Starting phenix.real_space_refine on Thu Aug 6 11:19:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xyi_72335/08_2026/9xyi_72335.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xyi_72335/08_2026/9xyi_72335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xyi_72335/08_2026/9xyi_72335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xyi_72335/08_2026/9xyi_72335.map" model { file = "/net/cci-nas-00/data/ceres_data/9xyi_72335/08_2026/9xyi_72335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xyi_72335/08_2026/9xyi_72335.cif" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 63 5.16 5 C 9129 2.51 5 N 2471 2.21 5 O 2825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14493 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4788 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 31, 'TRANS': 592} Chain: "B" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4788 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 31, 'TRANS': 592} Chain: "C" Number of atoms: 4779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4779 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 31, 'TRANS': 591} Chain: "D" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 123 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.46, per 1000 atoms: 0.24 Number of scatterers: 14493 At special positions: 0 Unit cell: (105.75, 108.288, 108.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 5 15.00 O 2825 8.00 N 2471 7.00 C 9129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 794.1 milliseconds 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 14 sheets defined 43.9% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 164 through 180 removed outlier: 4.044A pdb=" N LEU A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 237 through 266 removed outlier: 3.645A pdb=" N GLN A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 301 removed outlier: 5.657A pdb=" N GLU A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 328 removed outlier: 3.569A pdb=" N GLN A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 356 removed outlier: 3.507A pdb=" N PHE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.858A pdb=" N ILE A 406 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 444 through 459 removed outlier: 3.580A pdb=" N LEU A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 482 through 499 Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 567 through 593 removed outlier: 3.578A pdb=" N VAL A 571 " --> pdb=" O PRO A 567 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 622 removed outlier: 4.437A pdb=" N ALA A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LYS A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 635 Processing helix chain 'A' and resid 653 through 669 Processing helix chain 'B' and resid 115 through 122 Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 164 through 180 removed outlier: 4.133A pdb=" N LEU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 237 through 267 removed outlier: 3.715A pdb=" N GLN B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 301 removed outlier: 5.773A pdb=" N GLU B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 328 removed outlier: 3.506A pdb=" N ASP B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 356 removed outlier: 3.540A pdb=" N ILE B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL B 352 " --> pdb=" O PHE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 410 through 415 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 444 through 459 Processing helix chain 'B' and resid 482 through 499 Processing helix chain 'B' and resid 534 through 540 Processing helix chain 'B' and resid 568 through 593 removed outlier: 3.680A pdb=" N THR B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 622 removed outlier: 4.358A pdb=" N ALA B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LYS B 619 " --> pdb=" O SER B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'B' and resid 653 through 669 removed outlier: 3.507A pdb=" N GLU B 659 " --> pdb=" O SER B 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 124 through 139 Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 164 through 180 removed outlier: 4.083A pdb=" N LEU C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 211 removed outlier: 3.840A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 237 through 267 removed outlier: 3.637A pdb=" N GLN C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 300 removed outlier: 5.597A pdb=" N GLU C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ARG C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 328 removed outlier: 3.609A pdb=" N GLU C 326 " --> pdb=" O GLU C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 356 removed outlier: 3.522A pdb=" N PHE C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 352 " --> pdb=" O PHE C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 405 Processing helix chain 'C' and resid 409 through 417 Processing helix chain 'C' and resid 430 through 435 Processing helix chain 'C' and resid 444 through 459 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 482 through 499 Processing helix chain 'C' and resid 534 through 541 Processing helix chain 'C' and resid 567 through 593 removed outlier: 3.502A pdb=" N VAL C 571 " --> pdb=" O PRO C 567 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 622 removed outlier: 4.390A pdb=" N ALA C 618 " --> pdb=" O LEU C 614 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS C 619 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 635 Processing helix