Starting phenix.real_space_refine on Sun Aug 24 16:32:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yid_33855/08_2025/7yid_33855.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yid_33855/08_2025/7yid_33855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yid_33855/08_2025/7yid_33855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yid_33855/08_2025/7yid_33855.map" model { file = "/net/cci-nas-00/data/ceres_data/7yid_33855/08_2025/7yid_33855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yid_33855/08_2025/7yid_33855.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.059 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 K 6 8.98 5 S 128 5.16 5 C 13796 2.51 5 N 3544 2.21 5 O 3852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21326 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' K': 6} Classifications: {'undetermined': 6, 'water': 2} Link IDs: {None: 7} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 5.88, per 1000 atoms: 0.28 Number of scatterers: 21326 At special positions: 0 Unit cell: (157.065, 157.065, 130.746, 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) K 6 19.00 S 128 16.00 O 3852 8.00 N 3544 7.00 C 13796 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: 1.98 Conformation dependent library (CDL) restraints added in 995.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 20 sheets defined 54.8% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 15 through 24 removed outlier: 4.039A pdb=" N SER A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.636A pdb=" N ILE A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 79 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 156 removed outlier: 4.317A pdb=" N ARG A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 186 Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.540A pdb=" N THR A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 248 through 265 removed outlier: 3.942A pdb=" N SER A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 280 through 293 removed outlier: 3.685A pdb=" N ARG A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N MET A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.870A pdb=" N VAL A 334 " --> pdb=" O ARG A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 Processing helix chain 'A' and resid 345 through 375 Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 414 through 429 removed outlier: 3.578A pdb=" N TYR A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 495 removed outlier: 3.519A pdb=" N MET A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 458 " --> pdb=" O MET A 454 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN A 477 " --> pdb=" O GLN A 473 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A 484 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 517 Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.674A pdb=" N VAL A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 527 " --> pdb=" O LYS A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 541 removed outlier: 3.980A pdb=" N ASP A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.821A pdb=" N LYS A 619 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 620 " --> pdb=" O PHE A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 616 through 620' Processing helix chain 'A' and resid 643 through 653 Processing helix chain 'A' and resid 654 through 664 Processing helix chain 'A' and resid 678 through 692 removed outlier: 3.664A pdb=" N GLU A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 24 removed outlier: 4.039A pdb=" N SER B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.636A pdb=" N ILE B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 156 removed outlier: 4.318A pdb=" N ARG B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 153 " --> pdb=" O PHE B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 186 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.540A pdb=" N THR B 215 " --> pdb=" O CYS B 211 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.942A pdb=" N SER B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 280 through 293 removed outlier: 3.685A pdb=" N ARG B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N MET B 286 " --> pdb=" O LYS B 282 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 300 Processing helix chain 'B' and resid 321 through 326 Processing helix chain 'B' and resid 327 through 329 No H-bonds generated for 'chain 'B' and resid 327 through 329' Processing helix chain 'B' and resid 330 through 338 removed outlier: 3.870A pdb=" N VAL B 334 " --> pdb=" O ARG B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 344 Processing helix chain 'B' and resid 345 through 375 Processing helix chain 'B' and resid 387 through 397 Processing helix chain 'B' and resid 414 through 429 removed outlier: 3.578A pdb=" N TYR B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 495 removed outlier: 3.519A pdb=" N MET B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 458 " --> pdb=" O MET B 454 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET B 474 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN B 477 " --> pdb=" O GLN B 473 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 484 " --> pdb=" O ARG B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 517 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.674A pdb=" N VAL B 524 " --> pdb=" O ASP B 520 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE B 527 " --> pdb=" O LYS B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 541 removed outlier: 3.980A pdb=" N ASP B 535 " --> pdb=" O ASP B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.821A pdb=" N LYS B 619 " --> pdb=" O ILE B 616 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 620 " --> pdb=" O PHE B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 620' Processing helix chain 'B' and resid 643 through 653 Processing helix chain 'B' and resid 654 through 664 Processing helix chain 'B' and resid 678 through 692 removed outlier: 3.664A pdb=" N GLU B 687 " --> pdb=" O LYS B 683 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 688 " --> pdb=" O LYS B 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 24 removed outlier: 4.039A pdb=" N SER