0.014 0.001 TYR A 623 PHE 0.012 0.001 PHE B 72 TRP 0.008 0.001 TRP B 593 HIS 0.004 0.001 HIS A 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (20084) covalent geometry : angle 0.66495 / 0.33 (27272) hydrogen bonds : bond 0.05848 / 3.86 ( 893) hydrogen bonds : angle 4.04739 / 2.77 ( 2571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 0.747 Fit side-chains REVERT: A 255 MET cc_start: 0.7581 (ppp) cc_final: 0.7362 (tmm) REVERT: A 340 MET cc_start: 0.8866 (tpp) cc_final: 0.8568 (tpp) REVERT: A 539 THR cc_start: 0.9564 (OUTLIER) cc_final: 0.9338 (p) REVERT: A 591 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7881 (tp30) REVERT: A 592 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8963 (tp) REVERT: B 539 THR cc_start: 0.9553 (OUTLIER) cc_final: 0.9321 (p) REVERT: B 591 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7817 (tp30) REVERT: B 592 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8901 (tp) REVERT: C 255 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6892 (tmm) REVERT: C 340 MET cc_start: 0.8852 (tpp) cc_final: 0.8515 (tpp) REVERT: C 415 TYR cc_start: 0.7951 (t80) cc_final: 0.7715 (t80) REVERT: C 483 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8289 (tm-30) REVERT: C 591 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7814 (tp30) REVERT: C 592 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8901 (tp) REVERT: D 340 MET cc_start: 0.8877 (tpp) cc_final: 0.8561 (tpp) REVERT: D 483 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8321 (tm-30) REVERT: D 539 THR cc_start: 0.9560 (OUTLIER) cc_final: 0.9357 (p) REVERT: D 591 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7887 (tp30) REVERT: D 592 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8971 (tp) outliers start: 56 outliers final: 29 residues processed: 277 average time/residue: 0.1078 time to fit residues: 49.8866 Evaluate side-chains 254 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 592 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 192 optimal weight: 0.0770 chunk 225 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 190 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 chunk 148 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.086794 restraints weight = 43173.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.088961 restraints weight = 23744.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.090426 restraints weight = 16198.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.091387 restraints weight = 12632.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.091922 restraints weight = 10750.410| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20084 Z= 0.114 Angle : 0.625 15.659 27272 Z= 0.300 Chirality : 0.039 0.254 3104 Planarity : 0.004 0.038 3432 Dihedral : 5.124 44.710 2716 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.95 % Allowed : 13.62 % Favored : 83.43 % 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 are not related in a simple way. whole: -1.44 (0.16), residues: 2412 helix: 0.14 (0.14), residues: 1368 sheet: -0.97 (0.53), residues: 68 loop : -2.60 (0.16), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 470 TYR 0.012 0.001 TYR A 377 PHE 0.010 0.001 PHE C 553 TRP 0.008 0.001 TRP A 583 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (20084) covalent geometry : angle 0.62475 / 0.30 (27272) hydrogen bonds : bond 0.04528 / 2.97 ( 893) hydrogen bonds : angle 3.74385 / 2.58 ( 2571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 245 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 MET cc_start: 0.8799 (tpp) cc_final: 0.8437 (tpp) REVERT: A 591 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7724 (tp30) REVERT: A 592 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8900 (tp) REVERT: B 255 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6831 (tmm) REVERT: B 539 THR cc_start: 0.9555 (OUTLIER) cc_final: 0.9345 (p) REVERT: B 591 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7704 (tp30) REVERT: B 592 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8800 (tp) REVERT: C 340 MET cc_start: 0.8822 (tpp) cc_final: 0.8418 (tpp) REVERT: C 591 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7704 (tp30) REVERT: C 592 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8851 (tp) REVERT: D 255 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6927 (tmm) REVERT: D 340 MET cc_start: 0.8820 (tpp) cc_final: 0.8453 (tpp) REVERT: D 418 GLN cc_start: 0.8221 (pt0) cc_final: 0.7901 (mt0) REVERT: D 591 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7701 (tp30) REVERT: D 592 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8879 (tp) outliers start: 62 outliers final: 33 residues processed: 292 average time/residue: 0.1053 time to fit residues: 52.3110 Evaluate side-chains 261 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 592 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 184 optimal weight: 0.0070 chunk 56 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 212 optimal weight: 0.0170 chunk 10 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.106645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.086559 restraints weight = 42931.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.088688 restraints weight = 24064.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.090171 restraints weight = 16505.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.091044 restraints weight = 12846.