Starting phenix.real_space_refine on Sun Aug 24 16:17:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yie_33856/08_2025/7yie_33856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yie_33856/08_2025/7yie_33856.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 { model { file = "/net/cci-nas-00/data/ceres_data/7yie_33856/08_2025/7yie_33856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yie_33856/08_2025/7yie_33856.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yie_33856/08_2025/7yie_33856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yie_33856/08_2025/7yie_33856.map" } 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= 0.055 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 32 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: 8 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: "B" 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: "C" 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: "D" 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} Time building chain proxies: 5.63, per 1000 atoms: 0.26 Number of scatterers: 21326 At special positions: 0 Unit cell: (157.065, 157.065, 131.595, 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: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 108 helices and 20 sheets defined 54.4% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 15 through 24 removed outlier: 3.960A pdb=" N SER A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.501A pdb=" N SER A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 146 through 156 removed outlier: 4.182A pdb=" N ARG A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.680A 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: 3.735A 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 247 through 265 removed outlier: 3.739A pdb=" N ASP A 251 " --> pdb=" O TRP A 247 " (cutoff:3.500A) removed outlier: 3.678A 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: 3.587A pdb=" N ARG A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 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: 3.949A 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: 3.585A pdb=" N TYR A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 495 removed outlier: 4.018A pdb=" N ALA A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 458 " --> pdb=" O MET A 454 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN A 477 " --> pdb=" O GLN A 473 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.938A pdb=" N ILE A 527 " --> pdb=" O LYS A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 541 removed outlier: 4.244A pdb=" N ASP A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 removed outlier: 3.620A pdb=" N PHE A 545 " --> pdb=" O ASN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.955A pdb=" N LYS A 619 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 3.514A 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: 3.565A pdb=" N GLU A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 24 removed outlier: 3.960A pdb=" N SER B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.501A pdb=" N SER B 51 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 146 through 156 removed outlier: 4.182A pdb=" N ARG B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.680A 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: 3.735A 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 247 through 265 removed outlier: 3.739A pdb=" N ASP B 251 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 3.678A 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: 3.587A pdb=" N ARG B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET B 286 " --> pdb=" O LYS B 282 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 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: 3.949A 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: 3.594A pdb=" N TYR B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 495 removed outlier: 4.019A pdb=" N ALA B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 458 " --> pdb=" O MET B 454 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET B 474 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN B 477 " --> pdb=" O GLN B 473 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.938A pdb=" N ILE B 527 " --> pdb=" O LYS B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 541 removed outlier: 4.244A pdb=" N ASP B 535 " --> pdb=" O ASP B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 removed outlier: 3.620A pdb=" N PHE B 545 " --> pdb=" O ASN B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.955A pdb=" N LYS B 619 " --> pdb=" O ILE B 616 " (cutoff:3.500A) removed outlier: 3.514A 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: 3.565A pdb=" N GLU B 687 " --> pdb=" O LYS B 683 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 688 " --> pdb=" O LYS B 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 24 removed outlier: 3.960A pdb=" N SER C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 removed outlier: 3.501A pdb=" N SER C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 Processing helix chain 'C' and resid 146 through 156 removed outlier: 4.182A pdb=" N ARG C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.680A 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: 3.735A 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 247 through 265 removed outlier: 3.739A pdb=" N ASP C 251 " --> pdb=" O TRP C 247 " (cutoff:3.500A) removed outlier: 3.678A 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: 3.587A pdb=" N ARG C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 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: 3.949A 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: 3.594A pdb=" N TYR C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 495 removed outlier: 4.019A pdb=" N ALA C 451 " --> pdb=" O MET C 447 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 458 " --> pdb=" O MET C 454 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET C 474 " --> pdb=" O ILE C 470 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN C 477 " --> pdb=" O GLN C 473 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.938A pdb=" N ILE C 527 " --> pdb=" O LYS C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 541 removed outlier: 4.244A pdb=" N ASP C 535 " --> pdb=" O ASP C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 removed outlier: 3.620A pdb=" N PHE C 545 " --> pdb=" O ASN C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.955A pdb=" N LYS C 619 " --> pdb=" O ILE C 616 " (cutoff:3.500A) removed outlier: 3.515A 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: 3.565A pdb=" N GLU C 687 " --> pdb=" O LYS C 683 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 688 " --> pdb=" O LYS C 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 24 removed outlier: 3.960A pdb=" N SER D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.502A pdb=" N SER D 51 " --> pdb=" O PHE D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.182A pdb=" N ARG D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.680A 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: 3.735A 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 247 through 265 removed outlier: 3.739A pdb=" N ASP D 251 " --> pdb=" O TRP D 247 " (cutoff:3.500A) removed outlier: 3.678A 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: 3.587A pdb=" N ARG D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET D 286 " --> pdb=" O LYS D 282 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 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: 3.949A 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: 3.594A pdb=" N TYR D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 495 removed outlier: 4.019A pdb=" N ALA D 451 " --> pdb=" O MET D 447 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 458 " --> pdb=" O MET D 454 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET D 474 " --> pdb=" O ILE D 470 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN D 477 " --> pdb=" O GLN D 473 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.938A pdb=" N ILE D 527 " --> pdb=" O LYS D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 541 removed outlier: 4.244A pdb=" N ASP D 535 " --> pdb=" O ASP D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 removed outlier: 3.620A pdb=" N PHE D 545 " --> pdb=" O ASN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 566 Processing helix chain 'D' and resid 616 through 620 removed outlier: 3.955A pdb=" N LYS D 619 " --> pdb=" O ILE D 616 " (cutoff:3.500A) removed outlier: 3.515A 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: 3.565A pdb=" N GLU D 687 " --> pdb=" O LYS D 683 " (cutoff:3.500A) removed outlier: 3.572A 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: 3.798A pdb=" N LEU A 123 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR A 127 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 271 removed outlier: 3.690A pdb=" N PHE A 270 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 401 removed outlier: 3.959A pdb=" N GLU A 410 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 568 through 570 removed outlier: 6.519A pdb=" N ASP A 637 " --> pdb=" O VAL A 591 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP A 611 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N CYS A 668 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 614 " --> pdb=" O CYS A 668 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 603 through 607 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 32 removed outlier: 3.798A pdb=" N LEU B 123 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR B 127 " --> pdb=" O GLN B 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 270 through 271 removed outlier: 3.690A pdb=" N PHE B 270 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 400 through 401 removed outlier: 3.959A pdb=" N GLU B 410 " --> pdb=" O ARG B 401 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 568 through 570 removed outlier: 6.519A pdb=" N ASP B 637 " --> pdb=" O VAL B 591 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP B 611 " --> pdb=" O VAL B 590 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N CYS B 668 " --> pdb=" O VAL B 612 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 614 " --> pdb=" O CYS B 668 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 603 through 607 Processing sheet with id=AB2, first strand: chain 'C' and resid 31 through 32 removed outlier: 3.796A pdb=" N LEU C 123 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR C 127 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 270 through 271 removed outlier: 3.690A pdb=" N PHE C 270 " --> pdb=" O ILE C 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 400 through 401 removed outlier: 3.959A pdb=" N GLU C 410 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 568 through 570 removed outlier: 6.519A pdb=" N ASP C 637 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP C 611 " --> pdb=" O VAL C 590 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N CYS C 668 " --> pdb=" O VAL C 612 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 614 " --> pdb=" O CYS C 668 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 603 through 607 Processing sheet with id=AB7, first strand: chain 'D' and resid 31 through 32 removed outlier: 3.798A pdb=" N LEU D 123 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR D 127 " --> pdb=" O GLN D 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 270 through 271 removed outlier: 3.690A pdb=" N PHE D 270 " --> pdb=" O ILE D 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 400 through 401 removed outlier: 3.959A pdb=" N GLU D 410 " --> pdb=" O ARG D 401 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 568 through 570 removed outlier: 6.519A pdb=" N ASP D 637 " --> pdb=" O VAL D 591 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP D 611 " --> pdb=" O VAL D 590 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N CYS D 668 " --> pdb=" O VAL D 612 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 614 " --> pdb=" O CYS D 668 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 603 through 607 1044 hydrogen bonds defined for protein. 