chain 'C' and resid 653 through 668 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 51 removed outlier: 6.428A pdb=" N ALA A 79 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 99 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N CYS A 154 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASP A 101 " --> pdb=" O CYS A 154 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LEU A 156 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ARG A 103 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N ALA A 158 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 202 removed outlier: 3.999A pdb=" N ILE A 195 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU A 214 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN A 215 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA A 231 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL A 217 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU A 229 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA A 219 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A 227 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE A 561 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 229 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR A 555 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET A 543 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU A 513 " --> pdb=" O MET A 543 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP A 526 " --> pdb=" O LYS A 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 374 removed outlier: 6.282A pdb=" N GLN A 392 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N MET A 424 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N SER A 474 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS A 426 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL A 476 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLU A 428 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLU A 478 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 611 Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.376A pdb=" N ALA B 79 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 99 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N CYS B 154 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP B 101 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU B 156 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N ARG B 103 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N ALA B 158 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 202 removed outlier: 4.174A pdb=" N ILE B 195 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU B 214 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN B 215 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA B 231 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B 217 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU B 229 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA B 219 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL B 227 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE B 561 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 229 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR B 555 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N MET B 543 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 513 " --> pdb=" O MET B 543 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ALA B 510 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N THR B 531 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY B 512 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU B 529 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 514 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR B 527 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS B 516 " --> pdb=" O GLU B 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 199 through 202 removed outlier: 4.174A pdb=" N ILE B 195 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU B 214 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN B 215 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA B 231 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B 217 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU B 229 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA B 219 " --> pdb=" O VAL B 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 370 through 374 removed outlier: 6.291A pdb=" N GLN B 392 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 606 through 611 Processing sheet with id=AB1, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.399A pdb=" N ALA C 79 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU C 156 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AB3, first strand: chain 'C' and resid 199 through 202 removed outlier: 4.022A pdb=" N ILE C 195 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU C 214 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN C 215 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA C 231 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 217 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU C 229 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA C 219 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL C 227 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE C 561 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 229 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR C 555 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET C 543 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU C 513 " --> pdb=" O MET C 543 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP C 526 " --> pdb=" O LYS C 516 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 370 through 374 removed outlier: 6.351A pdb=" N GLN C 392 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 606 through 611 860 hydrogen bonds defined for protein. 