Starting phenix.real_space_refine on Wed May 21 08:57:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yie_33856/05_2025/7yie_33856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yie_33856/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yie_33856/05_2025/7yie_33856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yie_33856/05_2025/7yie_33856.map" model { file = "/net/cci-nas-00/data/ceres_data/7yie_33856/05_2025/7yie_33856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yie_33856/05_2025/7yie_33856.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.055 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.25, per 1000 atoms: 0.62 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: 4.81 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.28 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: 7.48 Time building geometry restraints manager: 5.74 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: 4.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 47.260 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.770 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (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 TRP 0.007 0.001 TRP D 513 HIS 0.003 0.001 HIS C 118 PHE 0.021 0.001 PHE D 566 TYR 0.023 0.001 TYR C 460 ARG 0.006 0.000 ARG D 677 Details of bonding type rmsd hydrogen bonds : bond 0.15154 ( 1044) hydrogen bonds : angle 5.13013 ( 3060) covalent geometry : bond 0.00282 (21804) covalent geometry : angle 0.54759 (29584) *********************** 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 : 2.462 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: 0.2978 time to fit residues: 118.8913 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 : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 0.0980 chunk 134 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 chunk 206 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 239 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.188960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.164035 restraints weight = 22762.190| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.22 r_work: 0.3173 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21804 Z= 0.125 Angle : 0.499 7.639 29584 Z= 0.271 Chirality : 0.040 0.145 3404 Planarity : 0.003 0.025 3668 Dihedral : 4.197 25.226 2864 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.49 % Favored : 92.20 % Rotamer: Outliers : 1.01 % Allowed : 7.23 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2616 helix: 1.36 (0.15), residues: 1384 sheet: -1.35 (0.32), residues: 260 loop : -2.31 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 367 HIS 0.004 0.001 HIS D 267 PHE 0.014 0.001 PHE A 566 TYR 0.018 0.001 TYR B 460 ARG 0.003 0.000 ARG B 480 Details of bonding type rmsd hydrogen bonds : bond 0.05252 ( 1044) hydrogen bonds : angle 4.11145 ( 3060) covalent geometry : bond 0.00271 (21804) covalent geometry : angle 0.49885 (29584) *********************** 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 233 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 2.192 Fit side-chains REVERT: A 169 MET cc_start: 0.4410 (ppp) cc_final: 0.3390 (ptm) REVERT: A 231 MET cc_start: 0.8402 (tpp) cc_final: 0.8042 (tpt) REVERT: A 480 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7994 (ttm170) REVERT: A 523 LYS cc_start: 0.8627 (mtpp) cc_final: 0.8303 (tptp) REVERT: A 601 ASP cc_start: 0.7837 (t0) cc_final: 0.7394 (t0) REVERT: B 169 MET cc_start: 0.3993 (ppp) cc_final: 0.3267 (ptm) REVERT: B 231 MET cc_start: 0.8414 (tpp) cc_final: 0.8054 (tpt) REVERT: B 480 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7986 (ttm170) REVERT: B 523 LYS cc_start: 0.8647 (mtpp) cc_final: 0.8309 (tptp) REVERT: B 601 ASP cc_start: 0.7843 (t0) cc_final: 0.7400 (t0) REVERT: C 169 MET cc_start: 0.3981 (ppp) cc_final: 0.3253 (ptm) REVERT: C 231 MET cc_start: 0.8393 (tpp) cc_final: 0.8033 (tpt) REVERT: C 480 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7997 (ttm170) REVERT: C 523 LYS cc_start: 0.8639 (mtpp) cc_final: 0.8306 (tptp) REVERT: C 601 ASP cc_start: 0.7833 (t0) cc_final: 0.7393 (t0) REVERT: D 169 MET cc_start: 0.3981 (ppp) cc_final: 0.3249 (ptm) REVERT: D 231 MET cc_start: 0.8400 (tpp) cc_final: 0.8038 (tpt) REVERT: D 480 ARG cc_start: 0.8235 (ttm-80) cc_final: 0.8016 (ttm170) REVERT: D 523 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8299 (tptp) REVERT: D 601 ASP cc_start: 0.7844 (t0) cc_final: 0.7400 (t0) outliers start: 24 outliers final: 16 residues processed: 225 average time/residue: 0.2882 time to fit residues: 105.0212 Evaluate side-chains 200 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 2.322 ------------------------------------------------------------------------------- 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 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 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 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 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 85 optimal weight: 0.0060 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.0070 chunk 10 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 14 optimal weight: 0.0670 chunk 238 optimal weight: 0.0170 chunk 157 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 overall best weight: 0.1790 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.191127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.159614 restraints weight = 22687.589| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.71 r_work: 0.3287 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 21804 Z= 0.094 Angle : 0.450 6.763 29584 Z= 0.243 Chirality : 0.039 0.135 3404 Planarity : 0.002 0.024 3668 Dihedral : 3.988 21.855 2864 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.88 % Favored : 92.81 % Rotamer: Outliers : 0.67 % Allowed : 10.92 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.17), residues: 2616 helix: 1.67 (0.15), residues: 1372 sheet: -0.99 (0.33), residues: 256 loop : -2.23 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 513 HIS 0.004 0.001 HIS D 267 PHE 0.008 0.001 PHE C 656 TYR 0.010 0.001 TYR A 460 ARG 0.003 0.000 ARG C 677 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 1044) hydrogen bonds : angle 3.65969 ( 3060) covalent geometry : bond 0.00181 (21804) covalent geometry : angle 0.44969 (29584) *********************** 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 250 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 234 time to evaluate : 2.065 Fit side-chains REVERT: A 169 MET cc_start: 0.3673 (ppp) cc_final: 0.3072 (ptm) REVERT: A 499 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8186 (ttmm) REVERT: A 523 LYS cc_start: 0.8592 (mtpp) cc_final: 0.8222 (tptp) REVERT: A 601 ASP cc_start: 0.8014 (t0) cc_final: 0.7523 (t0) REVERT: B 169 MET cc_start: 0.3577 (ppp) cc_final: 0.3191 (ptm) REVERT: B 437 ASN cc_start: 0.8037 (m110) cc_final: 0.7399 (m-40) REVERT: B 499 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8189 (ttmm) REVERT: B 523 LYS cc_start: 0.8597 (mtpp) cc_final: 0.8228 (tptp) REVERT: B 601 ASP cc_start: 0.8010 (t0) cc_final: 0.7514 (t0) REVERT: C 169 MET cc_start: 0.3590 (ppp) cc_final: 0.3202 (ptm) REVERT: C 437 ASN cc_start: 0.8039 (m110) cc_final: 0.7386 (m-40) REVERT: C 499 LYS cc_start: 0.8474 (ttmm) cc_final: 0.8200 (ttmm) REVERT: C 523 LYS cc_start: 0.8591 (mtpp) cc_final: 0.8222 (tptp) REVERT: C 601 ASP cc_start: 0.8002 (t0) cc_final: 0.7505 (t0) REVERT: D 169 MET cc_start: 0.3597 (ppp) cc_final: 0.3214 (ptm) REVERT: D 437 ASN cc_start: 0.8055 (m110) cc_final: 0.7433 (m-40) REVERT: D 499 LYS cc_start: 0.8455 (ttmm) cc_final: 0.8176 (ttmm) REVERT: D 523 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8221 (tptp) REVERT: D 601 ASP cc_start: 0.8011 (t0) cc_final: 0.7515 (t0) outliers start: 16 outliers final: 4 residues processed: 242 average time/residue: 0.3103 time to fit residues: 117.9431 Evaluate side-chains 200 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 196 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain D residue 118 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 173 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 250 optimal weight: 0.6980 chunk 246 optimal weight: 5.9990 chunk 233 optimal weight: 0.0970 chunk 199 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.187131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.157978 restraints weight = 23110.777| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.52 r_work: 0.3360 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1305 