Starting phenix.real_space_refine on Wed Jun 18 12:27:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yie_33856/06_2025/7yie_33856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yie_33856/06_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_33856/06_2025/7yie_33856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yie_33856/06_2025/7yie_33856.map" model { file = "/net/cci-nas-00/data/ceres_data/7yie_33856/06_2025/7yie_33856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yie_33856/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 16.67, per 1000 atoms: 0.78 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: 5.79 Conformation dependent library (CDL) restraints added in 3.1 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: 2.47 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: 7.88 Time building geometry restraints manager: 6.85 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: 4.570 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: 0.030 Extract box with map and model: 1.060 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 55.200 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.150 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.390 ------------------------------------------------------------------------------- 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 : 4.042 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: 0.3165 time to fit residues: 127.1029 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 : 2.512 ------------------------------------------------------------------------------- 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 = 0.188961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.164036 restraints weight = 22762.161| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.22 r_work: 0.3172 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 2.369 Fit side-chains REVERT: A 169 MET cc_start: 0.4408 (ppp) cc_final: 0.3392 (ptm) REVERT: A 231 MET cc_start: 0.8396 (tpp) cc_final: 0.8036 (tpt) REVERT: A 480 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7990 (ttm170) REVERT: A 523 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8304 (tptp) REVERT: A 601 ASP cc_start: 0.7837 (t0) cc_final: 0.7393 (t0) REVERT: B 169 MET cc_start: 0.3990 (ppp) cc_final: 0.3268 (ptm) REVERT: B 231 MET cc_start: 0.8408 (tpp) cc_final: 0.8047 (tpt) REVERT: B 480 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7983 (ttm170) REVERT: B 523 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8311 (tptp) REVERT: B 601 ASP cc_start: 0.7845 (t0) cc_final: 0.7404 (t0) REVERT: C 169 MET cc_start: 0.3977 (ppp) cc_final: 0.3253 (ptm) REVERT: C 231 MET cc_start: 0.8388 (tpp) cc_final: 0.8028 (tpt) REVERT: C 480 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7992 (ttm170) REVERT: C 523 LYS cc_start: 0.8634 (mtpp) cc_final: 0.8307 (tptp) REVERT: C 601 ASP cc_start: 0.7830 (t0) cc_final: 0.7388 (t0) REVERT: D 169 MET cc_start: 0.3975 (ppp) cc_final: 0.3247 (ptm) REVERT: D 231 MET cc_start: 0.8395 (tpp) cc_final: 0.8034 (tpt) REVERT: D 480 ARG cc_start: 0.8232 (ttm-80) cc_final: 0.8012 (ttm170) REVERT: D 523 LYS cc_start: 0.8632 (mtpp) cc_final: 0.8299 (tptp) REVERT: D 601 ASP cc_start: 0.7842 (t0) cc_final: 0.7398 (t0) outliers start: 24 outliers final: 16 residues processed: 225 average time/residue: 0.3016 time to fit residues: 109.7311 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 : 2.225 ------------------------------------------------------------------------------- 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: 0.0030 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 238 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 267 HIS C 267 HIS D 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.187157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.155625 restraints weight = 22689.356| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.57 r_work: 0.3321 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1006 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= 0.110 Angle : 0.466 6.741 29584 Z= 0.253 Chirality : 0.039 0.134 3404 Planarity : 0.003 0.024 3668 Dihedral : 4.103 23.460 2864 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.30 % Favored : 92.39 % Rotamer: Outliers : 1.34 % Allowed : 10.63 % Favored : 88.03 % 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: -0.17 (0.17), residues: 2616 helix: 1.49 (0.15), residues: 1384 sheet: -1.14 (0.33), residues: 260 loop : -2.27 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 513 HIS 0.003 0.001 HIS