2412 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: 3.08 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4798 1.34 - 1.46: 2080 1.46 - 1.58: 7751 1.58 - 1.70: 10 1.70 - 1.82: 99 Bond restraints: 14738 Sorted by residual: bond pdb=" CB GLU C 293 " pdb=" CG GLU C 293 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.91e+00 bond pdb=" CB GLU C 330 " pdb=" CG GLU C 330 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.40e+00 bond pdb=" CB GLU B 330 " pdb=" CG GLU B 330 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.36e+00 bond pdb=" N1 C D 4 " pdb=" C2 C D 4 " ideal model delta sigma weight residual 1.397 1.409 -0.012 1.00e-02 1.00e+04 1.33e+00 bond pdb=" CB PRO C 97 " pdb=" CG PRO C 97 " ideal model delta sigma weight residual 1.492 1.537 -0.045 5.00e-02 4.00e+02 8.16e-01 ... (remaining 14733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 19647 1.46 - 2.92: 265 2.92 - 4.39: 54 4.39 - 5.85: 15 5.85 - 7.31: 4 Bond angle restraints: 19985 Sorted by residual: angle pdb=" C1' C D 4 " pdb=" N1 C D 4 " pdb=" C2 C D 4 " ideal model delta sigma weight residual 118.80 125.24 -6.44 1.10e+00 8.26e-01 3.42e+01 angle pdb=" N1 C D 4 " pdb=" C2 C D 4 " pdb=" O2 C D 4 " ideal model delta sigma weight residual 118.90 121.83 -2.93 6.00e-01 2.78e+00 2.39e+01 angle pdb=" O2 C D 4 " pdb=" C2 C D 4 " pdb=" N3 C D 4 " ideal model delta sigma weight residual 121.90 118.89 3.01 7.00e-01 2.04e+00 1.85e+01 angle pdb=" C2 C D 4 " pdb=" N1 C D 4 " pdb=" C6 C D 4 " ideal model delta sigma weight residual 120.30 118.68 1.62 4.00e-01 6.25e+00 1.65e+01 angle pdb=" C1' C D 4 " pdb=" N1 C D 4 " pdb=" C6 C D 4 " ideal model delta sigma weight residual 120.80 116.09 4.71 1.20e+00 6.94e-01 1.54e+01 ... (remaining 19980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 8751 35.10 - 70.19: 285 70.19 - 105.29: 32 105.29 - 140.39: 0 140.39 - 175.48: 2 Dihedral angle restraints: 9070 sinusoidal: 3667 harmonic: 5403 Sorted by residual: dihedral pdb=" O4' C D 4 " pdb=" C1' C D 4 " pdb=" N1 C D 4 " pdb=" C2 C D 4 " ideal model delta sinusoidal sigma weight residual -160.00 11.04 -171.04 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' U D 5 " pdb=" C1' U D 5 " pdb=" N1 U D 5 " pdb=" C2 U D 5 " ideal model delta sinusoidal sigma weight residual 232.00 56.52 175.48 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA ALA B 107 " pdb=" C ALA B 107 " pdb=" N ALA B 108 " pdb=" CA ALA B 108 " ideal model delta harmonic sigma weight residual -180.00 -160.63 -19.37 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 9067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1882 0.052 - 0.105: 379 0.105 - 0.157: 82 0.157 - 0.209: 0 0.209 - 0.262: 1 Chirality restraints: 2344 Sorted by residual: chirality pdb=" CB ILE A 112 " pdb=" CA ILE A 112 " pdb=" CG1 ILE A 112 " pdb=" CG2 ILE A 112 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ASP B 375 " pdb=" N ASP B 375 " pdb=" C ASP B 375 " pdb=" CB ASP B 375 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE B 112 " pdb=" N ILE B 112 " pdb=" C ILE B 112 " pdb=" CB ILE B 112 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 2341 not shown) Planarity restraints: 2567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 293 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" CD GLU C 293 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU C 293 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU C 293 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 332 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A 333 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 112 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO B 113 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " -0.022 5.00e-02 4.00e+02 ... (remaining 2564 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 7091 2.98 - 3.46: 14790 3.46 - 3.94: 24741 3.94 - 4.42: 28874 4.42 - 4.90: 45736 Nonbonded interactions: 121232 Sorted by model distance: nonbonded pdb=" N GLU C 293 " pdb=" OE1 GLU C 293 " model vdw 2.504 3.120 nonbonded pdb=" N GLU C 330 " pdb=" OE1 GLU C 330 " model vdw 2.515 3.120 nonbonded pdb=" N GLU B 330 " pdb=" OE1 GLU B 330 " model vdw 2.522 3.120 nonbonded pdb=" O ARG B 464 " pdb=" OD1 ASP B 465 " model vdw 2.534 3.040 nonbonded pdb=" O VAL B 374 " pdb=" OD1 ASP B 375 " model vdw 2.539 3.040 ... (remaining 121227 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 46 through 668 or resid 901)) selection = (chain 'B' and (resid 46 through 668 or resid 901)) selection = chain 'C' } 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: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.760 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 27.