3060 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: 4.58 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6696 1.34 - 1.46: 5176 1.46 - 1.58: 9740 1.58 - 1.70: 0 1.70 - 1.81: 192 Bond restraints: 21804 Sorted by residual: bond pdb=" N GLN C 567 " pdb=" CA GLN C 567 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.55e+00 bond pdb=" N GLN B 567 " pdb=" CA GLN B 567 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.55e+00 bond pdb=" N GLN D 567 " pdb=" CA GLN D 567 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.55e+00 bond pdb=" N GLN A 567 " pdb=" CA GLN A 567 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.55e+00 bond pdb=" C MET B 474 " pdb=" O MET B 474 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.28e-02 6.10e+03 1.26e+00 ... (remaining 21799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 29058 1.74 - 3.48: 446 3.48 - 5.21: 60 5.21 - 6.95: 12 6.95 - 8.69: 8 Bond angle restraints: 29584 Sorted by residual: angle pdb=" N ILE B 245 " pdb=" CA ILE B 245 " pdb=" C ILE B 245 " ideal model delta sigma weight residual 113.43 107.72 5.71 1.09e+00 8.42e-01 2.74e+01 angle pdb=" N ILE C 245 " pdb=" CA ILE C 245 " pdb=" C ILE C 245 " ideal model delta sigma weight residual 113.43 107.72 5.71 1.09e+00 8.42e-01 2.74e+01 angle pdb=" N ILE D 245 " pdb=" CA ILE D 245 " pdb=" C ILE D 245 " ideal model delta sigma weight residual 113.43 107.72 5.71 1.09e+00 8.42e-01 2.74e+01 angle pdb=" N ILE A 245 " pdb=" CA ILE A 245 " pdb=" C ILE A 245 " ideal model delta sigma weight residual 113.43 107.72 5.71 1.09e+00 8.42e-01 2.74e+01 angle pdb=" C PHE A 566 " pdb=" N GLN A 567 " pdb=" CA GLN A 567 " ideal model delta sigma weight residual 121.54 129.11 -7.57 1.91e+00 2.74e-01 1.57e+01 ... (remaining 29579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 11506 17.41 - 34.82: 1198 34.82 - 52.23: 192 52.23 - 69.64: 16 69.64 - 87.05: 20 Dihedral angle restraints: 12932 sinusoidal: 5144 harmonic: 7788 Sorted by residual: 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 -156.30 -23.70 0 5.00e+00 4.00e-02 2.25e+01 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 -156.30 -23.70 0 5.00e+00 4.00e-02 2.25e+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 -156.30 -23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 12929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2043 0.031 - 0.063: 949 0.063 - 0.094: 277 0.094 - 0.125: 111 0.125 - 0.157: 24 Chirality restraints: 3404 Sorted by residual: chirality pdb=" CA ILE C 527 " pdb=" N ILE C 527 " pdb=" C ILE C 527 " pdb=" CB ILE C 527 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA ILE D 527 " pdb=" N ILE D 527 " pdb=" C ILE D 527 " pdb=" CB ILE D 527 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA ILE B 527 " pdb=" N ILE B 527 " pdb=" C ILE B 527 " pdb=" CB ILE B 527 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 3401 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 460 " 0.012 2.00e-02 2.50e+03 9.54e-03 1.82e+00 pdb=" CG TYR C 460 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 460 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR C 460 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 460 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 460 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 460 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 460 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 460 " 0.012 2.00e-02 2.50e+03 9.54e-03 1.82e+00 pdb=" CG TYR B 460 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR B 460 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 460 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 460 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 460 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 460 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 460 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 460 " 0.012 2.00e-02 2.50e+03 9.50e-03 1.80e+00 pdb=" CG TYR A 460 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 460 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 460 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 460 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 460 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 460 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 460 " 0.001 2.00e-02 2.50e+03 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 6136 2.82 - 3.40: 22699 3.40 - 3.98: 37297 3.98 - 4.56: 52427 4.56 - 5.14: 78962 Nonbonded interactions: 197521 Sorted by model distance: nonbonded pdb=" OD1 ASN D 235 " pdb=" OG1 THR D 240 " model vdw 2.239 3.040 nonbonded pdb=" OD1 ASN A 235 " pdb=" OG1 THR A 240 " model vdw 2.239 3.040 nonbonded pdb=" OD1 ASN C 235 " pdb=" OG1 THR C 240 " model vdw 2.239 3.040 nonbonded pdb=" OD1 ASN B 235 " pdb=" OG1 THR B 240 " model vdw 2.239 3.040 nonbonded pdb=" O LYS D 144 " pdb=" OG1 THR D 147 " model vdw 2.244 3.040 ... (remaining 197516 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: 6.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 22.770 Find NCS groups from input model: 0.490 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:2.