C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 74 through 87 removed outlier: 3.636A pdb=" N ILE C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU C 79 " --> pdb=" O LYS C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 156 removed outlier: 4.317A pdb=" N ARG C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 153 " --> pdb=" O PHE C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 186 Processing helix chain 'C' and resid 211 through 238 removed outlier: 3.540A pdb=" N THR C 215 " --> pdb=" O CYS C 211 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 248 through 265 removed outlier: 3.942A pdb=" N SER C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 280 through 293 removed outlier: 3.685A pdb=" N ARG C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N MET C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 327 through 329 No H-bonds generated for 'chain 'C' and resid 327 through 329' Processing helix chain 'C' and resid 330 through 338 removed outlier: 3.870A pdb=" N VAL C 334 " --> pdb=" O ARG C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 344 Processing helix chain 'C' and resid 345 through 375 Processing helix chain 'C' and resid 387 through 397 Processing helix chain 'C' and resid 414 through 429 removed outlier: 3.578A pdb=" N TYR C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 495 removed outlier: 3.518A pdb=" N MET C 447 " --> pdb=" O ASP C 443 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA C 451 " --> pdb=" O MET C 447 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 458 " --> pdb=" O MET C 454 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET C 474 " --> pdb=" O ILE C 470 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN C 477 " --> pdb=" O GLN C 473 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET C 484 " --> pdb=" O ARG C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 517 Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.674A pdb=" N VAL C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE C 527 " --> pdb=" O LYS C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 541 removed outlier: 3.980A pdb=" N ASP C 535 " --> pdb=" O ASP C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.821A pdb=" N LYS C 619 " --> pdb=" O ILE C 616 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 620 " --> pdb=" O PHE C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' Processing helix chain 'C' and resid 643 through 653 Processing helix chain 'C' and resid 654 through 664 Processing helix chain 'C' and resid 678 through 692 removed outlier: 3.664A pdb=" N GLU C 687 " --> pdb=" O LYS C 683 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU C 688 " --> pdb=" O LYS C 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 24 removed outlier: 4.039A pdb=" N SER D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 74 through 87 removed outlier: 3.636A pdb=" N ILE D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.318A pdb=" N ARG D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR D 153 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 186 Processing helix chain 'D' and resid 211 through 238 removed outlier: 3.540A pdb=" N THR D 215 " --> pdb=" O CYS D 211 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 248 through 265 removed outlier: 3.942A pdb=" N SER D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.685A pdb=" N ARG D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N MET D 286 " --> pdb=" O LYS D 282 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 300 Processing helix chain 'D' and resid 321 through 326 Processing helix chain 'D' and resid 327 through 329 No H-bonds generated for 'chain 'D' and resid 327 through 329' Processing helix chain 'D' and resid 330 through 338 removed outlier: 3.870A pdb=" N VAL D 334 " --> pdb=" O ARG D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 344 Processing helix chain 'D' and resid 345 through 375 Processing helix chain 'D' and resid 387 through 397 Processing helix chain 'D' and resid 414 through 429 removed outlier: 3.578A pdb=" N TYR D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 495 removed outlier: 3.519A pdb=" N MET D 447 " --> pdb=" O ASP D 443 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA D 451 " --> pdb=" O MET D 447 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 458 " --> pdb=" O MET D 454 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET D 474 " --> pdb=" O ILE D 470 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN D 477 " --> pdb=" O GLN D 473 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 517 Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.674A pdb=" N VAL D 524 " --> pdb=" O ASP D 520 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 527 " --> pdb=" O LYS D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 541 removed outlier: 3.980A pdb=" N ASP D 535 " --> pdb=" O ASP D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 555 through 566 Processing helix chain 'D' and resid 616 through 620 removed outlier: 3.821A pdb=" N LYS D 619 " --> pdb=" O ILE D 616 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 620 " --> pdb=" O PHE D 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 616 through 620' Processing helix chain 'D' and resid 643 through 653 Processing helix chain 'D' and resid 654 through 664 Processing helix chain 'D' and resid 678 through 692 removed outlier: 3.664A pdb=" N GLU D 687 " --> pdb=" O LYS D 683 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU D 688 " --> pdb=" O LYS D 684 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 4.646A pdb=" N LEU A 123 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 568 through 570 removed outlier: 6.514A pdb=" N ASP A 637 " --> pdb=" O VAL A 591 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS A 668 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 614 " --> pdb=" O CYS A 668 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 576 through 578 removed outlier: 6.870A pdb=" N VAL A 630 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU A 595 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE A 606 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 597 