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.091703 restraints weight = 11006.089| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20084 Z= 0.111 Angle : 0.628 16.079 27272 Z= 0.299 Chirality : 0.038 0.248 3104 Planarity : 0.004 0.037 3432 Dihedral : 4.901 41.854 2716 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.33 % Allowed : 15.33 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.16), residues: 2412 helix: 0.40 (0.14), residues: 1360 sheet: -0.69 (0.56), residues: 68 loop : -2.48 (0.16), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 470 TYR 0.013 0.001 TYR D 415 PHE 0.013 0.001 PHE B 553 TRP 0.007 0.001 TRP B 583 HIS 0.002 0.001 HIS A 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (20084) covalent geometry : angle 0.62826 / 0.30 (27272) hydrogen bonds : bond 0.04496 / 2.97 ( 893) hydrogen bonds : angle 3.62991 / 2.50 ( 2571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 MET cc_start: 0.8788 (tpp) cc_final: 0.8426 (tpp) REVERT: A 591 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7701 (tp30) REVERT: B 44 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8456 (tt) REVERT: B 255 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6969 (tmm) REVERT: B 539 THR cc_start: 0.9481 (OUTLIER) cc_final: 0.9239 (p) REVERT: B 591 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7693 (tp30) REVERT: C 98 LEU cc_start: 0.8395 (tt) cc_final: 0.8172 (mp) REVERT: C 99 MET cc_start: 0.7853 (tpp) cc_final: 0.7598 (tpp) REVERT: C 264 LYS cc_start: 0.8752 (ttmm) cc_final: 0.8444 (ttmt) REVERT: C 340 MET cc_start: 0.8808 (tpp) cc_final: 0.8407 (tpp) REVERT: C 591 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7692 (tp30) REVERT: D 255 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.7052 (tmm) REVERT: D 340 MET cc_start: 0.8834 (tpp) cc_final: 0.8468 (tpp) REVERT: D 591 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7695 (tp30) outliers start: 49 outliers final: 33 residues processed: 279 average time/residue: 0.1161 time to fit residues: 53.6691 Evaluate side-chains 251 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 564 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 162 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 184 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 HIS C 122 HIS C 157 HIS D 157 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.102075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.081741 restraints weight = 43222.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.083787 restraints weight = 24924.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.085132 restraints weight = 17350.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.085940 restraints weight = 13755.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.086551 restraints weight = 11908.740| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20084 Z= 0.178 Angle : 0.688 16.426 27272 Z= 0.338 Chirality : 0.042 0.252 3104 Planarity : 0.004 0.039 3432 Dihedral : 4.975 36.489 2716 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.33 % Allowed : 15.62 % Favored : 81.05 % 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 are not related in a simple way. whole: -1.04 (0.17), residues: 2412 helix: 0.48 (0.14), residues: 1368 sheet: -0.78 (0.55), residues: 68 loop : -2.45 (0.17), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 470 TYR 0.019 0.002 TYR C 415 PHE 0.012 0.001 PHE C 553 TRP 0.006 0.001 TRP B 629 HIS 0.005 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (20084) covalent geometry : angle 0.68768 / 0.34 (27272) hydrogen bonds : bond 0.06309 / 4.18 ( 893) hydrogen bonds : angle 3.82396 / 2.62 ( 2571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 211 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 MET cc_start: 0.8870 (tpp) cc_final: 0.8579 (tpp) REVERT: A 365 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8701 (tp) REVERT: A 591 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7879 (tp30) REVERT: A 625 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8101 (mm) REVERT: B 255 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.7018 (tmm) REVERT: B 377 TYR cc_start: 0.8087 (m-80) cc_final: 0.7818 (m-80) REVERT: B 591 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7906 (tp30) REVERT: C 264 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8497 (ttmm) REVERT: C 340 MET cc_start: 0.8905 (tpp) cc_final: 0.8588 (tpp) REVERT: C 591 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7897 (tp30) REVERT: D 255 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.7037 (tmm) REVERT: D 340 MET cc_start: 0.8880 (tpp) cc_final: 0.8593 (tpp) REVERT: D 591 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7890 (tp30) outliers start: 70 outliers final: 40 residues processed: 270 average time/residue: 0.1146 time to fit residues: 52.6344 Evaluate side-chains 249 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 564 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 103 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 205 optimal weight: 0.2980 chunk 148 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.084066 restraints weight = 43057.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.086165 restraints weight = 24651.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.087563 restraints weight = 17046.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.088439 restraints weight = 13461.