D 267 PHE 0.009 0.001 PHE D 660 TYR 0.014 0.001 TYR C 460 ARG 0.002 0.000 ARG A 480 Details of bonding type rmsd hydrogen bonds : bond 0.04803 ( 1044) hydrogen bonds : angle 3.84109 ( 3060) covalent geometry : bond 0.00235 (21804) covalent geometry : angle 0.46580 (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 243 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 2.456 Fit side-chains REVERT: A 169 MET cc_start: 0.4146 (ppp) cc_final: 0.3470 (ptm) REVERT: A 437 ASN cc_start: 0.8051 (m110) cc_final: 0.7470 (m-40) REVERT: A 480 ARG cc_start: 0.8252 (ttm-80) cc_final: 0.8051 (ttm170) REVERT: A 523 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8298 (tptp) REVERT: A 601 ASP cc_start: 0.8109 (t0) cc_final: 0.7621 (t0) REVERT: B 169 MET cc_start: 0.3808 (ppp) cc_final: 0.3343 (ptm) REVERT: B 437 ASN cc_start: 0.8043 (m110) cc_final: 0.7450 (m-40) REVERT: B 480 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.8046 (ttm170) REVERT: B 523 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8325 (tptp) REVERT: B 601 ASP cc_start: 0.8109 (t0) cc_final: 0.7621 (t0) REVERT: C 169 MET cc_start: 0.3810 (ppp) cc_final: 0.3338 (ptm) REVERT: C 437 ASN cc_start: 0.8064 (m110) cc_final: 0.7472 (m-40) REVERT: C 480 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.8071 (ttm170) REVERT: C 523 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8312 (tptp) REVERT: C 601 ASP cc_start: 0.8099 (t0) cc_final: 0.7608 (t0) REVERT: D 169 MET cc_start: 0.3815 (ppp) cc_final: 0.3341 (ptm) REVERT: D 437 ASN cc_start: 0.8065 (m110) cc_final: 0.7477 (m-40) REVERT: D 523 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8304 (tptp) REVERT: D 601 ASP cc_start: 0.8103 (t0) cc_final: 0.7612 (t0) outliers start: 32 outliers final: 16 residues processed: 235 average time/residue: 0.3131 time to fit residues: 116.9396 Evaluate side-chains 211 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 2.480 ------------------------------------------------------------------------------- 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 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 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 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 526 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 173 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 194 optimal weight: 0.3980 chunk 250 optimal weight: 1.9990 chunk 246 optimal weight: 7.9990 chunk 233 optimal weight: 0.9980 chunk 199 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.186380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.152604 restraints weight = 23085.978| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.80 r_work: 0.3280 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21804 Z= 0.115 Angle : 0.470 7.104 29584 Z= 0.254 Chirality : 0.039 0.131 3404 Planarity : 0.002 0.023 3668 Dihedral : 4.052 24.142 2864 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.19 % Favored : 92.51 % Rotamer: Outliers : 1.51 % Allowed : 12.56 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.11 (0.17), residues: 2616 helix: 1.58 (0.15), residues: 1380 sheet: -1.14 (0.43), residues: 144 loop : -2.21 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 513 HIS 0.004 0.001 HIS D 267 PHE 0.010 0.001 PHE A 660 TYR 0.013 0.001 TYR B 460 ARG 0.003 0.000 ARG D 102 Details of bonding type rmsd hydrogen bonds : bond 0.04733 ( 1044) hydrogen bonds : angle 3.76720 ( 3060) covalent geometry : bond 0.00252 (21804) covalent geometry : angle 0.46995 (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 251 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 2.271 Fit side-chains REVERT: A 169 MET cc_start: 0.4080 (ppp) cc_final: 0.3486 (ptm) REVERT: A 437 ASN cc_start: 0.8002 (m110) cc_final: 0.7359 (m-40) REVERT: A 499 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8317 (ttmm) REVERT: A 523 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8412 (tptp) REVERT: A 601 ASP cc_start: 0.8035 (t0) cc_final: 0.7564 (t0) REVERT: B 169 MET cc_start: 0.3992 (ppp) cc_final: 0.3648 (ptm) REVERT: B 437 ASN cc_start: 0.7990 (m110) cc_final: 0.7334 (m-40) REVERT: B 499 LYS cc_start: 0.8519 (ttmm) cc_final: 0.8308 (ttmm) REVERT: B 523 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8411 (tptp) REVERT: B 601 ASP cc_start: 0.8063 (t0) cc_final: 0.7592 (t0) REVERT: C 169 MET cc_start: 0.3979 (ppp) cc_final: 0.3638 (ptm) REVERT: C 437 ASN cc_start: 0.8002 (m110) cc_final: 0.7363 (m-40) REVERT: C 499 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8320 (ttmm) REVERT: C 523 