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 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 : 0.002 0.045 14738 Z= 0.109 Angle : 0.473 7.312 19985 Z= 0.269 Chirality : 0.043 0.262 2344 Planarity : 0.004 0.042 2567 Dihedral : 16.965 175.481 5586 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.76 % Allowed : 20.14 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.19), residues: 1865 helix: 0.78 (0.18), residues: 734 sheet: 1.62 (0.25), residues: 427 loop : 0.39 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 617 TYR 0.012 0.001 TYR A 427 PHE 0.014 0.001 PHE B 663 TRP 0.008 0.002 TRP A 184 HIS 0.002 0.000 HIS C 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (14738) covalent geometry : angle 0.47253 / 0.27 (19985) hydrogen bonds : bond 0.21473 / 14.38 ( 847) hydrogen bonds : angle 7.89597 / 5.68 ( 2412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.584 Fit side-chains REVERT: A 112 ILE cc_start: 0.5194 (OUTLIER) cc_final: 0.4924 (tp) REVERT: A 223 LYS cc_start: 0.8913 (mttp) cc_final: 0.8442 (mtmm) REVERT: A 230 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8008 (mm-30) REVERT: A 282 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7736 (tp30) REVERT: A 424 MET cc_start: 0.8950 (ptp) cc_final: 0.8135 (tmt) REVERT: A 428 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8419 (mp0) REVERT: A 544 ASP cc_start: 0.8322 (t0) cc_final: 0.8049 (t0) REVERT: B 164 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: B 311 GLU cc_start: 0.7987 (tp30) cc_final: 0.7629 (tp30) REVERT: B 315 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8326 (tmmm) REVERT: B 547 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8645 (tp) REVERT: C 118 ARG cc_start: 0.8293 (ttp80) cc_final: 0.7960 (ttm-80) REVERT: C 264 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8578 (ttpt) REVERT: C 415 ILE cc_start: 0.7472 (mt) cc_final: 0.7236 (mp) REVERT: C 632 GLN cc_start: 0.7480 (tm-30) cc_final: 0.7159 (tm-30) REVERT: C 645 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6314 (tp30) outliers start: 28 outliers final: 13 residues processed: 131 average time/residue: 0.6879 time to fit residues: 98.8352 Evaluate side-chains 123 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 645 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN B 155 ASN C 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.110682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.085346 restraints weight = 21411.721| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.19 r_work: 0.3034 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14738 Z= 0.218 Angle : 0.547 6.360 19985 Z= 0.302 Chirality : 0.046 0.223 2344 Planarity : 0.004 0.040 2567 Dihedral : 8.761 174.413 2129 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.96 % Allowed : 18.00 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.20), residues: 1865 helix: 1.87 (0.18), residues: 735 sheet: 1.81 (0.25), residues: 425 loop : 0.31 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 617 TYR 0.019 0.002 TYR A 334 PHE 0.019 0.001 PHE B 545 TRP 0.006 0.001 TRP C 184 HIS 0.003 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.22 (14738) covalent geometry : angle 0.54653 / 0.30 (19985) hydrogen bonds : bond 0.07026 / 4.63 ( 847) hydrogen bonds : angle 5.73482 / 4.13 ( 2412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 109 time to evaluate : 0.603 Fit side-chains REVERT: A 112 ILE cc_start: 0.5256 (OUTLIER) cc_final: 0.4966 (tp) REVERT: A 223 LYS cc_start: 0.9035 (mttp) cc_final: 0.8656 (mtmm) REVERT: A 230 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: A 282 GLU cc_start: 0.7786 (pm20) cc_final: 0.7167 (tp30) REVERT: A 424 MET cc_start: 0.8977 (ptp) cc_final: 0.8436 (tmt) REVERT: A 617 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7179 (tpt90) REVERT: B 81 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8752 (ttm) REVERT: B 164 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: B 311 GLU cc_start: 0.8051 (tp30) cc_final: 0.7749 (tp30) REVERT: B 315 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8363 (tmmm) REVERT: B 547 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8704 (tp) REVERT: B 606 VAL cc_start: 0.9008 (OUTLIER) cc_final: 0.8767 (m) REVERT: B 664 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7722 (mp) REVERT: C 346 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: C 410 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.5601 (tp40) REVERT: C 632 GLN cc_start: 0.7544 (tm-30) cc_final: 0.7319 (tm-30) outliers start: 63 outliers final: 22 residues processed: 161 average time/residue: 0.6515 time to fit residues: 115.4629 Evaluate side-chains 133 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 73 optimal weight: 0.0980 chunk 44 optimal weight: 4.9990 chunk 31 optimal weight: 0.0030 chunk 132 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 175 optimal weight: 0.8980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.112861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.088152 restraints weight = 21362.087| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.16 r_work: 0.3077 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14738 Z= 0.130 Angle : 0.481 6.357 19985 Z= 0.264 Chirality : 0.044 0.177 2344 Planarity : 0.004 0.057 2567 Dihedral : 8.464 176.986 2112 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.59 % Allowed : 18.57 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.20), residues: 1865 helix: 2.19 (0.18), residues: 742 sheet: 1.83 (0.25), residues: 427 loop : 0.40 (0.26), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 118 TYR 0.017 0.001 TYR C 334 PHE 0.021 0.001 PHE B 663 TRP 0.006 0.001 TRP A 184 HIS 0.002 0.000 HIS C 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (14738) covalent geometry : angle 0.48138 / 0.26 (19985) hydrogen bonds : bond 0.05728 / 3.78 ( 847) hydrogen bonds : angle 5.26357 / 3.78 ( 2412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 116 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 112 ILE cc_start: 0.5152 (OUTLIER) cc_final: 0.4891 (tp) REVERT: A 223 LYS cc_start: 0.9012 (mttp) cc_final: 0.8630 (mtmm) REVERT: A 230 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7958 (mm-30) REVERT: A 282 