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 0.031 21804 Z= 0.130 Angle : 0.548 8.691 29584 Z= 0.302 Chirality : 0.041 0.157 3404 Planarity : 0.003 0.028 3668 Dihedral : 14.094 87.047 7884 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.84 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -0.45 (0.17), residues: 2616 helix: 1.34 (0.15), residues: 1344 sheet: -1.49 (0.32), residues: 260 loop : -2.30 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 677 TYR 0.023 0.001 TYR C 460 PHE 0.021 0.001 PHE D 566 TRP 0.007 0.001 TRP D 513 HIS 0.003 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00282 (21804) covalent geometry : angle 0.54759 (29584) hydrogen bonds : bond 0.15154 ( 1044) hydrogen bonds : angle 5.13013 ( 3060) *********************** 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 247 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.901 Fit side-chains REVERT: A 231 MET cc_start: 0.7710 (tpp) cc_final: 0.7396 (tpt) REVERT: A 480 ARG cc_start: 0.7236 (ttm-80) cc_final: 0.7012 (ttm170) REVERT: B 231 MET cc_start: 0.7720 (tpp) cc_final: 0.7412 (tpt) REVERT: B 480 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.7012 (ttm170) REVERT: C 231 MET cc_start: 0.7743 (tpp) cc_final: 0.7417 (tpt) REVERT: C 480 ARG cc_start: 0.7248 (ttm-80) cc_final: 0.7024 (ttm170) REVERT: D 231 MET cc_start: 0.7739 (tpp) cc_final: 0.7406 (tpt) REVERT: D 480 ARG cc_start: 0.7236 (ttm-80) cc_final: 0.7015 (ttm170) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.1488 time to fit residues: 59.4242 Evaluate side-chains 196 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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: 3.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.0170 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 267 HIS C 267 HIS D 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.188342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.155974 restraints weight = 22828.805| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.68 r_work: 0.3297 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21804 Z= 0.116 Angle : 0.490 7.742 29584 Z= 0.266 Chirality : 0.040 0.144 3404 Planarity : 0.003 0.025 3668 Dihedral : 4.160 24.851 2864 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.19 % Favored : 92.51 % Rotamer: Outliers : 1.01 % Allowed : 6.72 % Favored : 92.27 % 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: -0.31 (0.17), residues: 2616 helix: 1.39 (0.15), residues: 1384 sheet: -1.36 (0.32), residues: 260 loop : -2.30 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 480 TYR 0.017 0.001 TYR B 460 PHE 0.013 0.001 PHE D 566 TRP 0.006 0.001 TRP B 367 HIS 0.004 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00240 (21804) covalent geometry : angle 0.49041 (29584) hydrogen bonds : bond 0.05137 ( 1044) hydrogen bonds : angle 4.07519 ( 3060) *********************** 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 235 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.873 Fit side-chains REVERT: A 169 MET cc_start: 0.4320 (ppp) cc_final: 0.3285 (ptm) REVERT: A 231 MET cc_start: 0.8513 (tpp) cc_final: 0.8162 (tpt) REVERT: A 480 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.8110 (ttm170) REVERT: A 523 LYS cc_start: 0.8698 (mtpp) cc_final: 0.8335 (tptp) REVERT: A 601 ASP cc_start: 0.8088 (t0) cc_final: 0.7651 (t0) REVERT: B 169 MET cc_start: 0.3975 (ppp) cc_final: 0.3232 (ptm) REVERT: B 231 MET cc_start: 0.8524 (tpp) cc_final: 0.8172 (tpt) REVERT: B 480 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.8107 (ttm170) REVERT: B 523 LYS cc_start: 0.8725 (mtpp) cc_final: 0.8363 (tptp) REVERT: B 601 ASP cc_start: 0.8080 (t0) cc_final: 0.7638 (t0) REVERT: C 169 MET cc_start: 0.3965 (ppp) cc_final: 0.3226 (ptm) REVERT: C 231 MET cc_start: 0.8508 (tpp) cc_final: 0.8157 (tpt) REVERT: C 480 ARG cc_start: 0.8325 (ttm-80) cc_final: 0.8108 (ttm170) REVERT: C 523 LYS cc_start: 0.8706 (mtpp) cc_final: 0.8338 (tptp) REVERT: C 601 ASP cc_start: 0.8089 (t0) cc_final: 0.7650 (t0) REVERT: D 169 MET cc_start: 0.3976 (ppp) cc_final: 0.3250 (ptm) REVERT: D 231 MET cc_start: 0.8513 (tpp) cc_final: 0.8163 (tpt) REVERT: D 480 ARG cc_start: 0.8340 (ttm-80) cc_final: 0.8132 (ttm170) REVERT: D 523 LYS cc_start: 0.8706 (mtpp) cc_final: 0.8335 (tptp) REVERT: D 601 ASP cc_start: 0.8093 (t0) cc_final: 0.7657 (t0) outliers start: 24 outliers final: 20 residues processed: 227 average time/residue: 0.1504 time to fit residues: 54.9177 Evaluate side-chains 208 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 526 SER 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: 0.0070 chunk 190 optimal weight: 3.9990 chunk 237 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 134 optimal weight: 0.2980 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 267 HIS C 267 HIS D 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.187119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.154449 restraints weight = 22862.209| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.68 r_work: 0.3228 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1007 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= 0.131 Angle : 0.487 6.861 29584 Z= 0.264 Chirality : 0.040 0.136 3404 Planarity : 0.003 0.023 3668 Dihedral : 4.161 24.472 2864 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.30 % Favored : 92.39 % Rotamer: Outliers : 1.51 % Allowed : 10.63 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.17), residues: 2616 helix: 1.46 (0.15), residues: 1384 sheet: -1.45 (0.41), residues: 148 loop : -2.24 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 480 TYR 0.017 0.001 TYR B 460 PHE 0.011 0.001 PHE D 660 TRP 0.006 0.001 TRP C 513 HIS 0.004 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00296 (21804) covalent geometry : angle 0.48669 (29584) hydrogen bonds : bond 0.05139 ( 1044) hydrogen bonds : angle 3.90750 ( 3060) *********************** 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 249 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 0.698 Fit side-chains REVERT: A 169 MET cc_start: 0.3890 (ppp) cc_final: 0.3272 (ptm) REVERT: A 231 MET cc_start: 0.8555 (tpp) cc_final: 0.8218 (tpt) REVERT: A 295 ILE cc_start: 0.8385 (mm) cc_final: 0.8155 (mm) REVERT: A 437 ASN cc_start: 0.8170 (m110) cc_final: 0.7803 (m110) REVERT: A 480 ARG cc_start: 0.8290 (ttm-80) cc_final: 0.8078 (ttm170) REVERT: A 523 LYS cc_start: 0.8621 (mtpp) cc_final: 0.8228 (tptp) REVERT: A 601 ASP cc_start: 0.8067 (t0) cc_final: 0.7578 (t0) REVERT: B 169 MET cc_start: 0.3645 (ppp) cc_final: 0.3243 (ptm) REVERT: B 231 MET