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8410 (tptp) REVERT: C 601 ASP cc_start: 0.8036 (t0) cc_final: 0.7568 (t0) REVERT: D 169 MET cc_start: 0.3973 (ppp) cc_final: 0.3632 (ptm) REVERT: D 437 ASN cc_start: 0.8012 (m110) cc_final: 0.7381 (m-40) REVERT: D 499 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8304 (ttmm) REVERT: D 523 LYS cc_start: 0.8667 (mtpp) cc_final: 0.8411 (tptp) REVERT: D 601 ASP cc_start: 0.8044 (t0) cc_final: 0.7577 (t0) outliers start: 36 outliers final: 28 residues processed: 239 average time/residue: 0.3114 time to fit residues: 119.3671 Evaluate side-chains 232 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 2.360 ------------------------------------------------------------------------------- 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 A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 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 299 SER Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 83 optimal weight: 0.5980 chunk 255 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 247 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 267 HIS C 267 HIS D 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.188229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.160098 restraints weight = 22821.938| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.48 r_work: 0.3279 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1353 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= 0.114 Angle : 0.458 7.162 29584 Z= 0.249 Chirality : 0.040 0.144 3404 Planarity : 0.002 0.023 3668 Dihedral : 3.999 23.781 2864 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.15 % Favored : 92.55 % Rotamer: Outliers : 1.68 % Allowed : 13.82 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.01 (0.17), residues: 2616 helix: 1.67 (0.15), residues: 1368 sheet: -1.22 (0.43), residues: 148 loop : -2.08 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 513 HIS 0.004 0.001 HIS D 267 PHE 0.018 0.001 PHE C 93 TYR 0.012 0.001 TYR B 460 ARG 0.002 0.000 ARG A 677 Details of bonding type rmsd hydrogen bonds : bond 0.04693 ( 1044) hydrogen bonds : angle 3.71590 ( 3060) covalent geometry : bond 0.00251 (21804) covalent geometry : angle 0.45780 (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 265 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 2.889 Fit side-chains REVERT: A 169 MET cc_start: 0.3683 (ppp) cc_final: 0.3206 (ptm) REVERT: A 437 ASN cc_start: 0.8178 (m110) cc_final: 0.7412 (m-40) REVERT: A 499 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8306 (ttmm) REVERT: A 523 LYS cc_start: 0.8595 (mtpp) cc_final: 0.8244 (tptp) REVERT: A 601 ASP cc_start: 0.8094 (t0) cc_final: 0.7607 (t0) REVERT: B 169 MET cc_start: 0.3605 (ppp) cc_final: 0.3323 (ptm) REVERT: B 437 ASN cc_start: 0.8155 (m110) cc_final: 0.7365 (m-40) REVERT: B 499 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8308 (ttmm) REVERT: B 523 LYS cc_start: 0.8599 (mtpp) cc_final: 0.8251 (tptp) REVERT: B 601 ASP cc_start: 0.8088 (t0) cc_final: 0.7603 (t0) REVERT: C 169 MET cc_start: 0.3590 (ppp) cc_final: 0.3305 (ptm) REVERT: C 437 ASN cc_start: 0.8171 (m110) cc_final: 0.7382 (m-40) REVERT: C 499 LYS cc_start: 0.8584 (ttmm) cc_final: 0.8316 (ttmm) REVERT: C 523 LYS cc_start: 0.8602 (mtpp) cc_final: 0.8243 (tptp) REVERT: C 601 ASP cc_start: 0.8069 (t0) cc_final: 0.7583 (t0) REVERT: D 169 MET cc_start: 0.3606 (ppp) cc_final: 0.3323 (ptm) REVERT: D 437 ASN cc_start: 0.8173 (m110) cc_final: 0.7390 (m-40) REVERT: D 499 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8303 (ttmm) REVERT: D 523 LYS cc_start: 0.8597 (mtpp) cc_final: 0.8237 (tptp) REVERT: D 601 ASP cc_start: 0.8075 (t0) cc_final: 0.7590 (t0) outliers start: 40 outliers final: 28 residues processed: 253 average time/residue: 0.3485 time to fit residues: 136.7887 Evaluate side-chains 228 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 2.303 ------------------------------------------------------------------------------- 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 A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 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 299 SER Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 41 optimal weight: 0.9980 chunk 174 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 248 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.183637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.148688 restraints weight = 22763.034| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.90 r_work: 0.3153 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21804 