GLU cc_start: 0.7719 (pm20) cc_final: 0.6917 (tp30) REVERT: A 424 MET cc_start: 0.8968 (ptp) cc_final: 0.8399 (tmt) REVERT: A 616 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.7926 (mmmm) REVERT: A 617 ARG cc_start: 0.8076 (mtp85) cc_final: 0.7430 (tpt90) REVERT: B 103 ARG cc_start: 0.8117 (mmm160) cc_final: 0.7913 (mmp-170) REVERT: B 164 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8550 (mp0) REVERT: B 311 GLU cc_start: 0.8027 (tp30) cc_final: 0.7693 (tp30) REVERT: B 315 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8358 (tmmm) REVERT: B 547 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8726 (tp) REVERT: B 664 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7774 (mp) REVERT: C 96 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8074 (tmm) REVERT: C 105 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8379 (mmtp) REVERT: C 346 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: C 415 ILE cc_start: 0.7810 (mt) cc_final: 0.7475 (mp) REVERT: C 632 GLN cc_start: 0.7516 (tm-30) cc_final: 0.7293 (tm-30) REVERT: C 645 GLU cc_start: 0.7091 (tp30) cc_final: 0.6368 (tp30) outliers start: 57 outliers final: 23 residues processed: 164 average time/residue: 0.6596 time to fit residues: 119.2783 Evaluate side-chains 133 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 609 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 131 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 73 optimal weight: 0.0020 chunk 88 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 38 optimal weight: 0.0040 chunk 122 optimal weight: 4.9990 overall best weight: 1.9204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.110917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.086056 restraints weight = 21435.950| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.16 r_work: 0.3044 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14738 Z= 0.209 Angle : 0.525 6.290 19985 Z= 0.286 Chirality : 0.045 0.207 2344 Planarity : 0.004 0.047 2567 Dihedral : 8.536 174.599 2110 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.03 % Allowed : 18.38 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.20), residues: 1865 helix: 2.18 (0.18), residues: 740 sheet: 1.74 (0.25), residues: 430 loop : 0.35 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 118 TYR 0.016 0.002 TYR C 334 PHE 0.019 0.001 PHE B 663 TRP 0.006 0.001 TRP C 184 HIS 0.003 0.001 HIS C 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (14738) covalent geometry : angle 0.52513 / 0.29 (19985) hydrogen bonds : bond 0.05897 / 3.88 ( 847) hydrogen bonds : angle 5.22648 / 3.76 ( 2412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 104 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.5264 (OUTLIER) cc_final: 0.4985 (tp) REVERT: A 223 LYS cc_start: 0.9030 (mttp) cc_final: 0.8645 (mtmm) REVERT: A 230 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7995 (mm-30) REVERT: A 282 GLU cc_start: 0.7735 (pm20) cc_final: 0.6996 (tp30) REVERT: A 424 MET cc_start: 0.8988 (ptp) cc_final: 0.8432 (tmt) REVERT: A 428 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8499 (mp0) REVERT: A 616 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7886 (mmmm) REVERT: A 617 ARG cc_start: 0.8131 (mtp85) cc_final: 0.7273 (tpt90) REVERT: B 164 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: B 311 GLU cc_start: 0.8058 (tp30) cc_final: 0.7725 (tp30) REVERT: B 315 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8369 (tmmm) REVERT: B 547 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8714 (tp) REVERT: B 664 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7754 (mp) REVERT: C 96 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8177 (tmm) REVERT: C 346 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7996 (tm-30) REVERT: C 415 ILE cc_start: 0.7740 (mt) cc_final: 0.7519 (mp) REVERT: C 632 GLN cc_start: 0.7510 (tm-30) cc_final: 0.7280 (tm-30) outliers start: 64 outliers final: 34 residues processed: 156 average time/residue: 0.6210 time to fit residues: 106.7506 Evaluate side-chains 143 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 100 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 128 optimal weight: 0.0670 chunk 26 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 38 optimal weight: 0.1980 chunk 145 optimal weight: 2.9990 overall best weight: 3.0524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.109487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.084118 restraints weight = 21565.965| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.19 r_work: 0.3012 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 14738 Z= 0.293 Angle : 0.583 6.191 19985 Z= 0.318 Chirality : 0.048 0.226 2344 Planarity : 0.005 0.055 2567 Dihedral : 8.718 176.653 2110 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.47 % Allowed : 18.19 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.20), residues: 1865 helix: 2.02 (0.18), residues: 733 sheet: 1.65 (0.25), residues: 432 loop : 0.23 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 118 TYR 0.019 0.002 TYR C 427 PHE 0.020 0.002 PHE A 545 TRP 0.006 0.002 TRP C 184 HIS 0.004 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.29 (14738) covalent geometry : angle 0.58296 / 0.32 (19985) hydrogen bonds : bond 0.06441 / 4.24 ( 847) hydrogen bonds : angle 5.34804 / 3.85 ( 2412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 101 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.5297 (OUTLIER) cc_final: 0.5006 (tp) REVERT: A 223 LYS cc_start: 0.9020 (mttp) cc_final: 0.8649 (mtmm) REVERT: A 230 