cc_start: 0.8548 (tpp) cc_final: 0.8205 (tpt) REVERT: B 295 ILE cc_start: 0.8367 (mm) cc_final: 0.8136 (mm) REVERT: B 437 ASN cc_start: 0.8158 (m110) cc_final: 0.7778 (m110) REVERT: B 480 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.8071 (ttm170) REVERT: B 523 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8245 (tptp) REVERT: B 601 ASP cc_start: 0.8059 (t0) cc_final: 0.7573 (t0) REVERT: C 169 MET cc_start: 0.3638 (ppp) cc_final: 0.3233 (ptm) REVERT: C 231 MET cc_start: 0.8552 (tpp) cc_final: 0.8212 (tpt) REVERT: C 295 ILE cc_start: 0.8367 (mm) cc_final: 0.8141 (mm) REVERT: C 437 ASN cc_start: 0.8184 (m110) cc_final: 0.7806 (m110) REVERT: C 480 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.8096 (ttm170) REVERT: C 523 LYS cc_start: 0.8626 (mtpp) cc_final: 0.8225 (tptp) REVERT: C 601 ASP cc_start: 0.8031 (t0) cc_final: 0.7541 (t0) REVERT: D 169 MET cc_start: 0.3637 (ppp) cc_final: 0.3240 (ptm) REVERT: D 231 MET cc_start: 0.8546 (tpp) cc_final: 0.8210 (tpt) REVERT: D 295 ILE cc_start: 0.8362 (mm) cc_final: 0.8135 (mm) REVERT: D 437 ASN cc_start: 0.8173 (m110) cc_final: 0.7802 (m110) REVERT: D 480 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.8102 (ttm170) REVERT: D 523 LYS cc_start: 0.8620 (mtpp) cc_final: 0.8228 (tptp) REVERT: D 601 ASP cc_start: 0.8050 (t0) cc_final: 0.7558 (t0) outliers start: 36 outliers final: 20 residues processed: 241 average time/residue: 0.1576 time to fit residues: 60.1861 Evaluate side-chains 228 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 526 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 251 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 0.0070 chunk 39 optimal weight: 0.5980 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 267 HIS C 267 HIS D 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.185601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.154604 restraints weight = 22936.392| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.64 r_work: 0.3360 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21804 Z= 0.129 Angle : 0.488 7.116 29584 Z= 0.264 Chirality : 0.040 0.133 3404 Planarity : 0.003 0.023 3668 Dihedral : 4.118 24.440 2864 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.34 % Favored : 92.35 % Rotamer: Outliers : 2.02 % Allowed : 12.82 % Favored : 85.17 % 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: -0.16 (0.17), residues: 2616 helix: 1.52 (0.15), residues: 1376 sheet: -1.30 (0.42), residues: 148 loop : -2.18 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 102 TYR 0.014 0.001 TYR B 460 PHE 0.011 0.001 PHE D 660 TRP 0.007 0.001 TRP C 513 HIS 0.004 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00295 (21804) covalent geometry : angle 0.48759 (29584) hydrogen bonds : bond 0.05001 ( 1044) hydrogen bonds : angle 3.84364 ( 3060) *********************** 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 260 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.874 Fit side-chains REVERT: A 169 MET cc_start: 0.4142 (ppp) cc_final: 0.3502 (ptm) REVERT: A 231 MET cc_start: 0.8428 (tpp) cc_final: 0.8088 (tpt) REVERT: A 295 ILE cc_start: 0.8702 (mm) cc_final: 0.8480 (mm) REVERT: A 437 ASN cc_start: 0.8047 (m110) cc_final: 0.7375 (m-40) REVERT: A 601 ASP cc_start: 0.8096 (t0) cc_final: 0.7638 (t0) REVERT: B 169 MET cc_start: 0.4056 (ppp) cc_final: 0.3691 (ptm) REVERT: B 231 MET cc_start: 0.8453 (tpp) cc_final: 0.8107 (tpt) REVERT: B 295 ILE cc_start: 0.8691 (mm) cc_final: 0.8469 (mm) REVERT: B 437 ASN cc_start: 0.8042 (m110) cc_final: 0.7344 (m-40) REVERT: B 601 ASP cc_start: 0.8118 (t0) cc_final: 0.7662 (t0) REVERT: C 169 MET cc_start: 0.4052 (ppp) cc_final: 0.3682 (ptm) REVERT: C 231 MET cc_start: 0.8429 (tpp) cc_final: 0.8086 (tpt) REVERT: C 295 ILE cc_start: 0.8693 (mm) cc_final: 0.8473 (mm) REVERT: C 437 ASN cc_start: 0.8052 (m110) cc_final: 0.7380 (m-40) REVERT: C 601 ASP cc_start: 0.8094 (t0) cc_final: 0.7643 (t0) REVERT: D 169 MET cc_start: 0.4037 (ppp) cc_final: 0.3679 (ptm) REVERT: D 231 MET cc_start: 0.8426 (tpp) cc_final: 0.8085 (tpt) REVERT: D 295 ILE cc_start: 0.8702 (mm) cc_final: 0.8482 (mm) REVERT: D 437 ASN cc_start: 0.8067 (m110) cc_final: 0.7400 (m-40) REVERT: D 601 ASP cc_start: 0.8100 (t0) cc_final: 0.7647 (t0) outliers start: 48 outliers final: 36 residues processed: 244 average time/residue: 0.1487 time to fit residues: 58.1796 Evaluate side-chains 239 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 259 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 258 optimal weight: 0.5980 chunk 146 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 235 optimal weight: 0.0870 chunk 187 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 267 HIS C 267 HIS D 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.187430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.152544 restraints weight = 22853.661| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.92 r_work: 0.3261 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1372 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= 0.111 Angle : 0.457 7.165 29584 Z= 0.250 Chirality : 0.039 0.130 3404 Planarity : 0.002 0.023 3668 Dihedral : 4.016 23.793 2864 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.15 % Favored : 92.55 % Rotamer: Outliers : 1.51 % Allowed : 14.03 % 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: 0.03 (0.17), residues: 2616 helix: 1.70 (0.15), residues: 1368 sheet: -1.06 (0.44), residues: 144 loop : -2.12 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 677 TYR 0.011 0.001 TYR B 460 PHE 0.016 0.001 PHE C 93 TRP 0.007 0.001 TRP A 513 HIS 0.004 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00241 (21804) covalent geometry : angle 0.45744 (29584) hydrogen bonds : bond 0.04690 ( 1044) hydrogen bonds : angle 3.70511 ( 3060) *********************** 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 267 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 0.849 Fit side-chains REVERT: A 169 MET cc_start: 0.4102 (ppp) cc_final: 