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 583 through 584 removed outlier: 3.543A pdb=" N VAL A 584 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA A 624 " --> pdb=" O VAL A 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 32 removed outlier: 4.646A pdb=" N LEU B 123 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 98 Processing sheet with id=AA8, first strand: chain 'B' and resid 568 through 570 removed outlier: 6.514A pdb=" N ASP B 637 " --> pdb=" O VAL B 591 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS B 668 " --> pdb=" O VAL B 612 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 614 " --> pdb=" O CYS B 668 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 576 through 578 removed outlier: 6.870A pdb=" N VAL B 630 " --> pdb=" O ILE B 577 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU B 595 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE B 606 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 597 " --> pdb=" O VAL B 604 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 583 through 584 removed outlier: 3.543A pdb=" N VAL B 584 " --> pdb=" O ALA B 624 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA B 624 " --> pdb=" O VAL B 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 31 through 32 removed outlier: 4.646A pdb=" N LEU C 123 " --> pdb=" O ILE C 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 93 through 98 Processing sheet with id=AB4, first strand: chain 'C' and resid 568 through 570 removed outlier: 6.514A pdb=" N ASP C 637 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS C 668 " --> pdb=" O VAL C 612 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY C 614 " --> pdb=" O CYS C 668 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 576 through 578 removed outlier: 6.870A pdb=" N VAL C 630 " --> pdb=" O ILE C 577 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU C 595 " --> pdb=" O ILE C 606 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE C 606 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 597 " --> pdb=" O VAL C 604 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 583 through 584 removed outlier: 3.543A pdb=" N VAL C 584 " --> pdb=" O ALA C 624 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA C 624 " --> pdb=" O VAL C 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 31 through 32 removed outlier: 4.647A pdb=" N LEU D 123 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 93 through 98 Processing sheet with id=AB9, first strand: chain 'D' and resid 568 through 570 removed outlier: 6.514A pdb=" N ASP D 637 " --> pdb=" O VAL D 591 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS D 668 " --> pdb=" O VAL D 612 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 614 " --> pdb=" O CYS D 668 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 576 through 578 removed outlier: 6.870A pdb=" N VAL D 630 " --> pdb=" O ILE D 577 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU D 595 " --> pdb=" O ILE D 606 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE D 606 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL D 597 " --> pdb=" O VAL D 604 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 583 through 584 removed outlier: 3.543A pdb=" N VAL D 584 " --> pdb=" O ALA D 624 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA D 624 " --> pdb=" O VAL D 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 1004 hydrogen bonds defined for protein. 2916 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: 4.18 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6668 1.34 - 1.46: 3354 1.46 - 1.57: 11590 1.57 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 21804 Sorted by residual: bond pdb=" N GLN B 567 " pdb=" CA GLN B 567 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 bond pdb=" N GLN C 567 " pdb=" CA GLN C 567 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 bond pdb=" N GLN D 567 " pdb=" CA GLN D 567 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 bond pdb=" N GLN A 567 " pdb=" CA GLN A 567 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 bond pdb=" C MET D 474 " pdb=" O MET D 474 " ideal model delta sigma weight residual 1.236 1.250 -0.015 1.28e-02 6.10e+03 1.32e+00 ... (remaining 21799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 28857 1.46 - 2.93: 587 2.93 - 4.39: 92 4.39 - 5.86: 36 5.86 - 7.32: 12 Bond angle restraints: 29584 Sorted by residual: angle pdb=" N ASP B 531 " pdb=" CA ASP B 531 " pdb=" C ASP B 531 " ideal model delta sigma weight residual 113.18 106.81 6.37 1.33e+00 5.65e-01 2.30e+01 angle pdb=" N ASP D 531 " pdb=" CA ASP D 531 " pdb=" C ASP D 531 " ideal model delta sigma weight residual 113.18 106.81 6.37 1.33e+00 5.65e-01 2.30e+01 angle pdb=" N ASP A 531 " pdb=" CA ASP A 531 " pdb=" C ASP A 531 " ideal model delta sigma weight residual 113.18 106.81 6.37 1.33e+00 5.65e-01 2.30e+01 angle pdb=" N ASP C 531 " pdb=" CA ASP C 531 " pdb=" C ASP C 531 " ideal model delta sigma weight residual 113.18 106.81 6.37 1.33e+00 5.65e-01 2.30e+01 angle pdb=" C PHE D 566 " pdb=" N GLN D 567 " pdb=" CA GLN D 567 " ideal model delta sigma weight residual 121.54 128.86 -7.32 1.91e+00 2.74e-01 1.47e+01 ... (remaining 29579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 11596 17.67 - 35.34: 1132 35.34 - 53.01: 168 53.01 - 70.68: 24 70.68 - 88.35: 12 Dihedral angle restraints: 12932 sinusoidal: 5144 harmonic: 7788 Sorted by residual: dihedral pdb=" CA PRO D 529 " pdb=" C PRO D 529 " pdb=" N LYS D 530 " pdb=" CA LYS D 530 " ideal model delta harmonic sigma weight residual -180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PRO B 529 " pdb=" C PRO B 529 " pdb=" N LYS B 530 " pdb=" CA LYS B 530 " ideal model delta harmonic sigma weight residual -180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PRO C 529 " pdb=" C PRO C 529 " pdb=" N LYS C 530 " pdb=" CA LYS C 530 " ideal model delta harmonic sigma weight residual 180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 12929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1962 0.030 - 0.060: 953 0.060 - 0.091: 361 0.091 - 0.121: 112 0.121 - 0.151: 16 Chirality restraints: 3404 Sorted by residual: chirality pdb=" CA ILE C 438 " pdb=" N ILE C 438 " pdb=" C ILE C 438 " pdb=" CB