Starting phenix.real_space_refine on Fri Jul 3 16:12:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xyi_72335/07_2026/9xyi_72335.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xyi_72335/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9xyi_72335/07_2026/9xyi_72335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xyi_72335/07_2026/9xyi_72335.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xyi_72335/07_2026/9xyi_72335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xyi_72335/07_2026/9xyi_72335.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 3.36, per 1000 atoms: 0.23 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: 1.01 Conformation dependent library (CDL) restraints added in 668.6 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: 0.56 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: 2.47 Time building geometry restraints manager: 1.41 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: 19661 1.46 - 2.92: 251 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: 1888 0.052 - 0.105: 377 0.105 - 0.157: 78 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: 3.170 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.710 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 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:7.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- 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 : 0.468 7.312 19985 Z= 0.262 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 0.00239 / 0.11 (14738) covalent geometry : angle 0.46798 / 0.26 (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 : 0.561 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: 0.5936 time to fit residues: 85.5519 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 : 0.397 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.110673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.085320 restraints weight = 21413.677| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.20 r_work: 0.3033 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14738 Z= 0.219 Angle : 0.545 6.379 19985 Z= 0.302 Chirality : 0.046 0.220 2344 Planarity : 0.004 0.041 2567 Dihedral : 8.792 173.794 2129 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.90 % Allowed : 18.06 % 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: 1.89 (0.20), residues: 1865 helix: 1.88 (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 0.003 0.000 ARG B 111 TYR 0.019 0.002 TYR A 334 PHE 0.020 0.001 PHE B 545 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 0.00481 / 0.22 (14738) covalent geometry : angle 0.54534 / 0.30 (19985) hydrogen bonds : bond 0.07069 / 4.66 ( 847) hydrogen bonds : angle 5.73324 / 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 169 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 107 time to evaluate : 0.576 Fit side-chains REVERT: A 112 ILE cc_start: 0.5247 (OUTLIER) cc_final: 0.4960 (tp) REVERT: A 223 LYS cc_start: 0.9031 (mttp) cc_final: 0.8656 (mtmm) REVERT: A 230 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8031 (mm-30) REVERT: A 282 GLU cc_start: 0.7790 (pm20) cc_final: 0.7174 (tp30) REVERT: A 424 MET cc_start: 0.8971 (ptp) cc_final: 0.8434 (tmt) REVERT: A 617 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7166 (tpt90) REVERT: B 81 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8746 (ttm) REVERT: B 164 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8278 (mp0) REVERT: B 311 GLU cc_start: 0.8048 (tp30) cc_final: 0.7736 (tp30) REVERT: B 315 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8360 (tmmm) REVERT: B 547 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8705 (tp) REVERT: B 606 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8766 (m) REVERT: B 664 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7702 (mp) REVERT: C 346 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: C 410 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.5570 (tp40) REVERT: C 632 GLN cc_start: 0.7534 (tm-30) cc_final: 0.7310 (tm-30) outliers start: 62 outliers final: 24 residues processed: 158 average time/residue: 0.5975 time to fit residues: 103.9356 Evaluate side-chains 133 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 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 602 GLU 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: 0.0770 chunk 44 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 175 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.112667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.087974 restraints weight = 21353.389| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.15 r_work: 0.3073 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1001 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= 0.133 Angle : 0.483 6.363 19985 Z= 0.265 Chirality : 0.044 0.182 2344 Planarity : 0.004 0.055 2567 Dihedral : 8.507 176.190 2112 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.40 % Allowed : 18.57 % 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: 2.16 (0.20), residues: 1865 