Z= 0.148 Angle : 0.503 7.542 29584 Z= 0.272 Chirality : 0.041 0.128 3404 Planarity : 0.003 0.022 3668 Dihedral : 4.126 25.794 2864 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.84 % Favored : 91.86 % Rotamer: Outliers : 2.02 % Allowed : 14.66 % Favored : 83.32 % 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: -0.13 (0.17), residues: 2616 helix: 1.48 (0.15), residues: 1380 sheet: -1.23 (0.42), residues: 148 loop : -2.09 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 388 HIS 0.005 0.001 HIS A 267 PHE 0.013 0.001 PHE A 660 TYR 0.014 0.001 TYR D 460 ARG 0.002 0.000 ARG B 560 Details of bonding type rmsd hydrogen bonds : bond 0.05290 ( 1044) hydrogen bonds : angle 3.85336 ( 3060) covalent geometry : bond 0.00348 (21804) covalent geometry : angle 0.50334 (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 271 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 223 time to evaluate : 2.806 Fit side-chains REVERT: A 169 MET cc_start: 0.4080 (ppp) cc_final: 0.3592 (ptm) REVERT: A 499 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8393 (ttmm) REVERT: A 523 LYS cc_start: 0.8664 (mtpp) cc_final: 0.8387 (tptp) REVERT: A 601 ASP cc_start: 0.7998 (t0) cc_final: 0.7577 (t0) REVERT: B 169 MET cc_start: 0.3868 (ppp) cc_final: 0.3612 (ptm) REVERT: B 499 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8388 (ttmm) REVERT: B 523 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8396 (tptp) REVERT: B 601 ASP cc_start: 0.8007 (t0) cc_final: 0.7586 (t0) REVERT: C 169 MET cc_start: 0.3847 (ppp) cc_final: 0.3597 (ptm) REVERT: C 499 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8399 (ttmm) REVERT: C 523 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8381 (tptp) REVERT: C 601 ASP cc_start: 0.7983 (t0) cc_final: 0.7564 (t0) REVERT: D 169 MET cc_start: 0.3853 (ppp) cc_final: 0.3599 (ptm) REVERT: D 499 LYS cc_start: 0.8602 (ttmm) cc_final: 0.8373 (ttmm) REVERT: D 523 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8386 (tptp) REVERT: D 601 ASP cc_start: 0.8002 (t0) cc_final: 0.7582 (t0) outliers start: 48 outliers final: 28 residues processed: 259 average time/residue: 0.3437 time to fit residues: 142.7246 Evaluate side-chains 242 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 2.343 ------------------------------------------------------------------------------- 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 A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 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 299 SER Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 107 optimal weight: 0.5980 chunk 236 optimal weight: 0.7980 chunk 238 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 162 optimal weight: 0.0870 chunk 164 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 229 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.186963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.159286 restraints weight = 22666.867| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.45 r_work: 0.3252 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1567 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 : 0.477 7.775 29584 Z= 0.253 Chirality : 0.040 0.132 3404 Planarity : 0.002 0.023 3668 Dihedral : 4.003 23.692 2864 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.38 % Favored : 92.32 % Rotamer: Outliers : 1.81 % Allowed : 15.21 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.04 (0.17), residues: 2616 helix: 1.66 (0.15), residues: 1372 sheet: -1.19 (0.42), residues: 148 loop : -2.03 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 513 HIS 0.004 0.001 HIS B 267 PHE 0.011 0.001 PHE D 93 TYR 0.010 0.001 TYR A 368 ARG 0.001 0.000 ARG B 560 Details of bonding type rmsd hydrogen bonds : bond 0.04618 ( 1044) hydrogen bonds : angle 3.62329 ( 3060) covalent geometry : bond 0.00228 (21804) covalent geometry : angle 0.47727 (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 256 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 2.516 Fit side-chains REVERT: A 169 MET cc_start: 0.3591 (ppp) cc_final: 0.3183 (ptm) REVERT: A 437 ASN cc_start: 0.8140 (m110) cc_final: 0.7238 (m-40) REVERT: A 499 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8266 (ttmm) REVERT: A 523 LYS cc_start: 0.8560 (mtpp) cc_final: 0.8229 (tptp) REVERT: A 601 ASP cc_start: 0.8054 (t0) cc_final: 0.7613 (t0) REVERT: B 437 ASN cc_start: 0.8150 (m110) cc_final: 0.7257 (m-40) REVERT: B 499 LYS cc_start: 0.8537 (ttmm) cc_final: 0.8265 (ttmm) REVERT: B 523 LYS cc_start: 0.8560 (mtpp) cc_final: 0.8232 (tptp) REVERT: B 601 ASP cc_start: 