ILE C 438 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA MET B 286 " pdb=" N MET B 286 " pdb=" C MET B 286 " pdb=" CB MET B 286 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA MET A 286 " pdb=" N MET A 286 " pdb=" C MET A 286 " pdb=" CB MET A 286 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 3401 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 460 " 0.020 2.00e-02 2.50e+03 1.38e-02 3.81e+00 pdb=" CG TYR B 460 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 460 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 460 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 460 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 460 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 460 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 460 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 460 " 0.020 2.00e-02 2.50e+03 1.37e-02 3.76e+00 pdb=" CG TYR A 460 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 460 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 460 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 460 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 460 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 460 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 460 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 460 " 0.020 2.00e-02 2.50e+03 1.35e-02 3.65e+00 pdb=" CG TYR C 460 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR C 460 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 460 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 460 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 460 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 460 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 460 " 0.004 2.00e-02 2.50e+03 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 5406 2.80 - 3.39: 23084 3.39 - 3.97: 37651 3.97 - 4.56: 52724 4.56 - 5.14: 79781 Nonbonded interactions: 198646 Sorted by model distance: nonbonded pdb=" O LYS A 144 " pdb=" OG1 THR A 147 " model vdw 2.216 3.040 nonbonded pdb=" O LYS C 144 " pdb=" OG1 THR C 147 " model vdw 2.216 3.040 nonbonded pdb=" O LYS B 144 " pdb=" OG1 THR B 147 " model vdw 2.216 3.040 nonbonded pdb=" O LYS D 144 " pdb=" OG1 THR D 147 " model vdw 2.216 3.040 nonbonded pdb=" OE2 GLU A 596 " pdb=" OH TYR C 195 " model vdw 2.257 3.040 ... (remaining 198641 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 692) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.520 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: 0.040 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.090 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.003 0.037 21804 Z= 0.129 Angle : 0.558 7.324 29584 Z= 0.312 Chirality : 0.041 0.151 3404 Planarity : 0.003 0.040 3668 Dihedral : 13.957 88.352 7884 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.57 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.17), residues: 2616 helix: 1.00 (0.15), residues: 1276 sheet: -1.61 (0.31), residues: 260 loop : -2.09 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 677 TYR 0.033 0.001 TYR B 460 PHE 0.018 0.002 PHE A 566 TRP 0.007 0.001 TRP B 367 HIS 0.003 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00271 (21804) covalent geometry : angle 0.55811 (29584) hydrogen bonds : bond 0.15413 ( 1004) hydrogen bonds : angle 5.31572 ( 2916) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.894 Fit side-chains REVERT: A 601 ASP cc_start: 0.6927 (t0) cc_final: 0.6485 (t0) REVERT: B 601 ASP cc_start: 0.6939 (t0) cc_final: 0.6496 (t0) REVERT: C 601 ASP cc_start: 0.6918 (t0) cc_final: 0.6480 (t0) REVERT: D 601 ASP cc_start: 0.6925 (t0) cc_final: 0.6485 (t0) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1314 time to fit residues: 50.7943 Evaluate side-chains 204 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.0030 chunk 111 optimal weight: 2.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 403 ASN B 267 HIS B 403 ASN C 267 HIS C 403 ASN D 267 HIS D 403 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.184490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.163476 restraints weight = 22176.941| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.68 r_work: 0.3267 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21804 Z= 0.144 Angle : 0.536 8.596 29584 Z= 0.290 Chirality : 0.042 0.150 3404 Planarity : 0.003 0.036 3668 Dihedral : 4.281 24.647 2864 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.03 % Favored : 92.66 % Rotamer: Outliers : 0.17 % Allowed : 8.57 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.17), residues: 2616 helix: 0.95 (0.15), residues: 1344 sheet: -1.66 (0.31), residues: 260 loop : -2.38 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.029 0.001 TYR B 460 PHE 0.013 0.002 PHE C 471 TRP 0.007 0.001 TRP B 367 HIS 0.005 0.001 HIS D 570 Details of bonding type rmsd covalent geometry : bond 0.00329 (21804) covalent geometry : angle 0.53605 (29584) hydrogen bonds : bond 0.05679 ( 1004) hydrogen bonds : angle 4.26703 ( 2916) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 0.799 Fit side-chains REVERT: A 290 LYS cc_start: 0.8358 (ptpt) cc_final: 0.8134 (ptpt) REVERT: A 373 TYR cc_start: 0.8332 (t80) cc_final: 0.8104 (t80) REVERT: A 484 MET cc_start: 0.8731 (tmm) cc_final: 0.8507 (tmm) REVERT: A 601 ASP cc_start: 0.7859 (t0) cc_final: 0.7215 (t0) REVERT: B 290 LYS cc_start: 0.8376 (ptpt) cc_final: 0.8153 (ptpt) REVERT: B 373 TYR cc_start: 0.8341 (t80) cc_final: 0.8116 (t80) REVERT: B 484 MET cc_start: 0.8737 (tmm) cc_final: 0.8515 (tmm) REVERT: B 601 ASP cc_start: 0.7840 (t0) cc_final: 0.7194 (t0) REVERT: C 290 LYS cc_start: 0.8371 (ptpt) cc_final: 0.8148 (ptpt) REVERT: C 373 TYR cc_start: 0.8331 (t80) cc_final: 0.8105 (t80) REVERT: C 484 MET cc_start: 0.8732 (tmm) cc_final: 0.8503 (tmm) REVERT: C 601 ASP cc_start: 0.7847 (t0) cc_final: 0.7198 (t0) REVERT: D 290 LYS cc_start: 0.8382 (ptpt) cc_final: 0.8157 (ptpt) REVERT: D 373 TYR cc_start: 0.8332 (t80) cc_final: 0.8106 (t80) REVERT: D 484 MET cc_start: 0.8729 (tmm) cc_final: 0.8499 (tmm) REVERT: D 601 ASP cc_start: 0.7865 (t0) cc_final: 0.7216 (t0) outliers start: 4 outliers final: 4 residues processed: 192 average time/residue: 0.1238 time to fit residues: 38.5033 Evaluate