0.3520 (ptm) REVERT: A 437 ASN cc_start: 0.8066 (m110) cc_final: 0.7352 (m-40) REVERT: A 499 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8327 (ttmm) REVERT: A 601 ASP cc_start: 0.8132 (t0) cc_final: 0.7669 (t0) REVERT: B 169 MET cc_start: 0.3988 (ppp) cc_final: 0.3598 (ptm) REVERT: B 437 ASN cc_start: 0.8041 (m110) cc_final: 0.7316 (m-40) REVERT: B 499 LYS cc_start: 0.8534 (ttmm) cc_final: 0.8320 (ttmm) REVERT: B 601 ASP cc_start: 0.8160 (t0) cc_final: 0.7697 (t0) REVERT: C 169 MET cc_start: 0.3977 (ppp) cc_final: 0.3582 (ptm) REVERT: C 437 ASN cc_start: 0.8060 (m110) cc_final: 0.7352 (m-40) REVERT: C 499 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8327 (ttmm) REVERT: C 601 ASP cc_start: 0.8127 (t0) cc_final: 0.7668 (t0) REVERT: D 169 MET cc_start: 0.3954 (ppp) cc_final: 0.3573 (ptm) REVERT: D 437 ASN cc_start: 0.8076 (m110) cc_final: 0.7370 (m-40) REVERT: D 499 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8316 (ttmm) REVERT: D 601 ASP cc_start: 0.8149 (t0) cc_final: 0.7690 (t0) outliers start: 36 outliers final: 24 residues processed: 255 average time/residue: 0.1675 time to fit residues: 65.7560 Evaluate side-chains 231 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 566 PHE 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: 1.9990 chunk 194 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 chunk 214 optimal weight: 40.0000 chunk 2 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 236 optimal weight: 1.9990 chunk 147 optimal weight: 0.0970 chunk 131 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 267 HIS C 267 HIS D 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.187433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.149974 restraints weight = 22816.346| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.09 r_work: 0.3158 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1526 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= 0.109 Angle : 0.459 7.508 29584 Z= 0.250 Chirality : 0.039 0.129 3404 Planarity : 0.002 0.023 3668 Dihedral : 3.971 23.992 2864 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.19 % Favored : 92.51 % Rotamer: Outliers : 2.14 % Allowed : 14.45 % Favored : 83.40 % 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: 0.06 (0.17), residues: 2616 helix: 1.74 (0.15), residues: 1368 sheet: -1.05 (0.43), residues: 144 loop : -2.12 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 327 TYR 0.011 0.001 TYR D 460 PHE 0.012 0.001 PHE C 93 TRP 0.007 0.001 TRP C 513 HIS 0.005 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00237 (21804) covalent geometry : angle 0.45937 (29584) hydrogen bonds : bond 0.04568 ( 1044) hydrogen bonds : angle 3.65322 ( 3060) *********************** 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 280 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 229 time to evaluate : 0.812 Fit side-chains REVERT: A 169 MET cc_start: 0.4002 (ppp) cc_final: 0.3512 (ptm) REVERT: A 437 ASN cc_start: 0.8073 (m110) cc_final: 0.7277 (m-40) REVERT: A 499 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8339 (ttmm) REVERT: A 601 ASP cc_start: 0.8085 (t0) cc_final: 0.7630 (t0) REVERT: B 169 MET cc_start: 0.3821 (OUTLIER) cc_final: 0.3552 (ptm) REVERT: B 437 ASN cc_start: 0.8078 (m110) cc_final: 0.7282 (m-40) REVERT: B 499 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8332 (ttmm) REVERT: B 601 ASP cc_start: 0.8111 (t0) cc_final: 0.7652 (t0) REVERT: C 169 MET cc_start: 0.3804 (OUTLIER) cc_final: 0.3539 (ptm) REVERT: C 437 ASN cc_start: 0.8096 (m110) cc_final: 0.7304 (m-40) REVERT: C 499 LYS cc_start: 0.8547 (ttmm) cc_final: 0.8334 (ttmm) REVERT: C 601 ASP cc_start: 0.8080 (t0) cc_final: 0.7624 (t0) REVERT: D 169 MET cc_start: 0.3807 (OUTLIER) cc_final: 0.3537 (ptm) REVERT: D 437 ASN cc_start: 0.8102 (m110) cc_final: 0.7321 (m-40) REVERT: D 499 LYS cc_start: 0.8541 (ttmm) cc_final: 0.8326 (ttmm) REVERT: D 601 ASP cc_start: 0.8091 (t0) cc_final: 0.7637 (t0) outliers start: 51 outliers final: 28 residues processed: 261 average time/residue: 0.1474 time to fit residues: 61.3801 Evaluate side-chains 243 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 566 PHE 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: 0.9980 chunk 151 optimal weight: 6.9990 chunk 223 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 192 optimal weight: 0.7980 chunk 104 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 267 HIS C 267 HIS D 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.187193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.155403 restraints weight = 22760.403| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.68 r_work: 0.3260 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21804 Z= 0.125 Angle : 0.493 7.302 29584 Z= 0.261 Chirality : 0.040 0.128 3404 Planarity : 0.002 0.022 3668 Dihedral : 4.013 24.865 2864 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.22 % Favored : 92.47 % Rotamer: Outliers : 1.64 % Allowed : 15.97 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.04 (0.17), residues: 2616 helix: 1.67 (0.15), residues: 1372 sheet: -1.14 (0.43), residues: 148 loop : -2.04 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 560 TYR 0.011 0.001 TYR A 368 PHE 0.010 0.001 PHE B 660 TRP 0.006 0.001 TRP B 513 HIS 0.004 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00286 (21804) covalent geometry : angle 0.49331 (29584) hydrogen bonds : bond 0.04799 ( 1044) hydrogen bonds : angle 3.64895 ( 3060) *********************** 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 258 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.861 Fit side-chains REVERT: A 169 MET cc_start: 0.3905 (ppp) cc_final: 0.3333 (ptm) REVERT: A 499 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8332 (ttmm) REVERT: A 601 ASP cc_start: 0.8182 (t0) cc_final: 0.7748 (t0) REVERT: B 169 MET cc_start: 0.3854 (ppp) cc_final: 0.3596 (ptm) REVERT: B 437 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7323 (m-40) REVERT: B 499 LYS