0.8054 (t0) cc_final: 0.7614 (t0) REVERT: C 437 ASN cc_start: 0.8155 (m110) cc_final: 0.7269 (m-40) REVERT: C 499 LYS cc_start: 0.8548 (ttmm) cc_final: 0.8282 (ttmm) REVERT: C 523 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8232 (tptp) REVERT: C 601 ASP cc_start: 0.8037 (t0) cc_final: 0.7600 (t0) REVERT: D 437 ASN cc_start: 0.8165 (m110) cc_final: 0.7280 (m-40) REVERT: D 499 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8266 (ttmm) REVERT: D 523 LYS cc_start: 0.8570 (mtpp) cc_final: 0.8235 (tptp) REVERT: D 601 ASP cc_start: 0.8051 (t0) cc_final: 0.7613 (t0) outliers start: 43 outliers final: 27 residues processed: 245 average time/residue: 0.3141 time to fit residues: 122.0305 Evaluate side-chains 235 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 2.524 ------------------------------------------------------------------------------- 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 A residue 527 ILE Chi-restraints excluded: chain A residue 566 PHE 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 B residue 527 ILE Chi-restraints excluded: chain B residue 566 PHE 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 C residue 527 ILE Chi-restraints excluded: chain C residue 566 PHE 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 Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 566 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 27 optimal weight: 0.0770 chunk 122 optimal weight: 0.9990 chunk 262 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 0.0040 chunk 214 optimal weight: 40.0000 chunk 263 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8154 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.185921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.150224 restraints weight = 22788.203| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.79 r_work: 0.3191 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1639 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= 0.124 Angle : 0.492 7.523 29584 Z= 0.261 Chirality : 0.040 0.129 3404 Planarity : 0.002 0.022 3668 Dihedral : 4.021 24.818 2864 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.76 % Favored : 91.93 % Rotamer: Outliers : 1.97 % Allowed : 15.71 % Favored : 82.31 % 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: 0.11 (0.17), residues: 2616 helix: 1.64 (0.15), residues: 1372 sheet: -0.88 (0.35), residues: 260 loop : -2.00 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 513 HIS 0.004 0.001 HIS D 267 PHE 0.010 0.001 PHE D 660 TYR 0.012 0.001 TYR A 368 ARG 0.002 0.000 ARG B 560 Details of bonding type rmsd hydrogen bonds : bond 0.04812 ( 1044) hydrogen bonds : angle 3.66347 ( 3060) covalent geometry : bond 0.00283 (21804) covalent geometry : angle 0.49199 (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 263 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 2.382 Fit side-chains REVERT: A 80 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7844 (mttt) REVERT: A 169 MET cc_start: 0.3996 (ppp) cc_final: 0.3427 (ptm) REVERT: A 437 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7304 (m-40) REVERT: A 499 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8298 (ttmm) REVERT: A 523 LYS cc_start: 0.8627 (mtpp) cc_final: 0.8392 (tptp) REVERT: A 601 ASP cc_start: 0.7905 (t0) cc_final: 0.7529 (t0) REVERT: B 80 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7839 (mttt) REVERT: B 437 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7283 (m-40) REVERT: B 499 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8300 (ttmm) REVERT: B 523 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8399 (tptp) REVERT: B 601 ASP cc_start: 0.7918 (t0) cc_final: 0.7540 (t0) REVERT: C 80 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7796 (mttt) REVERT: C 437 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7307 (m-40) REVERT: C 499 LYS cc_start: 0.8535 (ttmm) cc_final: 0.8307 (ttmm) REVERT: C 523 LYS cc_start: 0.8632 (mtpp) cc_final: 0.8391 (tptp) REVERT: C 601 ASP cc_start: 0.7910 (t0) cc_final: 0.7533 (t0) REVERT: D 80 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7839 (mttt) REVERT: D 437 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7321 (m-40) REVERT: D 499 LYS cc_start: 0.8519 (ttmm) cc_final: 0.8286 (ttmm) REVERT: D 523 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8394 (tptp) REVERT: D 601 ASP cc_start: 0.7920 (t0) cc_final: 0.7545 (t0) outliers start: 47 outliers final: 31 residues processed: 256 average time/residue: 0.3135 time to fit residues: 127.5792 Evaluate side-chains 251 