side-chains 196 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 394 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 30 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 146 optimal weight: 40.0000 chunk 190 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.177894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.145540 restraints weight = 22089.755| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.71 r_work: 0.3049 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21804 Z= 0.257 Angle : 0.620 5.631 29584 Z= 0.339 Chirality : 0.046 0.151 3404 Planarity : 0.003 0.038 3668 Dihedral : 4.625 27.537 2864 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.10 % Favored : 91.59 % Rotamer: Outliers : 1.34 % Allowed : 11.60 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.16), residues: 2616 helix: 0.63 (0.14), residues: 1352 sheet: -2.51 (0.37), residues: 148 loop : -2.43 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 22 TYR 0.034 0.002 TYR C 460 PHE 0.022 0.002 PHE C 660 TRP 0.010 0.001 TRP A 388 HIS 0.007 0.001 HIS D 570 Details of bonding type rmsd covalent geometry : bond 0.00638 (21804) covalent geometry : angle 0.61997 (29584) hydrogen bonds : bond 0.07052 ( 1004) hydrogen bonds : angle 4.39032 ( 2916) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.541 Fit side-chains REVERT: A 119 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8084 (mm-30) REVERT: A 286 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7263 (pmm) REVERT: A 290 LYS cc_start: 0.8289 (ptpt) cc_final: 0.8065 (ptpt) REVERT: A 373 TYR cc_start: 0.8251 (t80) cc_final: 0.7981 (t80) REVERT: A 601 ASP cc_start: 0.7658 (t0) cc_final: 0.7063 (t0) REVERT: B 119 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8084 (mm-30) REVERT: B 286 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7269 (pmm) REVERT: B 290 LYS cc_start: 0.8293 (ptpt) cc_final: 0.8068 (ptpt) REVERT: B 373 TYR cc_start: 0.8247 (t80) cc_final: 0.7980 (t80) REVERT: B 601 ASP cc_start: 0.7669 (t0) cc_final: 0.7070 (t0) REVERT: C 119 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8075 (mm-30) REVERT: C 286 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7275 (pmm) REVERT: C 290 LYS cc_start: 0.8273 (ptpt) cc_final: 0.8049 (ptpt) REVERT: C 373 TYR cc_start: 0.8250 (t80) cc_final: 0.7981 (t80) REVERT: C 601 ASP cc_start: 0.7633 (t0) cc_final: 0.7043 (t0) REVERT: D 119 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8087 (mm-30) REVERT: D 286 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7273 (pmm) REVERT: D 290 LYS cc_start: 0.8297 (ptpt) cc_final: 0.8073 (ptpt) REVERT: D 373 TYR cc_start: 0.8249 (t80) cc_final: 0.7981 (t80) REVERT: D 601 ASP cc_start: 0.7621 (t0) cc_final: 0.7037 (t0) outliers start: 32 outliers final: 12 residues processed: 220 average time/residue: 0.1293 time to fit residues: 46.2455 Evaluate side-chains 212 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 251 optimal weight: 0.8980 chunk 54 optimal weight: 0.0870 chunk 122 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 30.0000 chunk 39 optimal weight: 0.6980 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.179955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.143911 restraints weight = 22012.522| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.83 r_work: 0.2993 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21804 Z= 0.155 Angle : 0.524 6.156 29584 Z= 0.286 Chirality : 0.042 0.142 3404 Planarity : 0.003 0.034 3668 Dihedral : 4.394 24.278 2864 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.88 % Favored : 92.81 % Rotamer: Outliers : 1.51 % Allowed : 12.56 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.16), residues: 2616 helix: 0.94 (0.15), residues: 1340 sheet: -2.39 (0.38), residues: 156 loop : -2.37 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 82 TYR 0.020 0.001 TYR B 460 PHE 0.013 0.002 PHE B 134 TRP 0.009 0.001 TRP A 367 HIS 0.005 0.001 HIS D 570 Details of bonding type rmsd covalent geometry : bond 0.00365 (21804) covalent geometry : angle 0.52383 (29584) hydrogen bonds : bond 0.05878 ( 1004) hydrogen bonds : angle 4.05238 ( 2916) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.882 Fit side-chains REVERT: A 119 GLU cc_start: 0.8230 (mm-30) cc_final: 0.8014 (mm-30) REVERT: A 286 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7033 (pmm) REVERT: A 373 TYR cc_start: 0.8188 (t80) cc_final: 0.7861 (t80) REVERT: A 601 ASP cc_start: 0.7575 (t0) cc_final: 0.6979 (t0) REVERT: A 677 ARG cc_start: 0.8294 (ttp80) cc_final: 0.7980 (ttp80) REVERT: B 119 GLU cc_start: 0.8232 (mm-30) cc_final: 0.8021 (mm-30) REVERT: B 286 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7035 (pmm) REVERT: B 373 TYR cc_start: 0.8184 (t80) cc_final: 0.7857 (t80) REVERT: B 601 ASP cc_start: 0.7619 (t0) cc_final: 0.7014 (t0) REVERT: B 677 ARG cc_start: 0.8288 (ttp80) cc_final: 0.7971 (ttp80) REVERT: C 119 GLU cc_start: 0.8242 (mm-30) cc_final: 0.8026 (mm-30) REVERT: C 286 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7055 (pmm) REVERT: C 373 TYR cc_start: 0.8183 (t80) cc_final: 0.7855 (t80) REVERT: C 601 ASP cc_start: 0.7594 (t0) cc_final: 0.6996 (t0) REVERT: C 677 ARG cc_start: 0.8308 (ttp80) cc_final: 0.7994 (ttp80) REVERT: D 119 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8041 (mm-30) REVERT: D 286 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7047 (pmm) REVERT: D 373 TYR cc_start: 0.8185 (t80) cc_final: 0.7856 (t80) REVERT: D 601 ASP cc_start: 0.7609 (t0) cc_final: 0.7009 (t0) REVERT: D 677 ARG cc_start: 0.8304 (ttp80) cc_final: 0.7991 (ttp80) outliers start: 36 outliers final: 20 residues processed: 228 average time/residue: 0.1492 time to fit residues: 54.1452 Evaluate side-chains 204 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 598 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 258 optimal weight: 1.9990 chunk 146 optimal weight: 0.3980 chunk 152 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 235 optimal weight: 0.0770 chunk 187 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.183396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.157149 restraints weight = 21914.185| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.29 r_work: 0.3235 