helix: 2.20 (0.18), residues: 740 sheet: 1.83 (0.25), residues: 427 loop : 0.40 (0.26), residues: 698 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 0.019 0.001 PHE B 663 TRP 0.006 0.001 TRP A 184 HIS 0.002 0.001 HIS C 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (14738) covalent geometry : angle 0.48292 / 0.26 (19985) hydrogen bonds : bond 0.05804 / 3.83 ( 847) hydrogen bonds : angle 5.28322 / 3.80 ( 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 167 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 113 time to evaluate : 0.590 Fit side-chains REVERT: A 112 ILE cc_start: 0.5197 (OUTLIER) cc_final: 0.4928 (tp) REVERT: A 223 LYS cc_start: 0.9015 (mttp) cc_final: 0.8631 (mtmm) REVERT: A 230 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7983 (mm-30) REVERT: A 282 GLU cc_start: 0.7707 (pm20) cc_final: 0.6923 (tp30) REVERT: A 394 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8692 (tm) REVERT: A 424 MET cc_start: 0.8964 (ptp) cc_final: 0.8399 (tmt) REVERT: A 616 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.7905 (mmmm) REVERT: A 617 ARG cc_start: 0.8079 (mtp85) cc_final: 0.7430 (tpt90) REVERT: B 103 ARG cc_start: 0.8118 (mmm160) cc_final: 0.7915 (mmp-170) REVERT: B 164 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8549 (mp0) REVERT: B 311 GLU cc_start: 0.8015 (tp30) cc_final: 0.7684 (tp30) REVERT: B 315 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8349 (tmmm) REVERT: B 547 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8709 (tp) REVERT: B 606 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8657 (m) REVERT: B 664 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7779 (mp) REVERT: C 96 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8099 (tmm) REVERT: C 105 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8384 (mmtp) REVERT: C 346 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: C 415 ILE cc_start: 0.7778 (mt) cc_final: 0.7386 (mp) REVERT: C 632 GLN cc_start: 0.7518 (tm-30) cc_final: 0.7295 (tm-30) REVERT: C 645 GLU cc_start: 0.7080 (tp30) cc_final: 0.6383 (tp30) outliers start: 54 outliers final: 22 residues processed: 158 average time/residue: 0.6168 time to fit residues: 107.3796 Evaluate side-chains 133 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 394 LEU 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 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 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: 0.0970 chunk 111 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 0.0000 chunk 88 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 133 optimal weight: 0.0060 chunk 28 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 overall best weight: 0.4000 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.114347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.089356 restraints weight = 21392.138| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.20 r_work: 0.3100 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14738 Z= 0.116 Angle : 0.469 6.323 19985 Z= 0.255 Chirality : 0.044 0.166 2344 Planarity : 0.004 0.050 2567 Dihedral : 8.468 178.812 2111 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.46 % Allowed : 18.94 % 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: 2.25 (0.20), residues: 1865 helix: 2.33 (0.18), residues: 748 sheet: 1.85 (0.25), residues: 420 loop : 0.40 (0.26), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 118 TYR 0.016 0.001 TYR C 334 PHE 0.020 0.001 PHE B 663 TRP 0.007 0.001 TRP A 184 HIS 0.002 0.000 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (14738) covalent geometry : angle 0.46914 / 0.25 (19985) hydrogen bonds : bond 0.04888 / 3.23 ( 847) hydrogen bonds : angle 4.94739 / 3.55 ( 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 173 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 118 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.5088 (OUTLIER) cc_final: 0.4839 (tp) REVERT: A 223 LYS cc_start: 0.8990 (mttp) cc_final: 0.8606 (mtmm) REVERT: A 230 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7954 (mm-30) REVERT: A 282 GLU cc_start: 0.7646 (pm20) cc_final: 0.6879 (tp30) REVERT: A 394 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8675 (tm) REVERT: A 410 GLN cc_start: 0.5896 (OUTLIER) cc_final: 0.4830 (tm-30) REVERT: A 424 MET cc_start: 0.8941 (ptp) cc_final: 0.8380 (OUTLIER) REVERT: A 616 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.7931 (mmmm) REVERT: A 617 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7264 (tpt90) REVERT: B 164 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8528 (mp0) REVERT: B 311 GLU cc_start: 0.8042 (tp30) cc_final: 0.7689 (tp30) REVERT: B 315 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8358 (tmmm) REVERT: B 547 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8728 (tp) REVERT: B 664 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7809 (mp) REVERT: C 415 ILE cc_start: 0.7662 (mt) cc_final: 0.7455 (mp) REVERT: C 617 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7904 (ttm170) REVERT: C 632 GLN cc_start: 0.7568 (tm-30) cc_final: 0.7323 (tm-30) REVERT: C 645 GLU cc_start: 0.7031 (tp30) cc_final: 0.6314 (tp30) outliers start: 55 outliers final: 22 residues processed: 161 average time/residue: 0.5401 time to fit residues: 95.7635 Evaluate side-chains 137 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 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 56 LEU 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 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 B residue 664 ILE 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 376 MET Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 394 LEU 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 609 THR Chi-restraints excluded: chain C residue 617 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 128 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 59 optimal weight: 0.0470 chunk 126 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 38 optimal weight: 0.0070 chunk 145 optimal weight: 4.9990 overall best weight: 3.2102 ------------------------------------------------------------------------------- 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** C 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.109834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.084399 restraints weight = 21577.061| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.20 r_work: 0.3016 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 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 0.079 14738 Z= 0.303 Angle : 0.588 6.177 19985 Z= 0.320 Chirality : 0.048 0.226 2344 Planarity : 0.005 0.056 2567 Dihedral : 8.689 179.830 2110 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.09 % Allowed : 18.69 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.19), residues: 1865 helix: 2.10 (0.18), residues: 741 sheet: 1.73 (0.25), residues: 430 loop : 0.24 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 118 TYR 0.020 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 0.00686 / 0.30 (14738) covalent geometry : angle 0.58771 / 0.32 (19985) hydrogen bonds : bond 0.06281 / 4.12 ( 847) hydrogen bonds : angle 5.27113 / 3.79 ( 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 168 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 103 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 112 ILE cc_start: 0.5288 (OUTLIER) cc_final: 0.5020 (tp) REVERT: A 223 LYS cc_start: 0.9026 (mttp) cc_final: 0.8651 (mtmm) REVERT: A 230 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8037 (mm-30) REVERT: A 282 GLU cc_start: 0.7769 (pm20) cc_final: 0.7100 (tp30) REVERT: A 424 MET cc_start: 0.8965 (ptp) cc_final: 0.8437 (tmt) REVERT: A 616 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7897 (mmmm) REVERT: B 164 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: B 282 GLU cc_start: 0.8238 (pp20) cc_final: 0.7948 (pp20) REVERT: B 311 GLU cc_start: 0.8081 (tp30) cc_final: 0.7733 (tp30) REVERT: B 315 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8387 (tmmm) REVERT: B 547 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8741 (tp) REVERT: C 105 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8484 (mmtp) REVERT: C 346 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: C 410 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.5325 (tp40) REVERT: C 415 ILE cc_start: 0.7736 (mt) cc_final: 0.7463 (mp) REVERT: C 632 GLN cc_start: 0.7522 (tm-30) cc_final: 0.7297 (tm-30) outliers start: 65 outliers final: 30 residues processed: 157 average time/residue: 0.5285 time to fit residues: 92.0408 Evaluate side-chains 139 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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 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 400 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 547 ILE 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 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 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 440 VAL Chi-restraints excluded: chain C residue 448 LEU 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: 1.9990 chunk 173 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 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** C 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.111517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.086736 restraints weight = 21320.226| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.15 r_work: 0.3052 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14738 Z= 0.161 Angle : 0.511 6.220 19985 Z= 0.278 Chirality : 0.044 0.225 2344 Planarity : 0.004 0.047 2567 Dihedral : 8.609 176.920 2110 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.80 % Rotamer: Outliers : 3.65 % Allowed : 19.45 % Favored : 76.90 % 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: 2.12 (0.20), residues: 1865 helix: 2.26 (0.18), residues: 742 sheet: 1.73 (0.25), residues: 427 loop : 0.31 (0.26), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 118 TYR 0.017 0.001 TYR C 334 PHE 0.019 0.001 PHE