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= 0.115 Angle : 0.462 6.967 29584 Z= 0.250 Chirality : 0.039 0.131 3404 Planarity : 0.002 0.023 3668 Dihedral : 3.977 24.365 2864 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.88 % Favored : 92.81 % Rotamer: Outliers : 1.34 % Allowed : 12.06 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2616 helix: 1.68 (0.15), residues: 1380 sheet: -0.83 (0.34), residues: 256 loop : -2.22 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 513 HIS 0.004 0.001 HIS D 267 PHE 0.010 0.001 PHE B 660 TYR 0.013 0.001 TYR C 460 ARG 0.002 0.000 ARG C 480 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 1044) hydrogen bonds : angle 3.67426 ( 3060) covalent geometry : bond 0.00254 (21804) covalent geometry : angle 0.46201 (29584) *********************** 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 248 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 2.283 Fit side-chains REVERT: A 169 MET cc_start: 0.3911 (ppp) cc_final: 0.3388 (ptm) REVERT: A 437 ASN cc_start: 0.8138 (m110) cc_final: 0.7409 (m-40) REVERT: A 499 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8260 (ttmm) REVERT: A 523 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8372 (tptp) REVERT: A 601 ASP cc_start: 0.8150 (t0) cc_final: 0.7661 (t0) REVERT: A 677 ARG cc_start: 0.7585 (ttp80) cc_final: 0.7084 (mmm160) REVERT: B 169 MET cc_start: 0.3801 (ppp) cc_final: 0.3499 (ptm) REVERT: B 437 ASN cc_start: 0.8133 (m110) cc_final: 0.7383 (m-40) REVERT: B 499 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8272 (ttmm) REVERT: B 523 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8381 (tptp) REVERT: B 601 ASP cc_start: 0.8134 (t0) cc_final: 0.7644 (t0) REVERT: B 677 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7091 (mmm160) REVERT: C 169 MET cc_start: 0.3775 (ppp) cc_final: 0.3473 (ptm) REVERT: C 437 ASN cc_start: 0.8139 (m110) cc_final: 0.7400 (m-40) REVERT: C 499 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8281 (ttmm) REVERT: C 523 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8373 (tptp) REVERT: C 601 ASP cc_start: 0.8135 (t0) cc_final: 0.7644 (t0) REVERT: C 677 ARG cc_start: 0.7605 (ttp80) cc_final: 0.7079 (mmm160) REVERT: D 169 MET cc_start: 0.3764 (ppp) cc_final: 0.3464 (ptm) REVERT: D 437 ASN cc_start: 0.8132 (m110) cc_final: 0.7403 (m-40) REVERT: D 499 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8258 (ttmm) REVERT: D 523 LYS cc_start: 0.8688 (mtpp) cc_final: 0.8375 (tptp) REVERT: D 601 ASP cc_start: 0.8164 (t0) cc_final: 0.7676 (t0) REVERT: D 677 ARG cc_start: 0.7587 (ttp80) cc_final: 0.7091 (mmm160) outliers start: 32 outliers final: 20 residues processed: 236 average time/residue: 0.3202 time to fit residues: 117.7399 Evaluate side-chains 226 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 2.154 ------------------------------------------------------------------------------- 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 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 441 THR 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 441 THR 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 441 THR Chi-restraints excluded: chain D residue 526 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 83 optimal weight: 6.9990 chunk 255 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 106 optimal weight: 0.0980 chunk 247 optimal weight: 3.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.183681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.146637 restraints weight = 22953.700| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.03 r_work: 0.3149 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21804 Z= 0.178 Angle : 0.523 7.255 29584 Z= 0.284 Chirality : 0.042 0.132 3404 Planarity : 0.003 0.023 3668 Dihedral : 4.207 26.396 2864 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.80 % Favored : 91.90 % Rotamer: Outliers : 2.18 % Allowed : 13.78 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2616 helix: 1.47 (0.14), residues: 1380 sheet: -1.22 (0.42), residues: 148 loop : -2.18 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 388 HIS 0.005 0.001 HIS C 267 PHE 0.016 0.002 PHE C 93 TYR 0.018 0.002 TYR C 460 ARG 0.003 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.05692 ( 1044) hydrogen bonds : angle 3.95870 ( 3060) covalent geometry : bond 0.00431 (21804) covalent geometry : angle 0.52337 (29584) *********************** 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 294 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 242 time to evaluate : 2.491 Fit side-chains REVERT: A 169 MET cc_start: 0.3907 (ppp) cc_final: 0.3410 (ptm) REVERT: A 341 TYR cc_start: 0.6998 (m-80) cc_final: 0.6760 (m-80) REVERT: A 523 LYS cc_start: 0.8714 (mtpp) cc_final: 0.8394 (tptp) REVERT: A 601 ASP cc_start: 0.8120 (t0) cc_final: 0.7676 (t0) REVERT: B 169 MET cc_start: 0.3824 (ppp) cc_final: 0.3502 (ptm) REVERT: B 341 TYR cc_start: 0.6996 (m-80) cc_final: 0.6760 (m-80) REVERT: B 523 LYS cc_start: 0.8720 (mtpp) cc_final: 0.8392 (tptp) REVERT: B 601 ASP cc_start: 0.8103 (t0) cc_final: 0.7658 (t0) REVERT: C 169 MET cc_start: 0.3824 (ppp) cc_final: 0.3501 (ptm) REVERT: C 341 TYR cc_start: 0.6982 (m-80) cc_final: 0.6747 (m-80) REVERT: C 523 LYS cc_start: 0.8708 (mtpp) cc_final: 0.8387 (tptp) REVERT: C 601 ASP cc_start: 0.8113 (t0) cc_final: 0.7668 (t0) REVERT: D 169 MET cc_start: 0.3821 (ppp) cc_final: 0.3497 (ptm) REVERT: D 341 TYR cc_start: 0.6983 (m-80) cc_final: 0.6750 (m-80) REVERT: D 523 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8389 (tptp) REVERT: D 601 ASP cc_start: 0.8132 (t0) cc_final: 0.7693 (t0) outliers start: 52 outliers final: 40 residues processed: 274 average time/residue: 0.3084 time to fit residues: 133.8078 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 : 2.147 ------------------------------------------------------------------------------- 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 512 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 598 ILE 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 441 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 598 ILE 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 441 THR Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 598 ILE 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 441 THR Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 598 ILE 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 41 optimal weight: 0.6980 chunk 174 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 188 optimal weight: 2.9990 chunk 210 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.187894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.159980 restraints weight = 22777.569| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.50 r_work: 0.3254 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 21804 Z= 0.107 Angle : 0.461 7.493 29584 Z= 0.251 Chirality : 0.039 0.127 3404 Planarity : 0.002 0.022 3668 Dihedral : 4.066 23.502 2864 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.91 % Favored : 91.78 % Rotamer: Outliers : 2.48 % Allowed : 14.29 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2616 helix: 1.69 (0.15), residues: 1368 sheet: -0.99 (0.43), residues: 144 loop : -2.09 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 513 HIS 0.005 0.001 HIS D 267 PHE 0.012 0.001 PHE C 93 TYR 0.010 0.001 TYR C 210 ARG 0.002 0.000 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 1044) hydrogen bonds : angle 3.64701 ( 3060) covalent geometry : bond 0.00226 (21804) covalent geometry : angle 0.46070 (29584) *********************** 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 285 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 226 time to evaluate : 2.956 Fit side-chains REVERT: A 87 ASN cc_start: 0.7502 (OUTLIER) cc_final: 0.7233 (t0) REVERT: A 169 MET cc_start: 0.4233 (ppp) cc_final: 0.3727 (ptm) REVERT: A 341 TYR cc_start: 0.7059 (m-80) cc_final: 0.6831 (m-80) REVERT: A 437 ASN cc_start: 0.8015 (m110) cc_final: 0.7199 (m-40) REVERT: A 499 LYS cc_start: 0.8487 (ttmm) cc_final: 0.8270 (ttmm) REVERT: A 601 ASP cc_start: 0.8011 (t0) cc_final: 0.7608 (t0) REVERT: B 87 ASN cc_start: 0.7516 (OUTLIER) cc_final: 0.7248 (t0) REVERT: B 169 MET cc_start: 0.3988 (OUTLIER) cc_final: 0.3639 (ptp) REVERT: B 341 TYR cc_start: 0.7064 (m-80) cc_final: 0.6838 (m-80) REVERT: B 437 ASN cc_start: 0.8019 (m110) cc_final: 0.7183 (m-40) REVERT: B 499 LYS cc_start: 0.8498 (ttmm) cc_final: 0.8278 (ttmm) REVERT: B 601 ASP cc_start: 0.8009 (t0) cc_final: 0.7606 (t0) REVERT: C 87 