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21804 Z= 0.115 Angle : 0.492 8.806 29584 Z= 0.265 Chirality : 0.040 0.135 3404 Planarity : 0.003 0.031 3668 Dihedral : 4.194 23.615 2864 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.57 % Favored : 93.12 % Rotamer: Outliers : 1.68 % Allowed : 13.03 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.17), residues: 2616 helix: 1.17 (0.15), residues: 1340 sheet: -2.16 (0.41), residues: 148 loop : -2.31 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 327 TYR 0.015 0.001 TYR C 460 PHE 0.011 0.001 PHE B 471 TRP 0.008 0.001 TRP A 367 HIS 0.004 0.001 HIS C 570 Details of bonding type rmsd covalent geometry : bond 0.00250 (21804) covalent geometry : angle 0.49158 (29584) hydrogen bonds : bond 0.05081 ( 1004) hydrogen bonds : angle 3.81187 ( 2916) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 0.880 Fit side-chains REVERT: A 286 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6886 (pmm) REVERT: A 344 TYR cc_start: 0.7970 (m-80) cc_final: 0.7739 (m-80) REVERT: A 373 TYR cc_start: 0.8138 (t80) cc_final: 0.7879 (t80) REVERT: A 601 ASP cc_start: 0.7526 (t0) cc_final: 0.6938 (t0) REVERT: A 677 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7908 (ttp80) REVERT: B 286 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.6868 (pmm) REVERT: B 344 TYR cc_start: 0.7971 (m-80) cc_final: 0.7740 (m-80) REVERT: B 373 TYR cc_start: 0.8132 (t80) cc_final: 0.7870 (t80) REVERT: B 601 ASP cc_start: 0.7561 (t0) cc_final: 0.6968 (t0) REVERT: B 677 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7889 (ttp80) REVERT: C 286 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.6887 (pmm) REVERT: C 344 TYR cc_start: 0.7984 (m-80) cc_final: 0.7756 (m-80) REVERT: C 373 TYR cc_start: 0.8121 (t80) cc_final: 0.7860 (t80) REVERT: C 601 ASP cc_start: 0.7571 (t0) cc_final: 0.6979 (t0) REVERT: C 677 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7911 (ttp80) REVERT: D 286 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.6896 (pmm) REVERT: D 344 TYR cc_start: 0.7990 (m-80) cc_final: 0.7756 (m-80) REVERT: D 373 TYR cc_start: 0.8127 (t80) cc_final: 0.7867 (t80) REVERT: D 601 ASP cc_start: 0.7554 (t0) cc_final: 0.6971 (t0) REVERT: D 677 ARG cc_start: 0.8256 (ttp80) cc_final: 0.7909 (ttp80) outliers start: 40 outliers final: 20 residues processed: 224 average time/residue: 0.1453 time to fit residues: 52.5845 Evaluate side-chains 206 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 254 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 214 optimal weight: 30.0000 chunk 2 optimal weight: 0.5980 chunk 154 optimal weight: 0.6980 chunk 236 optimal weight: 0.4980 chunk 147 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 104 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.183740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.158299 restraints weight = 21919.414| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.27 r_work: 0.3261 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 21804 Z= 0.105 Angle : 0.479 7.652 29584 Z= 0.256 Chirality : 0.039 0.135 3404 Planarity : 0.003 0.028 3668 Dihedral : 4.055 23.387 2864 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.50 % Favored : 93.20 % Rotamer: Outliers : 2.02 % Allowed : 13.36 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.17), residues: 2616 helix: 1.40 (0.15), residues: 1332 sheet: -1.95 (0.42), residues: 148 loop : -2.22 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 82 TYR 0.013 0.001 TYR C 460 PHE 0.013 0.001 PHE D 93 TRP 0.008 0.001 TRP D 513 HIS 0.004 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00223 (21804) covalent geometry : angle 0.47938 (29584) hydrogen bonds : bond 0.04703 ( 1004) hydrogen bonds : angle 3.66722 ( 2916) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 190 time to evaluate : 0.778 Fit side-chains REVERT: A 286 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.6849 (pmm) REVERT: A 344 TYR cc_start: 0.7887 (m-80) cc_final: 0.7650 (m-80) REVERT: A 373 TYR cc_start: 0.8155 (t80) cc_final: 0.7871 (t80) REVERT: A 601 ASP cc_start: 0.7481 (t0) cc_final: 0.6900 (t0) REVERT: A 677 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7890 (ttp80) REVERT: B 286 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.6826 (pmm) REVERT: B 344 TYR cc_start: 0.7898 (m-80) cc_final: 0.7652 (m-80) REVERT: B 373 TYR cc_start: 0.8145 (t80) cc_final: 0.7857 (t80) REVERT: B 601 ASP cc_start: 0.7506 (t0) cc_final: 0.6921 (t0) REVERT: B 677 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7882 (ttp80) REVERT: C 286 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.6854 (pmm) REVERT: C 344 TYR cc_start: 0.7900 (m-80) cc_final: 0.7659 (m-80) REVERT: C 373 TYR cc_start: 0.8133 (t80) cc_final: 0.7848 (t80) REVERT: C 601 ASP cc_start: 0.7501 (t0) cc_final: 0.6920 (t0) REVERT: C 677 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7887 (ttp80) REVERT: D 286 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.6848 (pmm) REVERT: D 344 TYR cc_start: 0.7901 (m-80) cc_final: 0.7657 (m-80) REVERT: D 373 TYR cc_start: 0.8139 (t80) cc_final: 0.7854 (t80) REVERT: D 601 ASP cc_start: 0.7478 (t0) cc_final: 0.6904 (t0) REVERT: D 677 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7882 (ttp80) outliers start: 48 outliers final: 28 residues processed: 234 average time/residue: 0.1430 time to fit residues: 54.3142 Evaluate side-chains 216 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.5980 chunk 151 optimal weight: 0.5980 chunk 223 optimal weight: 3.9990 chunk 263 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 224 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.183347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.156276 restraints weight = 21893.814| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.37 r_work: 0.3222 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 21804 Z= 0.119 Angle : 0.500 8.813 29584 Z= 0.263 Chirality : 0.040 0.137 3404 Planarity : 0.003 0.029 3668 Dihedral : 4.040 24.074 2864 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.57 % Favored : 93.12 % Rotamer: Outliers : 1.51 % Allowed : 14.62 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.17), residues: 2616 helix: 1.35 (0.15), residues: 1340 sheet: -1.88 (0.42), residues: 148 loop : -2.22 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 336 TYR 0.013 0.001 TYR A 460 PHE 0.010 0.001 PHE B 471 TRP 0.007 0.001 TRP C 367 HIS 0.004 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00265 (21804) covalent geometry : angle 0.49966 (29584) hydrogen bonds : bond 0.04876 ( 1004) hydrogen bonds : angle 3.68086 ( 2916) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.873 Fit side-chains REVERT: A 107 PHE cc_start: 0.7790 (m-80) cc_final: 0.7513 (m-80) REVERT: A 286 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.6886 (pmm) REVERT: A 344 TYR cc_start: 0.7895 (m-80) cc_final: 0.7647 (m-80) REVERT: A 373 TYR cc_start: 0.8263 (t80) cc_final: 0.7943 (t80) REVERT: A 601 ASP cc_start: 0.7523 (t0) cc_final: 0.6910 (t0) REVERT: A 677 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7875 (ttp80) REVERT: B 107 PHE cc_start: 0.7756 (m-80) cc_final: 0.7479 (m-80) REVERT: B 286 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6886 (pmm) REVERT: B 344 TYR cc_start: 0.7918 (m-80) cc_final: 0.7662 (m-80) REVERT: B 373 TYR cc_start: 0.8254 (t80) cc_final: 0.7931 (t80) REVERT: B 601 ASP cc_start: 0.7551 (t0) cc_final: 0.6931 (t0) REVERT: B 677 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7846 (ttp80) REVERT: C 107 PHE cc_start: 0.7776 (m-80) cc_final: 0.7499 (m-80) REVERT: C 286 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.6884 (pmm) REVERT: C 344 TYR cc_start: 0.7907 (m-80) cc_final: 0.7661 (m-80) REVERT: C 373 TYR cc_start: 0.8244 (t80) cc_final: 0.7921 (t80) REVERT: C 601 ASP cc_start: 0.7582 (t0) cc_final: 0.6959 (t0) REVERT: C 677 ARG cc_start: 0.8263 (ttp80) cc_final: 0.7864 (ttp80) REVERT: D 107 PHE cc_start: 0.7747 (m-80) cc_final: 0.7472 (m-80) REVERT: D 286 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.6884 (pmm) REVERT: D 344 TYR cc_start: 0.7899 (m-80) cc_final: 0.7652 (m-80) REVERT: D 373 TYR cc_start: 0.8251 (t80) cc_final: 0.7929 (t80) REVERT: D 601 ASP cc_start: 0.7569 (t0) cc_final: 0.6951 (t0) REVERT: D 677 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7865 (ttp80) outliers start: 36 outliers final: 28 residues processed: 222 average time/residue: 0.1480 time to fit residues: 52.3254 Evaluate side-chains 220 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 138 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 260 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 232 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.183164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.153040 restraints weight = 21876.922| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.54 r_work: 0.3169 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21804 Z= 0.122 Angle : 0.503 8.070 29584 Z= 0.265 Chirality : 0.040 0.149 3404 Planarity : 0.003 0.029 3668 Dihedral : 4.034 24.098 2864 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.84 % Favored : 92.85 % Rotamer: Outliers : 1.85 % Allowed : 13.78 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.17), residues: 2616 helix: 1.35 (0.15), residues: 1344 sheet: -1.88 (0.42), residues: 148 loop : -2.22 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 82 TYR 0.014 0.001 TYR A 460 PHE 0.014 0.001 PHE D 93 TRP 0.007 0.001 TRP A 367 HIS 0.004 0.001 HIS C 570 Details of bonding type rmsd covalent geometry : bond 0.00276 (21804) covalent geometry : angle 0.50270 (29584) hydrogen bonds : bond 0.04943 ( 1004) hydrogen bonds : angle 3.68604 ( 2916) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 0.780 Fit side-chains REVERT: A 107 PHE cc_start: 0.7793 (m-80) cc_final: 0.7500 (m-80) REVERT: A 286 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.6887 (pmm) REVERT: A 344 TYR cc_start: 0.7896 (m-80) cc_final: 0.7634 (m-80) REVERT: A 373 TYR cc_start: 0.8257 (t80) cc_final: 0.7926 (t80) REVERT: A 601 ASP cc_start: 0.7529 (t0) cc_final: 0.6913 (t0) REVERT: A 677 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7843 (ttp80) REVERT: B 107 PHE cc_start: 0.7753 (m-80) cc_final: 0.7460 (m-80) REVERT: B 286 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.6888 (pmm) REVERT: B 373 TYR cc_start: 0.8246 (t80) cc_final: 0.7913 (t80) REVERT: B 601 ASP cc_start: 0.7588 (t0) cc_final: 0.6962 (t0) REVERT: B 677 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7824 (ttp80) REVERT: C 107 PHE cc_start: 0.7784 (m-80) cc_final: 0.7491 (m-80) REVERT: C 286 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.6887 (pmm) REVERT: C 344 TYR cc_start: 0.7892 (m-80) cc_final: 0.7636 (m-80) REVERT: C 373 TYR cc_start: 0.8243 (t80) cc_final: 0.7910 (t80) REVERT: C 601 ASP cc_start: 0.7609 (t0) cc_final: 0.6978 (t0) REVERT: C 677 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7833 (ttp80) REVERT: D 107 PHE cc_start: 0.7761 (m-80) cc_final: 0.7470 (m-80) REVERT: D 286 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.6894 (pmm) REVERT: D 344 TYR cc_start: 0.7898 (m-80) cc_final: 0.7641 (m-80) REVERT: D 373 TYR cc_start: 0.8244 (t80) cc_final: 0.7912 (t80) REVERT: D 601 ASP cc_start: 0.7603 (t0) cc_final: 0.6980 (t0) REVERT: D 677 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7829 (ttp80) outliers start: 44 outliers final: 28 residues processed: 234 average time/residue: 0.1337 time to fit residues: 50.1173 Evaluate side-chains 218 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 172 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 0.0570 chunk 3 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 206 optimal weight: 5.