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LYS 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 437 ASN Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 526 SER 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 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 526 SER 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 299 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 526 SER 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 87 ASN Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 526 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 262 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 237 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 chunk 249 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.185356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.150959 restraints weight = 22663.504| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.91 r_work: 0.3142 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21804 Z= 0.132 Angle : 0.505 8.218 29584 Z= 0.268 Chirality : 0.040 0.130 3404 Planarity : 0.002 0.022 3668 Dihedral : 4.058 24.528 2864 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.61 % Favored : 92.09 % Rotamer: Outliers : 1.97 % Allowed : 16.22 % 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: 0.10 (0.17), residues: 2616 helix: 1.62 (0.15), residues: 1372 sheet: -0.90 (0.35), residues: 260 loop : -1.98 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 513 HIS 0.005 0.001 HIS C 267 PHE 0.011 0.001 PHE C 660 TYR 0.012 0.001 TYR A 368 ARG 0.002 0.000 ARG C 560 Details of bonding type rmsd hydrogen bonds : bond 0.04933 ( 1044) hydrogen bonds : angle 3.69259 ( 3060) covalent geometry : bond 0.00306 (21804) covalent geometry : angle 0.50501 (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 : 2.506 Fit side-chains REVERT: A 80 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7752 (mmmt) REVERT: A 87 ASN cc_start: 0.7174 (OUTLIER) cc_final: 0.6890 (t0) REVERT: A 169 MET cc_start: 0.3857 (ppp) cc_final: 0.3309 (ptm) REVERT: A 437 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7306 (m-40) REVERT: A 499 LYS cc_start: 0.8539 (ttmm) cc_final: 0.8283 (ttmm) REVERT: A 523 LYS cc_start: 0.8593 (mtpp) cc_final: 0.8328 (tptp) REVERT: A 601 ASP cc_start: 0.7895 (t0) cc_final: 0.7512 (t0) REVERT: B 80 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7758 (mmmt) REVERT: B 87 ASN cc_start: 0.7161 (OUTLIER) cc_final: 0.6887 (t0) REVERT: B 437 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7293 (m-40) REVERT: B 499 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8281 (ttmm) REVERT: B 523 LYS cc_start: 0.8593 (mtpp) cc_final: 0.8333 (tptp) REVERT: B 601 ASP cc_start: 0.7897 (t0) cc_final: 0.7515 (t0) REVERT: C 80 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7759 (mttt) REVERT: C 437 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7286 (m-40) REVERT: C 499 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8286 (ttmm) REVERT: C 523 LYS cc_start: 0.8599 (mtpp) cc_final: 0.8326 (tptp) REVERT: C 601 ASP cc_start: 0.7894 (t0) cc_final: 0.7508 (t0) REVERT: D 80 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7760 (mmmt) REVERT: D 437 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7300 (m-40) REVERT: D 499 LYS cc_start: 0.8539 (ttmm) cc_final: 0.8279 (ttmm) REVERT: D 523 LYS cc_start: 0.8602 (mtpp) cc_final: 0.8338 (tptp) REVERT: D 601 ASP cc_start: 0.7891 (t0) cc_final: 0.7511 (t0) outliers start: 47 outliers final: 24 residues processed: 257 average time/residue: 0.3040 time to fit residues: 123.9799 Evaluate side-chains 246 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LYS 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 437 ASN Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 526 SER 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 299 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 526 SER 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 76 optimal weight: 0.0170 chunk 135 optimal weight: 0.0270 chunk 204 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 267 HIS C 267 HIS D 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.187373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.149713 restraints weight = 22775.905| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.17 r_work: 0.3119 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1766 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= 0.103 Angle : 0.478 8.739 29584 Z= 0.254 Chirality : 0.039 0.130 3404 Planarity : 0.002 0.023 3668 Dihedral : 3.949 23.673 2864 