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.088998 restraints weight = 11587.015| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20084 Z= 0.124 Angle : 0.660 17.011 27272 Z= 0.313 Chirality : 0.039 0.258 3104 Planarity : 0.004 0.039 3432 Dihedral : 4.809 33.714 2716 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.71 % Allowed : 16.43 % Favored : 80.86 % 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 are not related in a simple way. whole: -0.88 (0.17), residues: 2412 helix: 0.60 (0.14), residues: 1368 sheet: -0.55 (0.55), residues: 68 loop : -2.38 (0.17), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 470 TYR 0.012 0.001 TYR A 623 PHE 0.008 0.001 PHE C 553 TRP 0.009 0.001 TRP B 583 HIS 0.005 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (20084) covalent geometry : angle 0.66038 / 0.31 (27272) hydrogen bonds : bond 0.05103 / 3.36 ( 893) hydrogen bonds : angle 3.67193 / 2.53 ( 2571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 MET cc_start: 0.8845 (tpp) cc_final: 0.8509 (tpp) REVERT: A 365 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8741 (tp) REVERT: A 591 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7805 (tp30) REVERT: B 255 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6987 (tmm) REVERT: B 591 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7793 (tp30) REVERT: B 625 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8125 (mm) REVERT: C 340 MET cc_start: 0.8803 (tpp) cc_final: 0.8436 (tpp) REVERT: C 515 GLU cc_start: 0.8124 (mp0) cc_final: 0.7757 (mp0) REVERT: C 591 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7787 (tp30) REVERT: C 625 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8088 (mm) REVERT: D 255 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6926 (tmm) REVERT: D 340 MET cc_start: 0.8826 (tpp) cc_final: 0.8470 (tpp) REVERT: D 591 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7815 (tp30) REVERT: D 625 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7994 (mm) outliers start: 57 outliers final: 38 residues processed: 274 average time/residue: 0.1103 time to fit residues: 51.1242 Evaluate side-chains 262 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 104 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 200 optimal weight: 0.0170 chunk 191 optimal weight: 30.0000 chunk 82 optimal weight: 0.9980 chunk 157 optimal weight: 0.5980 chunk 208 optimal weight: 0.5980 chunk 189 optimal weight: 6.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.108225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.088579 restraints weight = 42362.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.090784 restraints weight = 23836.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.092269 restraints weight = 16259.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.093136 restraints weight = 12687.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.093829 restraints weight = 10865.933| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20084 Z= 0.105 Angle : 0.636 17.044 27272 Z= 0.297 Chirality : 0.038 0.250 3104 Planarity : 0.004 0.038 3432 Dihedral : 4.504 30.163 2716 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.67 % Allowed : 17.90 % Favored : 80.43 % 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 are not related in a simple way. whole: -0.68 (0.17), residues: 2412 helix: 0.75 (0.14), residues: 1364 sheet: -0.48 (0.56), residues: 68 loop : -2.26 (0.17), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 470 TYR 0.016 0.001 TYR C 415 PHE 0.010 0.001 PHE A 630 TRP 0.010 0.001 TRP B 583 HIS 0.004 0.000 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 (20084) covalent geometry : angle 0.63561 / 0.30 (27272) hydrogen bonds : bond 0.03638 / 2.39 ( 893) hydrogen bonds : angle 3.52689 / 2.45 ( 2571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8520 (tp) REVERT: A 591 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7612 (tp30) REVERT: B 591 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7559 (tp30) REVERT: B 625 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7967 (mm) REVERT: C 591 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7562 (tp30) REVERT: D 255 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.7017 (tmm) REVERT: D 447 MET cc_start: 0.8315 (mtt) cc_final: 0.8091 (mtp) REVERT: D 591 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7564 (tp30) outliers start: 35 outliers final: 21 residues processed: 278 average time/residue: 0.1101 time to fit residues: 52.1265 Evaluate side-chains 253 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 557 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 226 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 211 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 239 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 178 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN B 129 ASN C 129 ASN C 509 HIS D 129 ASN D 509 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.106685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.086797 restraints weight = 42593.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.088970 restraints weight = 24132.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.090430 restraints weight = 16602.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.091281 restraints weight = 12976.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.092008 restraints weight = 11145.349| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20084 Z= 0.109 Angle : 0.655 16.838 27272 Z= 0.306 Chirality : 0.039 0.249 3104 Planarity : 0.004 0.038 3432 Dihedral : 4.368 28.150 2716 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.67 % Allowed : 18.38 % Favored : 79.95 % 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 are not related in a simple way. whole: -0.56 (0.17), residues: 2412 helix: 0.87 (0.14), residues: 1356 sheet: -0.57 (0.56), residues: 68 loop : -2.20 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 470 TYR 0.011 0.001 TYR C 415 PHE 0.015 0.001 PHE D 553 TRP 0.007 0.001 TRP B 583 HIS 0.005 0.000 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (20084) covalent geometry : angle 0.65527 / 0.31 (27272) hydrogen bonds : bond 0.04105 / 2.72 ( 893) hydrogen bonds : angle 