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8034 (mm-30) REVERT: A 282 GLU cc_start: 0.7786 (pm20) cc_final: 0.7157 (tp30) REVERT: A 410 GLN cc_start: 0.5739 (OUTLIER) cc_final: 0.4828 (tm-30) REVERT: A 424 MET cc_start: 0.8998 (ptp) cc_final: 0.8442 (tmt) REVERT: A 616 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.7916 (mmmm) REVERT: B 81 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8718 (ttm) REVERT: B 164 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8253 (mp0) REVERT: B 311 GLU cc_start: 0.8086 (tp30) cc_final: 0.7744 (tp30) REVERT: B 315 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8393 (tmmm) REVERT: B 547 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8744 (tp) REVERT: C 96 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8290 (tmm) REVERT: C 105 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8518 (mmtp) REVERT: C 346 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: C 410 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.5369 (tp40) REVERT: C 415 ILE cc_start: 0.7748 (mt) cc_final: 0.7522 (mp) REVERT: C 632 GLN cc_start: 0.7546 (tm-30) cc_final: 0.7333 (tm-30) outliers start: 71 outliers final: 36 residues processed: 159 average time/residue: 0.5768 time to fit residues: 101.9798 Evaluate side-chains 148 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 100 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 23 optimal weight: 0.4980 chunk 173 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN C 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.111197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.086474 restraints weight = 21314.716| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.15 r_work: 0.3052 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14738 Z= 0.164 Angle : 0.514 6.277 19985 Z= 0.281 Chirality : 0.045 0.209 2344 Planarity : 0.004 0.041 2567 Dihedral : 8.675 179.899 2110 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.31 % Favored : 97.64 % Rotamer: Outliers : 3.46 % Allowed : 19.38 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.20), residues: 1865 helix: 2.24 (0.18), residues: 736 sheet: 1.66 (0.25), residues: 431 loop : 0.32 (0.26), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 118 TYR 0.017 0.001 TYR C 334 PHE 0.018 0.001 PHE B 545 TRP 0.006 0.001 TRP C 184 HIS 0.002 0.001 HIS C 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (14738) covalent geometry : angle 0.51373 / 0.28 (19985) hydrogen bonds : bond 0.05577 / 3.68 ( 847) hydrogen bonds : angle 5.11298 / 3.68 ( 2412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 110 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.5283 (OUTLIER) cc_final: 0.5020 (tp) REVERT: A 223 LYS cc_start: 0.9010 (mttp) cc_final: 0.8634 (mtmm) REVERT: A 230 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7994 (mm-30) REVERT: A 282 GLU cc_start: 0.7694 (pm20) cc_final: 0.7013 (tp30) REVERT: A 394 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8727 (tm) REVERT: A 410 GLN cc_start: 0.5874 (OUTLIER) cc_final: 0.4900 (tm-30) REVERT: A 424 MET cc_start: 0.8970 (ptp) cc_final: 0.8409 (tmt) REVERT: A 428 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8571 (mp0) REVERT: A 616 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7848 (mmmm) REVERT: B 164 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: B 311 GLU cc_start: 0.8053 (tp30) cc_final: 0.7703 (tp30) REVERT: B 315 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8380 (tmmm) REVERT: B 547 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8756 (tp) REVERT: C 96 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8167 (tmm) REVERT: C 105 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8527 (mmtp) REVERT: C 346 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: C 408 SER cc_start: 0.7488 (t) cc_final: 0.7071 (p) REVERT: C 415 ILE cc_start: 0.7809 (mt) cc_final: 0.7547 (mp) REVERT: C 632 GLN cc_start: 0.7513 (tm-30) cc_final: 0.7286 (tm-30) REVERT: C 645 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6819 (mm-30) outliers start: 55 outliers final: 25 residues processed: 155 average time/residue: 0.6356 time to fit residues: 108.7319 Evaluate side-chains 136 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 645 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 178 optimal weight: 0.2980 chunk 133 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 100 optimal weight: 0.0170 chunk 70 optimal weight: 5.9990 chunk 73 optimal weight: 0.0070 chunk 153 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.114558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.089740 restraints weight = 21196.352| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.18 r_work: 0.3106 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14738 Z= 0.113 Angle : 0.480 6.363 19985 Z= 0.261 Chirality : 0.044 0.162 2344 Planarity : 0.004 0.040 2567 Dihedral : 8.501 179.177 2110 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.25 % Favored : 97.69 % Rotamer: Outliers : 3.02 % Allowed : 20.33 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.20), residues: 1865 helix: 2.40 (0.18), residues: 746 sheet: 1.73 (0.25), residues: 429 loop : 0.36 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 118 TYR 0.016 0.001 TYR C 334 PHE 0.017 0.001 PHE A 545 TRP 0.009 0.002 TRP B 184 HIS 0.001 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (14738) covalent geometry : angle 0.47971 / 0.26 (19985) hydrogen bonds : bond 0.04577 / 3.04 ( 847) hydrogen bonds : angle 4.81028 / 3.45 ( 2412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 