cc_start: 0.8573 (ttmm) cc_final: 0.8328 (ttmm) REVERT: B 601 ASP cc_start: 0.8193 (t0) cc_final: 0.7765 (t0) REVERT: C 169 MET cc_start: 0.3852 (ppp) cc_final: 0.3595 (ptm) REVERT: C 437 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7328 (m-40) REVERT: C 499 LYS cc_start: 0.8599 (ttmm) cc_final: 0.8355 (ttmm) REVERT: C 601 ASP cc_start: 0.8170 (t0) cc_final: 0.7733 (t0) REVERT: D 169 MET cc_start: 0.3834 (ppp) cc_final: 0.3578 (ptm) REVERT: D 437 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7382 (m-40) REVERT: D 499 LYS cc_start: 0.8578 (ttmm) cc_final: 0.8328 (ttmm) REVERT: D 601 ASP cc_start: 0.8180 (t0) cc_final: 0.7745 (t0) outliers start: 39 outliers final: 24 residues processed: 250 average time/residue: 0.1507 time to fit residues: 60.0012 Evaluate side-chains 246 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 566 PHE 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: 8.9990 chunk 187 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 260 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 246 optimal weight: 0.0030 chunk 123 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 267 HIS C 267 HIS D 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.183289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.152186 restraints weight = 22820.985| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.59 r_work: 0.3161 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21804 Z= 0.157 Angle : 0.524 6.676 29584 Z= 0.280 Chirality : 0.041 0.151 3404 Planarity : 0.003 0.022 3668 Dihedral : 4.151 25.757 2864 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.22 % Favored : 91.48 % Rotamer: Outliers : 1.97 % Allowed : 16.43 % Favored : 81.60 % 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: 0.01 (0.17), residues: 2616 helix: 1.53 (0.15), residues: 1372 sheet: -0.87 (0.35), residues: 260 loop : -2.02 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 21 TYR 0.013 0.001 TYR A 368 PHE 0.013 0.001 PHE C 660 TRP 0.007 0.001 TRP B 388 HIS 0.005 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00374 (21804) covalent geometry : angle 0.52399 (29584) hydrogen bonds : bond 0.05363 ( 1044) hydrogen bonds : angle 3.82441 ( 3060) *********************** 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 279 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 0.714 Fit side-chains REVERT: A 80 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7902 (mttm) REVERT: A 169 MET cc_start: 0.3558 (ppp) cc_final: 0.3044 (ptm) REVERT: A 437 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7427 (m-40) REVERT: A 499 LYS cc_start: 0.8652 (ttmm) cc_final: 0.8371 (ttmm) REVERT: A 601 ASP cc_start: 0.8019 (t0) cc_final: 0.7594 (t0) REVERT: B 80 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7895 (mttm) REVERT: B 169 MET cc_start: 0.3509 (OUTLIER) cc_final: 0.3302 (ptm) REVERT: B 437 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.7447 (m-40) REVERT: B 499 LYS cc_start: 0.8653 (ttmm) cc_final: 0.8368 (ttmm) REVERT: B 601 ASP cc_start: 0.8009 (t0) cc_final: 0.7586 (t0) REVERT: C 80 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7891 (mttm) REVERT: C 169 MET cc_start: 0.3525 (OUTLIER) cc_final: 0.3314 (ptm) REVERT: C 437 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.7452 (m-40) REVERT: C 499 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8376 (ttmm) REVERT: C 601 ASP cc_start: 0.8016 (t0) cc_final: 0.7597 (t0) REVERT: D 80 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7896 (mttm) REVERT: D 169 MET cc_start: 0.3523 (OUTLIER) cc_final: 0.3309 (ptm) REVERT: D 437 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.7433 (m-40) REVERT: D 499 LYS cc_start: 0.8646 (ttmm) cc_final: 0.8361 (ttmm) REVERT: D 601 ASP cc_start: 0.8011 (t0) cc_final: 0.7588 (t0) outliers start: 47 outliers final: 24 residues processed: 268 average time/residue: 0.1398 time to fit residues: 58.9672 Evaluate side-chains 255 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 566 PHE 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: 0.4980 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 136 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 235 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 482 HIS B 267 HIS B 482 HIS C 267 HIS C 482 HIS D 267 HIS D 482 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.184569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.153115 restraints weight = 22755.196| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.64 r_work: 0.3159 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21804 Z= 0.141 Angle : 0.515 8.184 29584 Z= 0.275 Chirality : 0.041 0.129 3404 Planarity : 0.002 0.022 3668 Dihedral : 4.134 25.256 2864 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.49 % Favored : 92.20 % Rotamer: Outliers : 2.14 % Allowed : 16.55 % Favored : 81.30 % 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: 0.01 (0.17), residues: 2616 helix: 1.54 (0.15), residues: 1372 sheet: -0.86 (0.35), residues: 260 loop : -2.04 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 560 TYR 0.012 0.001 TYR A 368 PHE 0.011 0.001 PHE C 660 TRP 0.008 0.001 TRP C 513 HIS 0.005 0.001 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.00330 (21804) covalent geometry : angle 0.51466 (29584) hydrogen bonds : bond 0.05137 ( 1044) hydrogen bonds : angle 3.81089 ( 3060) *********************** 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 251 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 200 time to evaluate : 0.873 Fit side-chains REVERT: A 80 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7852 (mttm) REVERT: A 169 MET cc_start: 0.3472 (ppp) cc_final: 0.2973 (ptm) REVERT: A 437 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7370 (m-40) REVERT: A 499 LYS cc_start: 0.8645 (ttmm) cc_final: 0.8374 (ttmm) REVERT: A 601 ASP cc_start: 0.8095 (t0) cc_final: 0.7672 (t0) REVERT: B 80 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7849 (mttm) REVERT: B 169 MET cc_start: 