A 545 TRP 0.006 0.001 TRP C 184 HIS 0.002 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (14738) covalent geometry : angle 0.51098 / 0.28 (19985) hydrogen bonds : bond 0.05490 / 3.62 ( 847) hydrogen bonds : angle 5.07688 / 3.65 ( 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 162 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 104 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 112 ILE cc_start: 0.5239 (OUTLIER) cc_final: 0.4977 (tp) REVERT: A 223 LYS cc_start: 0.9012 (mttp) cc_final: 0.8633 (mtmm) REVERT: A 230 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7980 (mm-30) REVERT: A 282 GLU cc_start: 0.7691 (pm20) cc_final: 0.6980 (tp30) REVERT: A 424 MET cc_start: 0.8971 (ptp) cc_final: 0.8404 (tmt) REVERT: A 616 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7865 (mmmm) REVERT: B 164 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: B 311 GLU cc_start: 0.8054 (tp30) cc_final: 0.7696 (tp30) REVERT: B 315 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8387 (tmmm) REVERT: B 547 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8743 (tp) REVERT: C 105 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8498 (mmtp) REVERT: C 346 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: C 408 SER cc_start: 0.7624 (t) cc_final: 0.7233 (p) REVERT: C 415 ILE cc_start: 0.7717 (mt) cc_final: 0.7427 (mp) REVERT: C 632 GLN cc_start: 0.7467 (tm-30) cc_final: 0.7236 (tm-30) outliers start: 58 outliers final: 32 residues processed: 150 average time/residue: 0.5568 time to fit residues: 92.3381 Evaluate side-chains 140 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 610 VAL Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 112 ILE 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 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 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 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 394 LEU Chi-restraints excluded: chain C residue 398 THR 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 610 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 178 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 0.0570 chunk 70 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.111914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.087165 restraints weight = 21202.371| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.14 r_work: 0.3060 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14738 Z= 0.157 Angle : 0.503 6.461 19985 Z= 0.273 Chirality : 0.044 0.183 2344 Planarity : 0.004 0.046 2567 Dihedral : 8.537 175.334 2110 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.36 % Favored : 97.59 % Rotamer: Outliers : 3.65 % Allowed : 19.63 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.20), residues: 1865 helix: 2.35 (0.18), residues: 740 sheet: 1.74 (0.25), residues: 428 loop : 0.32 (0.26), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 118 TYR 0.016 0.001 TYR C 334 PHE 0.018 0.001 PHE A 545 TRP 0.006 0.001 TRP C 184 HIS 0.002 0.000 HIS C 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (14738) covalent geometry : angle 0.50258 / 0.27 (19985) hydrogen bonds : bond 0.05231 / 3.45 ( 847) hydrogen bonds : angle 4.98009 / 3.58 ( 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 160 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 102 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8017 (mp) REVERT: A 112 ILE cc_start: 0.5164 (OUTLIER) cc_final: 0.4902 (tp) REVERT: A 223 LYS cc_start: 0.9015 (mttp) cc_final: 0.8637 (mtmm) REVERT: A 230 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: A 282 GLU cc_start: 0.7675 (pm20) cc_final: 0.6961 (tp30) REVERT: A 410 GLN cc_start: 0.5978 (OUTLIER) cc_final: 0.4859 (tm-30) REVERT: A 424 MET cc_start: 0.8962 (ptp) cc_final: 0.8399 (tmt) REVERT: A 616 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7898 (mmmm) REVERT: B 164 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8573 (mp0) REVERT: B 282 GLU cc_start: 0.8223 (pp20) cc_final: 0.7944 (pp20) REVERT: B 311 GLU cc_start: 0.8042 (tp30) cc_final: 0.7681 (tp30) REVERT: B 315 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8388 (tmmm) REVERT: B 547 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8748 (tp) REVERT: C 96 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8126 (tmm) REVERT: C 105 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8312 (mmtp) REVERT: C 346 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: C 415 ILE cc_start: 0.7782 (mt) cc_final: 0.7539 (mp) REVERT: C 632 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7304 (tm-30) REVERT: C 645 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6263 (tp30) outliers start: 58 outliers final: 31 residues processed: 149 average time/residue: 0.5382 time to fit residues: 88.6578 Evaluate side-chains 141 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 610 VAL Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 112 ILE 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 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 