ASN cc_start: 0.7514 (OUTLIER) cc_final: 0.7242 (t0) REVERT: C 169 MET cc_start: 0.3963 (OUTLIER) cc_final: 0.3613 (ptp) REVERT: C 341 TYR cc_start: 0.7048 (m-80) cc_final: 0.6823 (m-80) REVERT: C 437 ASN cc_start: 0.8043 (m110) cc_final: 0.7227 (m-40) REVERT: C 499 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8288 (ttmm) REVERT: C 601 ASP cc_start: 0.8005 (t0) cc_final: 0.7596 (t0) REVERT: D 87 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.7235 (t0) REVERT: D 169 MET cc_start: 0.3963 (OUTLIER) cc_final: 0.3620 (ptp) REVERT: D 341 TYR cc_start: 0.7035 (m-80) cc_final: 0.6808 (m-80) REVERT: D 437 ASN cc_start: 0.8047 (m110) cc_final: 0.7240 (m-40) REVERT: D 499 LYS cc_start: 0.8479 (ttmm) cc_final: 0.8260 (ttmm) REVERT: D 601 ASP cc_start: 0.8035 (t0) cc_final: 0.7630 (t0) outliers start: 59 outliers final: 32 residues processed: 270 average time/residue: 0.2867 time to fit residues: 125.5130 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 : 2.201 ------------------------------------------------------------------------------- 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 442 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 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 442 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 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 442 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 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 442 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 107 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 chunk 238 optimal weight: 0.0170 chunk 121 optimal weight: 2.9990 chunk 162 optimal weight: 0.1980 chunk 164 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 229 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.187363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.156007 restraints weight = 22762.361| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.65 r_work: 0.3219 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1714 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= 0.108 Angle : 0.477 7.151 29584 Z= 0.254 Chirality : 0.039 0.128 3404 Planarity : 0.002 0.023 3668 Dihedral : 4.009 23.944 2864 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.22 % Favored : 92.47 % Rotamer: Outliers : 2.44 % Allowed : 14.75 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2616 helix: 1.73 (0.15), residues: 1372 sheet: -1.03 (0.43), residues: 144 loop : -2.03 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 513 HIS 0.004 0.001 HIS A 267 PHE 0.010 0.001 PHE D 93 TYR 0.015 0.001 TYR A 288 ARG 0.001 0.000 ARG D 560 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 1044) hydrogen bonds : angle 3.53883 ( 3060) covalent geometry : bond 0.00231 (21804) covalent geometry : angle 0.47719 (29584) *********************** 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 284 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 226 time to evaluate : 2.463 Fit side-chains REVERT: A 169 MET cc_start: 0.3512 (ppp) cc_final: 0.3022 (ptm) REVERT: A 341 TYR cc_start: 0.6752 (m-80) cc_final: 0.6484 (m-80) REVERT: A 437 ASN cc_start: 0.8187 (m110) cc_final: 0.7279 (m-40) REVERT: A 499 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8258 (ttmm) REVERT: A 601 ASP cc_start: 0.8067 (t0) cc_final: 0.7632 (t0) REVERT: B 169 MET cc_start: 0.3455 (ppp) cc_final: 0.3231 (ptm) REVERT: B 341 TYR cc_start: 0.6746 (m-80) cc_final: 0.6485 (m-80) REVERT: B 437 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7223 (m-40) REVERT: B 499 LYS cc_start: 0.8528 (ttmm) cc_final: 0.8257 (ttmm) REVERT: B 601 ASP cc_start: 0.8059 (t0) cc_final: 0.7621 (t0) REVERT: C 169 MET cc_start: 0.3452 (ppp) cc_final: 0.3225 (ptm) REVERT: C 437 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7237 (m-40) REVERT: C 499 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8273 (ttmm) REVERT: C 601 ASP cc_start: 0.8062 (t0) cc_final: 0.7626 (t0) REVERT: D 169 MET cc_start: 0.3456 (ppp) cc_final: 0.3229 (ptm) REVERT: D 341 TYR cc_start: 0.6748 (m-80) cc_final: 0.6488 (m-80) REVERT: D 437 ASN cc_start: 0.8186 (m110) cc_final: 0.7248 (m-40) REVERT: D 499 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8258 (ttmm) REVERT: D 601 ASP cc_start: 0.8064 (t0) cc_final: 0.7628 (t0) outliers start: 58 outliers final: 32 residues processed: 270 average time/residue: 0.3013 time to fit residues: 132.2740 Evaluate side-chains 256 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 442 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 118 HIS 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 442 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 118 HIS 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 442 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 118 HIS 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 442 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 27 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 49 optimal weight: 0.0270 chunk 214 optimal weight: 30.0000 chunk 263 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.186418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.154730 restraints weight = 22916.505| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.73 r_work: 0.3200 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1793 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= 0.123 Angle : 0.494 7.616 29584 Z= 0.263 Chirality : 0.040 0.127 3404 Planarity : 0.002 0.022 3668 Dihedral : 4.027 24.386 2864 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.68 % Favored : 92.01 % Rotamer: Outliers : 2.31 % Allowed : 15.42 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.17), residues: 2616 helix: 1.73 (0.15), residues: 1372 sheet: -0.66 (0.35), residues: 256 loop : -2.04 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 513 HIS 0.005 0.001 HIS C 267 PHE 0.010 0.001 PHE A 660 TYR 0.012 0.001 TYR C 288 ARG 0.001 0.000 ARG A 560 Details of bonding type rmsd hydrogen bonds : bond 0.04717 ( 1044) hydrogen bonds : angle 3.53976 ( 3060) covalent geometry : bond 0.00278 (21804) covalent geometry : angle 0.49425 (29584) *********************** 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 276 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 221 time to evaluate : 2.132 Fit side-chains REVERT: A 80 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7707 (mmmt) REVERT: A 169 MET cc_start: 0.3511 (ppp) cc_final: 0.3033 (ptm) REVERT: A 437 ASN cc_start: 0.8226 (OUTLIER) cc_final: 0.7318 (m-40) REVERT: A 499 LYS cc_start: 0.8559 (ttmm) cc_final: 0.8290 (ttmm) REVERT: A 601 ASP cc_start: 0.8095 (t0) cc_final: 0.7667 (t0) REVERT: B 80 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7703 (mmmt) REVERT: B 437 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7281 (m-40) REVERT: B 499 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8295 (ttmm) REVERT: B 601 ASP cc_start: 0.8074 (t0) cc_final: 0.7651 (t0) REVERT: C 80 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7723 (mttt) REVERT: C 437 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7291 (m-40) REVERT: C 499 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8306 (ttmm) REVERT: C 601 ASP cc_start: 0.8090 (t0) cc_final: 0.7664 (t0) REVERT: D 80 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7733 (mttt) REVERT: D 437 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7293 (m-40) REVERT: D 499 LYS cc_start: 0.8572 (ttmm) cc_final: 0.8302 (ttmm) REVERT: D 601 ASP cc_start: 0.8082 (t0) cc_final: 0.7662 (t0) outliers start: 55 outliers final: 32 residues processed: 265 average time/residue: 0.2987 time to fit residues: 127.5318 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 : 2.152 ------------------------------------------------------------------------------- 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 263 VAL 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 442 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 250 LEU Chi-restraints excluded: chain B residue 263 VAL 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 442 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 250 LEU Chi-restraints excluded: chain C residue 263 VAL 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 442 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 250 LEU Chi-restraints excluded: chain D residue 263 VAL 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 442 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 262 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 237 optimal weight: 0.9980 chunk 