3.43653 / 2.37 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 447 MET cc_start: 0.8350 (mtt) cc_final: 0.8091 (mtp) REVERT: A 591 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7692 (tp30) REVERT: A 625 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7956 (mm) REVERT: B 591 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7667 (tp30) REVERT: B 625 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7911 (mm) REVERT: C 447 MET cc_start: 0.8305 (mtt) cc_final: 0.8055 (mtp) REVERT: C 591 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7631 (tp30) REVERT: C 625 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7895 (mm) REVERT: D 255 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.7023 (tmm) REVERT: D 447 MET cc_start: 0.8335 (mtt) cc_final: 0.8083 (mtp) REVERT: D 591 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7644 (tp30) REVERT: D 625 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7892 (mm) outliers start: 35 outliers final: 18 residues processed: 261 average time/residue: 0.1086 time to fit residues: 48.4757 Evaluate side-chains 246 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 89 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 178 optimal weight: 0.0970 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 572 ASN D 509 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.107751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.087906 restraints weight = 42782.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.090139 restraints weight = 24095.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.091629 restraints weight = 16436.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.092537 restraints weight = 12796.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.093171 restraints weight = 10969.022| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 20084 Z= 0.110 Angle : 0.654 16.485 27272 Z= 0.304 Chirality : 0.038 0.251 3104 Planarity : 0.004 0.039 3432 Dihedral : 4.289 29.481 2716 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.29 % Allowed : 18.90 % Favored : 79.81 % 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 are not related in a simple way. whole: -0.60 (0.17), residues: 2412 helix: 0.78 (0.14), residues: 1400 sheet: -0.63 (0.57), residues: 68 loop : -2.26 (0.17), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 470 TYR 0.012 0.001 TYR C 415 PHE 0.021 0.001 PHE C 611 TRP 0.008 0.001 TRP B 583 HIS 0.006 0.000 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (20084) covalent geometry : angle 0.65400 / 0.30 (27272) hydrogen bonds : bond 0.03910 / 2.56 ( 893) hydrogen bonds : angle 3.42368 / 2.36 ( 2571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 246 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 447 MET cc_start: 0.8309 (mtt) cc_final: 0.8060 (mtp) REVERT: A 591 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7665 (tp30) REVERT: A 625 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7927 (mm) REVERT: B 591 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7645 (tp30) REVERT: B 625 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7930 (mm) REVERT: C 255 MET cc_start: 0.8443 (tpp) cc_final: 0.8199 (tpt) REVERT: C 447 MET cc_start: 0.8256 (mtt) cc_final: 0.8003 (mtp) REVERT: C 475 LEU cc_start: 0.8566 (mp) cc_final: 0.8365 (mt) REVERT: C 591 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7635 (tp30) REVERT: C 625 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7876 (mm) REVERT: D 447 MET cc_start: 0.8301 (mtt) cc_final: 0.8045 (mtp) REVERT: D 591 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7602 (tp30) REVERT: D 625 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7850 (mm) outliers start: 27 outliers final: 21 residues processed: 264 average time/residue: 0.1114 time to fit residues: 50.0877 Evaluate side-chains 254 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 112 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 40 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 234 optimal weight: 0.9990 chunk 226 optimal weight: 6.9990 chunk 223 optimal weight: 0.3980 chunk 191 optimal weight: 0.0980 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN B 380 HIS C 185 HIS C 572 ASN D 418 GLN D 509 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.108556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.088837 restraints weight = 42463.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.091052 restraints weight = 23971.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.092535 restraints weight = 16425.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.093410 restraints weight = 12854.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.094092 restraints weight = 11009.114| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 20084 Z= 0.108 Angle : 0.654 16.441 27272 Z= 0.303 Chirality : 0.038 0.250 3104 Planarity : 0.004 0.039 3432 Dihedral : 4.221 29.980 2716 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.38 % Allowed : 19.19 % Favored : 79.43 % 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 are not related in a simple way. whole: -0.54 (0.17), residues: 2412 helix: 0.81 (0.14), residues: 1404 sheet: -0.60 (0.57), residues: 68 loop : -2.21 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 470 TYR 0.011 0.001 TYR B 415 PHE 0.020 0.001 PHE D 611 TRP 0.007 0.001 TRP B 583 HIS 0.006 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (20084) covalent geometry : angle 0.65379 / 0.30 (27272) hydrogen bonds : bond 0.03649 / 2.39 ( 893) hydrogen bonds : angle 3.40553 / 2.35 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2529.82 seconds wall clock time: 44 minutes 39.40 seconds (2679.40 seconds total)