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.182156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.152667 restraints weight = 21807.867| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.58 r_work: 0.3154 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21804 Z= 0.128 Angle : 0.516 8.303 29584 Z= 0.270 Chirality : 0.041 0.155 3404 Planarity : 0.003 0.027 3668 Dihedral : 4.051 24.289 2864 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.11 % Favored : 92.58 % Rotamer: Outliers : 1.34 % Allowed : 13.95 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.17), residues: 2616 helix: 1.34 (0.15), residues: 1344 sheet: -1.91 (0.42), residues: 148 loop : -2.17 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 82 TYR 0.014 0.001 TYR A 460 PHE 0.011 0.001 PHE B 471 TRP 0.007 0.001 TRP C 367 HIS 0.004 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00293 (21804) covalent geometry : angle 0.51647 (29584) hydrogen bonds : bond 0.05060 ( 1004) hydrogen bonds : angle 3.71813 ( 2916) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.854 Fit side-chains REVERT: A 107 PHE cc_start: 0.7912 (m-80) cc_final: 0.7660 (m-80) REVERT: A 286 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.6881 (pmm) REVERT: A 373 TYR cc_start: 0.8320 (t80) cc_final: 0.7996 (t80) REVERT: A 601 ASP cc_start: 0.7679 (t0) cc_final: 0.7057 (t0) REVERT: B 107 PHE cc_start: 0.7875 (m-80) cc_final: 0.7619 (m-80) REVERT: B 286 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.6898 (pmm) REVERT: B 373 TYR cc_start: 0.8310 (t80) cc_final: 0.7984 (t80) REVERT: B 601 ASP cc_start: 0.7741 (t0) cc_final: 0.7108 (t0) REVERT: C 107 PHE cc_start: 0.7879 (m-80) cc_final: 0.7627 (m-80) REVERT: C 286 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.6913 (pmm) REVERT: C 373 TYR cc_start: 0.8304 (t80) cc_final: 0.7977 (t80) REVERT: C 601 ASP cc_start: 0.7754 (t0) cc_final: 0.7123 (t0) REVERT: C 677 ARG cc_start: 0.8299 (ttp80) cc_final: 0.8049 (ttp80) REVERT: D 107 PHE cc_start: 0.7864 (m-80) cc_final: 0.7612 (m-80) REVERT: D 286 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.6887 (pmm) REVERT: D 373 TYR cc_start: 0.8310 (t80) cc_final: 0.7986 (t80) REVERT: D 601 ASP cc_start: 0.7751 (t0) cc_final: 0.7123 (t0) REVERT: D 677 ARG cc_start: 0.8288 (ttp80) cc_final: 0.8036 (ttp80) outliers start: 32 outliers final: 24 residues processed: 220 average time/residue: 0.1344 time to fit residues: 47.1635 Evaluate side-chains 208 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 124 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 152 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 253 optimal weight: 0.0020 chunk 164 optimal weight: 0.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.183401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.159448 restraints weight = 21906.505| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.14 r_work: 0.3265 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21804 Z= 0.113 Angle : 0.505 8.058 29584 Z= 0.265 Chirality : 0.040 0.149 3404 Planarity : 0.003 0.028 3668 Dihedral : 3.991 23.381 2864 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.69 % Favored : 93.00 % Rotamer: Outliers : 1.51 % Allowed : 13.87 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.17), residues: 2616 helix: 1.41 (0.15), residues: 1336 sheet: -1.83 (0.42), residues: 148 loop : -2.13 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 677 TYR 0.012 0.001 TYR C 460 PHE 0.013 0.001 PHE D 93 TRP 0.008 0.001 TRP C 367 HIS 0.004 0.001 HIS D 570 Details of bonding type rmsd covalent geometry : bond 0.00250 (21804) covalent geometry : angle 0.50528 (29584) hydrogen bonds : bond 0.04767 ( 1004) hydrogen bonds : angle 3.66395 ( 2916) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.872 Fit side-chains REVERT: A 107 PHE cc_start: 0.7802 (m-80) cc_final: 0.7542 (m-80) REVERT: A 286 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.6757 (pmm) REVERT: A 344 TYR cc_start: 0.7946 (m-80) cc_final: 0.7698 (m-80) REVERT: A 373 TYR cc_start: 0.8219 (t80) cc_final: 0.7888 (t80) REVERT: A 601 ASP cc_start: 0.7478 (t0) cc_final: 0.6893 (t0) REVERT: B 107 PHE cc_start: 0.7772 (m-80) cc_final: 0.7511 (m-80) REVERT: B 286 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.6763 (pmm) REVERT: B 373 TYR cc_start: 0.8204 (t80) cc_final: 0.7869 (t80) REVERT: B 601 ASP cc_start: 0.7533 (t0) cc_final: 0.6930 (t0) REVERT: C 107 PHE cc_start: 0.7788 (m-80) cc_final: 0.7526 (m-80) REVERT: C 286 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.6770 (pmm) REVERT: C 344 TYR cc_start: 0.7955 (m-80) cc_final: 0.7708 (m-80) REVERT: C 373 TYR cc_start: 0.8198 (t80) cc_final: 0.7864 (t80) REVERT: C 601 ASP cc_start: 0.7545 (t0) cc_final: 0.6947 (t0) REVERT: C 677 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7937 (ttp80) REVERT: D 107 PHE cc_start: 0.7762 (m-80) cc_final: 0.7502 (m-80) REVERT: D 286 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.6783 (pmm) REVERT: D 344 TYR cc_start: 0.7949 (m-80) cc_final: 0.7701 (m-80) REVERT: D 373 TYR cc_start: 0.8206 (t80) cc_final: 0.7870 (t80) REVERT: D 601 ASP cc_start: 0.7531 (t0) cc_final: 0.6936 (t0) REVERT: D 677 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7920 (ttp80) outliers start: 36 outliers final: 28 residues processed: 218 average time/residue: 0.1385 time to fit residues: 48.7834 Evaluate side-chains 212 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 119 optimal weight: 0.9980 chunk 233 optimal weight: 0.1980 chunk 57 optimal weight: 0.7980 chunk 198 optimal weight: 0.8980 chunk 49 optimal weight: 0.0050 chunk 219 optimal weight: 0.8980 chunk 211 optimal weight: 0.1980 chunk 155 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 242 optimal weight: 0.7980 chunk 82 optimal weight: 30.0000 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.186097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.160138 restraints weight = 21805.931| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.16 r_work: 0.3305 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 21804 Z= 0.097 Angle : 0.483 7.887 29584 Z= 0.252 Chirality : 0.039 0.140 3404 Planarity : 0.003 0.025 3668 Dihedral : 3.849 22.401 2864 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.65 % Favored : 93.04 % Rotamer: Outliers : 1.34 % Allowed : 14.20 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.17), residues: 2616 helix: 1.51 (0.15), residues: 1336 sheet: -1.45 (0.34), residues: 260 loop : -2.04 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 677 TYR 0.011 0.001 TYR B 98 PHE 0.011 0.001 PHE B 448 TRP 0.008 0.001 TRP C 513 HIS 0.004 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00202 (21804) covalent geometry : angle 0.48286 (29584) hydrogen bonds : bond 0.04257 ( 1004) hydrogen bonds : angle 3.54527 ( 2916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5086.26 seconds wall clock time: 87 minutes 55.07 seconds (5275.07 seconds total)