111 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7970 (mp) REVERT: A 112 ILE cc_start: 0.5033 (OUTLIER) cc_final: 0.4766 (tp) REVERT: A 223 LYS cc_start: 0.8972 (mttp) cc_final: 0.8594 (mtmm) REVERT: A 230 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7932 (mm-30) REVERT: A 394 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8694 (tm) REVERT: A 410 GLN cc_start: 0.5845 (OUTLIER) cc_final: 0.4824 (tm-30) REVERT: A 424 MET cc_start: 0.8936 (ptp) cc_final: 0.8378 (tmt) REVERT: A 428 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8518 (mp0) REVERT: A 616 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7883 (mmmm) REVERT: B 123 THR cc_start: 0.7408 (OUTLIER) cc_final: 0.7151 (p) REVERT: B 164 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8539 (mp0) REVERT: B 282 GLU cc_start: 0.8232 (pp20) cc_final: 0.7922 (pp20) REVERT: B 311 GLU cc_start: 0.8043 (tp30) cc_final: 0.7670 (tp30) REVERT: B 315 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8415 (tmmm) REVERT: B 547 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8769 (tp) REVERT: C 105 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8252 (mmtp) REVERT: C 352 VAL cc_start: 0.8123 (t) cc_final: 0.7879 (p) REVERT: C 617 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7854 (ttm170) REVERT: C 641 GLN cc_start: 0.8755 (tp40) cc_final: 0.8010 (tm-30) REVERT: C 645 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6187 (tp30) outliers start: 48 outliers final: 20 residues processed: 150 average time/residue: 0.5514 time to fit residues: 92.2152 Evaluate side-chains 133 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 645 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 138 optimal weight: 0.0980 chunk 75 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.111266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.086484 restraints weight = 21269.458| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.14 r_work: 0.3047 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14738 Z= 0.215 Angle : 0.542 7.291 19985 Z= 0.294 Chirality : 0.046 0.194 2344 Planarity : 0.004 0.041 2567 Dihedral : 8.543 175.243 2110 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.36 % Favored : 97.59 % Rotamer: Outliers : 3.15 % Allowed : 20.33 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.20), residues: 1865 helix: 2.32 (0.18), residues: 741 sheet: 1.78 (0.25), residues: 429 loop : 0.30 (0.26), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 118 TYR 0.016 0.002 TYR C 334 PHE 0.018 0.001 PHE A 545 TRP 0.005 0.001 TRP C 184 HIS 0.003 0.001 HIS C 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 (14738) covalent geometry : angle 0.54230 / 0.29 (19985) hydrogen bonds : bond 0.05410 / 3.56 ( 847) hydrogen bonds : angle 5.02327 / 3.61 ( 2412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 102 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8030 (mp) REVERT: A 112 ILE cc_start: 0.5086 (OUTLIER) cc_final: 0.4802 (tp) REVERT: A 223 LYS cc_start: 0.9009 (mttp) cc_final: 0.8627 (mtmm) REVERT: A 230 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7982 (mm-30) REVERT: A 282 GLU cc_start: 0.7622 (pm20) cc_final: 0.6904 (tp30) REVERT: A 410 GLN cc_start: 0.5830 (OUTLIER) cc_final: 0.4843 (tm-30) REVERT: A 424 MET cc_start: 0.8974 (ptp) cc_final: 0.8413 (tmt) REVERT: A 428 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8555 (mp0) REVERT: A 616 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7914 (mmmm) REVERT: B 123 THR cc_start: 0.7661 (OUTLIER) cc_final: 0.7421 (p) REVERT: B 164 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: B 311 GLU cc_start: 0.8067 (tp30) cc_final: 0.7697 (tp30) REVERT: B 315 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8409 (tmmm) REVERT: B 547 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8753 (tp) REVERT: C 105 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8356 (mmtp) REVERT: C 408 SER cc_start: 0.7706 (t) cc_final: 0.7299 (p) REVERT: C 410 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6884 (tp40) REVERT: C 632 GLN cc_start: 0.7541 (tm-30) cc_final: 0.7308 (tm-30) REVERT: C 645 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6831 (mm-30) outliers start: 50 outliers final: 22 residues processed: 143 average time/residue: 0.6129 time to fit residues: 97.1777 Evaluate side-chains 132 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 645 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 169 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 183 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 179 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.113508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.088413 restraints weight = 21298.365| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.19 r_work: 0.3086 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14738 Z= 0.126 Angle : 0.498 7.855 19985 Z= 0.270 Chirality : 0.044 0.152 2344 Planarity : 0.004 0.049 2567 Dihedral : 8.430 177.628 2110 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.31 % Favored : 97.64 % Rotamer: Outliers : 2.33 % Allowed : 21.27 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.20), residues: 1865 helix: 2.40 (0.18), residues: 747 sheet: 1.78 (0.25), residues: 429 loop : 0.37 (0.26), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 118 TYR 0.016 0.001 TYR C 334 PHE 0.018 0.001 PHE A 545 TRP 0.007 0.001 TRP A 184 HIS 0.002 0.000 HIS C 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (14738) covalent geometry : angle 0.49763 / 0.27 (19985) hydrogen bonds : bond 0.04752 / 