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.45 % Favored : 92.24 % Rotamer: Outliers : 1.51 % Allowed : 17.06 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.18), residues: 2616 helix: 1.70 (0.15), residues: 1376 sheet: -0.80 (0.35), residues: 256 loop : -1.94 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 513 HIS 0.006 0.001 HIS B 267 PHE 0.011 0.001 PHE A 448 TYR 0.009 0.001 TYR A 368 ARG 0.001 0.000 ARG B 560 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 1044) hydrogen bonds : angle 3.55343 ( 3060) covalent geometry : bond 0.00218 (21804) covalent geometry : angle 0.47845 (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 251 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 2.536 Fit side-chains REVERT: A 80 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7750 (mmmt) REVERT: A 87 ASN cc_start: 0.7063 (OUTLIER) cc_final: 0.6838 (t0) REVERT: A 169 MET cc_start: 0.3753 (ppp) cc_final: 0.3210 (ptm) REVERT: A 437 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7120 (m-40) REVERT: A 499 LYS cc_start: 0.8481 (ttmm) cc_final: 0.8241 (ttmm) REVERT: A 523 LYS cc_start: 0.8607 (mtpp) cc_final: 0.8311 (tptp) REVERT: A 601 ASP cc_start: 0.7972 (t0) cc_final: 0.7575 (t0) REVERT: B 80 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7714 (mmmt) REVERT: B 87 ASN cc_start: 0.7058 (OUTLIER) cc_final: 0.6838 (t0) REVERT: B 437 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7115 (m-40) REVERT: B 499 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8241 (ttmm) REVERT: B 523 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8326 (tptp) REVERT: B 601 ASP cc_start: 0.7967 (t0) cc_final: 0.7572 (t0) REVERT: C 80 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7708 (mmmt) REVERT: C 437 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7139 (m-40) REVERT: C 499 LYS cc_start: 0.8482 (ttmm) cc_final: 0.8244 (ttmm) REVERT: C 523 LYS cc_start: 0.8606 (mtpp) cc_final: 0.8312 (tptp) REVERT: C 601 ASP cc_start: 0.7963 (t0) cc_final: 0.7567 (t0) REVERT: D 80 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7706 (mmmt) REVERT: D 437 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7148 (m-40) REVERT: D 499 LYS cc_start: 0.8476 (ttmm) cc_final: 0.8234 (ttmm) REVERT: D 523 LYS cc_start: 0.8611 (mtpp) cc_final: 0.8327 (tptp) REVERT: D 601 ASP cc_start: 0.7962 (t0) cc_final: 0.7567 (t0) outliers start: 36 outliers final: 22 residues processed: 243 average time/residue: 0.3246 time to fit residues: 126.4423 Evaluate side-chains 245 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LYS 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 437 ASN 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 80 LYS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 526 SER 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 299 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 526 SER 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 299 SER Chi-restraints excluded: chain D residue 437 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 224 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 173 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 217 optimal weight: 0.6980 chunk 191 optimal weight: 5.9990 chunk 226 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 168 optimal weight: 0.5980 chunk 219 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.185767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.150523 restraints weight = 22752.231| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.82 r_work: 0.3193 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1784 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= 0.122 Angle : 0.494 8.551 29584 Z= 0.262 Chirality : 0.040 0.128 3404 Planarity : 0.002 0.022 3668 Dihedral : 3.996 24.361 2864 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.57 % Favored : 92.13 % Rotamer: Outliers : 1.81 % Allowed : 16.47 % Favored : 81.72 % 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: 0.20 (0.18), residues: 2616 helix: 1.67 (0.15), residues: 1376 sheet: -0.86 (0.35), residues: 260 loop : -1.88 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 513 HIS 0.006 0.001 HIS D 267 PHE 0.017 0.001 PHE B 93 TYR 0.012 0.001 TYR A 368 ARG 0.002 0.000 ARG B 560 Details of bonding type rmsd hydrogen bonds : bond 0.04705 ( 1044) hydrogen bonds : angle 3.61049 ( 3060) covalent geometry : bond 0.00277 (21804) covalent geometry : angle 0.49395 (29584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10453.71 seconds wall clock time: 182 minutes 18.56 seconds (10938.56 seconds total)