136 optimal weight: 0.3980 chunk 249 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.187794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.159591 restraints weight = 22707.750| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.49 r_work: 0.3269 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1842 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 : 0.493 8.151 29584 Z= 0.261 Chirality : 0.040 0.126 3404 Planarity : 0.002 0.022 3668 Dihedral : 4.016 24.401 2864 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.45 % Favored : 92.24 % Rotamer: Outliers : 1.97 % Allowed : 16.05 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2616 helix: 1.75 (0.15), residues: 1372 sheet: -0.65 (0.36), residues: 256 loop : -2.04 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 513 HIS 0.005 0.001 HIS D 267 PHE 0.009 0.001 PHE C 660 TYR 0.010 0.001 TYR B 368 ARG 0.001 0.000 ARG D 560 Details of bonding type rmsd hydrogen bonds : bond 0.04611 ( 1044) hydrogen bonds : angle 3.49138 ( 3060) covalent geometry : bond 0.00263 (21804) covalent geometry : angle 0.49252 (29584) *********************** 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 260 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 213 time to evaluate : 2.167 Fit side-chains REVERT: A 80 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7718 (mmmt) REVERT: A 169 MET cc_start: 0.3624 (ppp) cc_final: 0.3128 (ptm) REVERT: A 437 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7240 (m-40) REVERT: A 499 LYS cc_start: 0.8563 (ttmm) cc_final: 0.8324 (ttmm) REVERT: A 601 ASP cc_start: 0.8096 (t0) cc_final: 0.7676 (t0) REVERT: B 80 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7721 (mmmt) REVERT: B 437 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7268 (m-40) REVERT: B 499 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8328 (ttmm) REVERT: B 601 ASP cc_start: 0.8099 (t0) cc_final: 0.7681 (t0) REVERT: C 80 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7716 (mmmt) REVERT: C 437 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7287 (m-40) REVERT: C 499 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8342 (ttmm) REVERT: C 601 ASP cc_start: 0.8089 (t0) cc_final: 0.7669 (t0) REVERT: D 80 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7722 (mmmt) REVERT: D 437 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7278 (m-40) REVERT: D 499 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8328 (ttmm) REVERT: D 601 ASP cc_start: 0.8104 (t0) cc_final: 0.7686 (t0) outliers start: 47 outliers final: 35 residues processed: 252 average time/residue: 0.2883 time to fit residues: 116.9505 Evaluate side-chains 250 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 2.089 ------------------------------------------------------------------------------- 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 263 VAL 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 442 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 250 LEU Chi-restraints excluded: chain B residue 263 VAL 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 442 THR Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 598 ILE 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 250 LEU Chi-restraints excluded: chain C residue 263 VAL 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 442 THR Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 598 ILE 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 250 LEU Chi-restraints excluded: chain D residue 263 VAL 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 442 THR Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 76 optimal weight: 0.0000 chunk 135 optimal weight: 0.0870 chunk 204 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 overall best weight: 0.5364 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.189603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.162468 restraints weight = 22848.349| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.47 r_work: 0.3113 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21804 Z= 0.107 Angle : 0.479 9.259 29584 Z= 0.255 Chirality : 0.039 0.126 3404 Planarity : 0.002 0.023 3668 Dihedral : 3.946 23.097 2864 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.22 % Favored : 92.47 % Rotamer: Outliers : 2.02 % Allowed : 16.09 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.18), residues: 2616 helix: 1.80 (0.15), residues: 1376 sheet: -0.63 (0.36), residues: 256 loop : -2.03 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 513 HIS 0.005 0.001 HIS C 267 PHE 0.010 0.001 PHE B 448 TYR 0.009 0.001 TYR B 368 ARG 0.001 0.000 ARG D 560 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 1044) hydrogen bonds : angle 3.40515 ( 3060) covalent geometry : bond 0.00233 (21804) covalent geometry : angle 0.47868 (29584) ********************** 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 273 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 225 time to evaluate : 2.272 Fit side-chains REVERT: A 80 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7756 (mmmt) REVERT: A 169 MET cc_start: 0.3712 (ppp) cc_final: 0.3194 (ptm) REVERT: A 231 MET cc_start: 0.8462 (tpp) cc_final: 0.8079 (tpt) REVERT: A 437 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7194 (m-40) REVERT: A 601 ASP cc_start: 0.7980 (t0) cc_final: 0.7589 (t0) REVERT: B 80 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7758 (mmmt) REVERT: B 231 MET cc_start: 0.8466 (tpp) cc_final: 0.8081 (tpt) REVERT: B 437 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7182 (m-40) REVERT: B 499 LYS cc_start: 0.8442 (ttmm) cc_final: 0.8194 (ttmm) REVERT: B 601 ASP cc_start: 0.7974 (t0) cc_final: 0.7584 (t0) REVERT: C 80 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7723 (mmmt) REVERT: C 231 MET cc_start: 0.8463 (tpp) cc_final: 0.8076 (tpt) REVERT: C 437 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7150 (m-40) REVERT: C 499 LYS cc_start: 0.8455 (ttmm) cc_final: 0.8206 (ttmm) REVERT: C 601 ASP cc_start: 0.7959 (t0) cc_final: 0.7566 (t0) REVERT: D 80 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7727 (mmmt) REVERT: D 231 MET cc_start: 0.8464 (tpp) cc_final: 0.8078 (tpt) REVERT: D 437 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7143 (m-40) REVERT: D 499 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8188 (ttmm) REVERT: D 601 ASP cc_start: 0.7961 (t0) cc_final: 0.7571 (t0) outliers start: 48 outliers final: 33 residues processed: 265 average time/residue: 0.2927 time to fit residues: 124.7756 Evaluate side-chains 267 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 2.518 ------------------------------------------------------------------------------- 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 263 VAL 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 250 LEU Chi-restraints excluded: chain B residue 263 VAL 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 250 LEU Chi-restraints excluded: chain C residue 263 VAL 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 250 LEU Chi-restraints excluded: chain D residue 263 VAL 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 224 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 217 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 226 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 219 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4029 r_free = 0.4029 target = 0.188207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.156104 restraints weight = 22809.701| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.66 r_work: 0.3253 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1943 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= 0.123 Angle : 0.501 9.870 29584 Z= 0.264 Chirality : 0.040 0.126 3404 Planarity : 0.002 0.022 3668 Dihedral : 3.989 24.367 2864 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.26 % Favored : 92.43 % Rotamer: Outliers : 2.02 % Allowed : 16.18 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2616 helix: 1.77 (0.15), residues: 1376 sheet: -0.64 (0.36), residues: 256 loop : -2.03 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 513 HIS 0.005 0.001 HIS B 267 PHE 0.020 0.001 PHE C 93 TYR 0.010 0.001 TYR B 368 ARG 0.001 0.000 ARG D 560 Details of bonding type rmsd hydrogen bonds : bond 0.04548 ( 1044) hydrogen bonds : angle 3.45631 ( 3060) covalent geometry : bond 0.00281 (21804) covalent geometry : angle 0.50111 (29584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10091.07 seconds wall clock time: 175 minutes 50.77 seconds (10550.77 seconds total)