3.15 ( 847) hydrogen bonds : angle 4.84537 / 3.48 ( 2412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7985 (mp) REVERT: A 112 ILE cc_start: 0.5042 (OUTLIER) cc_final: 0.4767 (tp) REVERT: A 223 LYS cc_start: 0.8982 (mttp) cc_final: 0.8606 (mtmm) REVERT: A 230 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7957 (mm-30) REVERT: A 282 GLU cc_start: 0.7602 (pm20) cc_final: 0.6796 (tp30) REVERT: A 394 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8688 (tm) REVERT: A 410 GLN cc_start: 0.5932 (OUTLIER) cc_final: 0.4904 (tm-30) REVERT: A 424 MET cc_start: 0.8942 (ptp) cc_final: 0.8385 (tmt) REVERT: A 428 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8518 (mp0) REVERT: A 616 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7882 (mmmm) REVERT: B 164 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8560 (mp0) REVERT: B 311 GLU cc_start: 0.8056 (tp30) cc_final: 0.7687 (tp30) REVERT: B 315 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8421 (tmmm) REVERT: B 547 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8764 (tp) REVERT: C 105 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8324 (mmtp) REVERT: C 346 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: C 352 VAL cc_start: 0.8179 (t) cc_final: 0.7935 (p) REVERT: C 641 GLN cc_start: 0.8871 (tp40) cc_final: 0.8306 (tm-30) REVERT: C 645 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6762 (mm-30) outliers start: 37 outliers final: 17 residues processed: 129 average time/residue: 0.5966 time to fit residues: 84.6276 Evaluate side-chains 124 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 645 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 133 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 153 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.0870 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.114930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.090437 restraints weight = 21960.818| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.16 r_work: 0.3145 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14738 Z= 0.123 Angle : 0.497 8.396 19985 Z= 0.269 Chirality : 0.044 0.171 2344 Planarity : 0.004 0.039 2567 Dihedral : 8.329 178.130 2110 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.36 % Favored : 97.59 % Rotamer: Outliers : 2.20 % Allowed : 21.46 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.20), residues: 1865 helix: 2.44 (0.18), residues: 748 sheet: 1.82 (0.25), residues: 423 loop : 0.38 (0.26), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 118 TYR 0.016 0.001 TYR C 334 PHE 0.016 0.001 PHE B 545 TRP 0.008 0.001 TRP A 184 HIS 0.002 0.000 HIS C 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (14738) covalent geometry : angle 0.49682 / 0.27 (19985) hydrogen bonds : bond 0.04541 / 3.01 ( 847) hydrogen bonds : angle 4.76286 / 3.42 ( 2412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8025 (mp) REVERT: A 112 ILE cc_start: 0.5058 (OUTLIER) cc_final: 0.4792 (tp) REVERT: A 223 LYS cc_start: 0.8921 (mttp) cc_final: 0.8567 (mtmm) REVERT: A 230 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7884 (mm-30) REVERT: A 282 GLU cc_start: 0.7542 (pm20) cc_final: 0.6701 (tp30) REVERT: A 394 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8705 (tm) REVERT: A 410 GLN cc_start: 0.5933 (OUTLIER) cc_final: 0.4884 (tm-30) REVERT: A 424 MET cc_start: 0.8880 (ptp) cc_final: 0.8399 (tmt) REVERT: A 428 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8504 (mp0) REVERT: A 616 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7886 (mmmm) REVERT: B 164 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8517 (mp0) REVERT: B 311 GLU cc_start: 0.8086 (tp30) cc_final: 0.7702 (tp30) REVERT: B 315 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8445 (tmmm) REVERT: B 547 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8753 (tp) REVERT: C 105 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8330 (mmtp) REVERT: C 346 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: C 641 GLN cc_start: 0.8812 (tp40) cc_final: 0.8334 (mm-40) REVERT: C 645 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6860 (mm-30) outliers start: 35 outliers final: 18 residues processed: 137 average time/residue: 0.4871 time to fit residues: 74.1181 Evaluate side-chains 128 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 645 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 225 GLN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.111616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.086908 restraints weight = 22312.697| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.18 r_work: 0.3081 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14738 Z= 0.265 Angle : 0.769 45.755 19985 Z= 0.382 Chirality : 0.048 0.198 2344 Planarity : 0.004 0.046 2567 Dihedral : 8.468 174.192 2110 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.68 % Favored : 97.27 % Rotamer: Outliers : 2.39 % Allowed : 21.40 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.20), residues: 1865 helix: 2.21 (0.18), residues: 742 sheet: 1.78 (0.25), residues: 431 loop : 0.25 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 118 TYR 0.018 0.002 TYR C 427 PHE 0.018 0.002 PHE A 545 TRP 0.006 0.002 TRP C 184 HIS 0.004 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.27 (14738) covalent geometry : angle 0.76941 / 0.38 (19985) hydrogen bonds : bond 0.05618 / 3.69 ( 847) hydrogen bonds : angle 5.06747 / 3.65 ( 2412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4647.53 seconds wall clock time: 80 minutes 18.01 seconds (4818.01 seconds total)