0.3397 (OUTLIER) cc_final: 0.3182 (ptm) REVERT: B 437 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7373 (m-40) REVERT: B 499 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8369 (ttmm) REVERT: B 601 ASP cc_start: 0.8098 (t0) cc_final: 0.7678 (t0) REVERT: C 80 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7660 (mttt) REVERT: C 169 MET cc_start: 0.3406 (OUTLIER) cc_final: 0.3189 (ptm) REVERT: C 437 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7375 (m-40) REVERT: C 499 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8375 (ttmm) REVERT: C 601 ASP cc_start: 0.8091 (t0) cc_final: 0.7670 (t0) REVERT: D 80 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7666 (mttt) REVERT: D 169 MET cc_start: 0.3428 (OUTLIER) cc_final: 0.3211 (ptm) REVERT: D 437 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7385 (m-40) REVERT: D 499 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8375 (ttmm) REVERT: D 601 ASP cc_start: 0.8102 (t0) cc_final: 0.7680 (t0) outliers start: 51 outliers final: 28 residues processed: 244 average time/residue: 0.1338 time to fit residues: 51.4203 Evaluate side-chains 235 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 566 PHE 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: 1.9990 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 200 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 152 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 chunk 253 optimal weight: 0.2980 chunk 164 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 267 HIS C 267 HIS D 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.187543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.159208 restraints weight = 22789.062| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.47 r_work: 0.3260 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1791 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= 0.117 Angle : 0.500 8.051 29584 Z= 0.266 Chirality : 0.040 0.130 3404 Planarity : 0.002 0.022 3668 Dihedral : 4.051 23.954 2864 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.34 % Favored : 92.35 % Rotamer: Outliers : 1.68 % Allowed : 17.10 % Favored : 81.22 % 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: 0.11 (0.17), residues: 2616 helix: 1.64 (0.15), residues: 1372 sheet: -0.73 (0.35), residues: 256 loop : -2.04 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 560 TYR 0.010 0.001 TYR B 368 PHE 0.017 0.001 PHE B 93 TRP 0.008 0.001 TRP D 513 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00259 (21804) covalent geometry : angle 0.49976 (29584) hydrogen bonds : bond 0.04740 ( 1044) hydrogen bonds : angle 3.68926 ( 3060) ********************** 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 259 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 0.700 Fit side-chains REVERT: A 80 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7548 (mtmm) REVERT: A 169 MET cc_start: 0.3608 (ppp) cc_final: 0.3092 (ptm) REVERT: A 437 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7273 (m-40) REVERT: A 499 LYS cc_start: 0.8623 (ttmm) cc_final: 0.8384 (ttmm) REVERT: A 601 ASP cc_start: 0.8078 (t0) cc_final: 0.7658 (t0) REVERT: B 80 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7552 (mtmm) REVERT: B 169 MET cc_start: 0.3574 (OUTLIER) cc_final: 0.3370 (ptm) REVERT: B 437 ASN cc_start: 0.8171 (m110) cc_final: 0.7285 (m-40) REVERT: B 499 LYS cc_start: 0.8613 (ttmm) cc_final: 0.8364 (ttmm) REVERT: B 601 ASP cc_start: 0.8076 (t0) cc_final: 0.7658 (t0) REVERT: C 80 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7550 (mtmm) REVERT: C 169 MET cc_start: 0.3550 (OUTLIER) cc_final: 0.3346 (ptm) REVERT: C 437 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7301 (m-40) REVERT: C 499 LYS cc_start: 0.8629 (ttmm) cc_final: 0.8387 (ttmm) REVERT: C 601 ASP cc_start: 0.8085 (t0) cc_final: 0.7668 (t0) REVERT: D 80 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7550 (mtmm) REVERT: D 169 MET cc_start: 0.3574 (OUTLIER) cc_final: 0.3367 (ptm) REVERT: D 437 ASN cc_start: 0.8193 (m110) cc_final: 0.7318 (m-40) REVERT: D 499 LYS cc_start: 0.8631 (ttmm) cc_final: 0.8385 (ttmm) REVERT: D 601 ASP cc_start: 0.8088 (t0) cc_final: 0.7673 (t0) outliers start: 40 outliers final: 31 residues processed: 251 average time/residue: 0.1347 time to fit residues: 53.3683 Evaluate side-chains 252 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 267 HIS Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 566 PHE 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: 0.9990 chunk 233 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 219 optimal weight: 0.9980 chunk 211 optimal weight: 30.0000 chunk 155 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 82 optimal weight: 40.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 267 HIS C 267 HIS D 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.183862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.152096 restraints weight = 22876.527| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.67 r_work: 0.3147 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21804 Z= 0.172 Angle : 0.545 8.112 29584 Z= 0.288 Chirality : 0.042 0.128 3404 Planarity : 0.003 0.022 3668 Dihedral : 4.163 25.729 2864 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.91 % Favored : 91.78 % Rotamer: Outliers : 1.89 % Allowed : 17.23 % Favored : 80.88 % 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: -0.00 (0.17), residues: 2616 helix: 1.52 (0.15), residues: 1372 sheet: -0.87 (0.35), residues: 260 loop : -2.03 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 560 TYR 0.012 0.001 TYR A 368 PHE 0.017 0.002 PHE A 93 TRP 0.007 0.001 TRP B 388 HIS 0.008 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00416 (21804) covalent geometry : angle 0.54488 (29584) hydrogen bonds : bond 0.05303 ( 1044) hydrogen bonds : angle 3.84063 ( 3060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5284.73 seconds wall clock time: 91 minutes 26.59 seconds (5486.59 seconds total)