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 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 394 LEU Chi-restraints excluded: chain C residue 398 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 609 THR Chi-restraints excluded: chain C residue 610 VAL 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: 0.0970 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 138 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.111744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.086430 restraints weight = 21257.750| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.18 r_work: 0.3050 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14738 Z= 0.182 Angle : 0.518 6.374 19985 Z= 0.281 Chirality : 0.045 0.179 2344 Planarity : 0.004 0.045 2567 Dihedral : 8.525 174.767 2110 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.53 % Rotamer: Outliers : 3.40 % Allowed : 19.95 % 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: 2.16 (0.20), residues: 1865 helix: 2.32 (0.18), residues: 740 sheet: 1.75 (0.25), residues: 429 loop : 0.30 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 118 TYR 0.016 0.001 TYR C 334 PHE 0.019 0.001 PHE A 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 0.00402 / 0.18 (14738) covalent geometry : angle 0.51818 / 0.28 (19985) hydrogen bonds : bond 0.05356 / 3.53 ( 847) hydrogen bonds : angle 5.00640 / 3.60 ( 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 154 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 100 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8047 (mp) REVERT: A 112 ILE cc_start: 0.5113 (OUTLIER) cc_final: 0.4836 (tp) REVERT: A 223 LYS cc_start: 0.9015 (mttp) cc_final: 0.8633 (mtmm) REVERT: A 230 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7986 (mm-30) REVERT: A 282 GLU cc_start: 0.7678 (pm20) cc_final: 0.6995 (tp30) REVERT: A 410 GLN cc_start: 0.6108 (OUTLIER) cc_final: 0.4937 (tm-30) REVERT: A 424 MET cc_start: 0.8981 (ptp) cc_final: 0.8407 (tmt) REVERT: A 616 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7910 (mmmm) REVERT: B 123 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7356 (p) REVERT: B 164 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: B 311 GLU cc_start: 0.8057 (tp30) cc_final: 0.7690 (tp30) REVERT: B 315 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8408 (tmmm) REVERT: B 547 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8750 (tp) REVERT: C 96 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8159 (tmm) REVERT: C 105 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8349 (mmtp) REVERT: C 346 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8037 (tm-30) REVERT: C 410 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6960 (tp40) REVERT: C 415 ILE cc_start: 0.7718 (mt) cc_final: 0.7467 (mp) REVERT: C 632 GLN cc_start: 0.7559 (tm-30) cc_final: 0.7327 (tm-30) REVERT: C 645 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6776 (mm-30) outliers start: 54 outliers final: 29 residues processed: 145 average time/residue: 0.5519 time to fit residues: 88.9889 Evaluate side-chains 140 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 610 VAL 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 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 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 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 394 LEU Chi-restraints excluded: chain C residue 398 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 609 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 637 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: 0.0050 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 179 optimal weight: 0.5980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.113613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.089093 restraints weight = 21282.689| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.13 r_work: 0.3096 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1385 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= 0.122 Angle : 0.483 6.683 19985 Z= 0.262 Chirality : 0.044 0.161 2344 Planarity : 0.004 0.038 2567 Dihedral : 8.385 177.243 2110 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.36 % Favored : 97.59 % Rotamer: Outliers : 2.64 % Allowed : 20.96 % 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: 2.30 (0.20), residues: 1865 helix: 2.44 (0.18), residues: 746 sheet: 1.79 (0.25), residues: 428 loop : 0.37 (0.26), residues: 691 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 0.018 0.001 PHE A 545 TRP 0.008 0.002 TRP B 184 HIS 0.002 0.000 HIS C 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (14738) covalent geometry : angle 0.48328 / 0.26 (19985) hydrogen bonds : bond 0.04705 / 3.12 ( 847) hydrogen bonds : angle 4.81767 / 3.46 ( 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 150 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7987 (mp) REVERT: A 112 ILE cc_start: 0.5069 (OUTLIER) cc_final: 0.4787 (tp) REVERT: A 223 LYS cc_start: 0.8976 (mttp) cc_final: 0.8615 (mtmm) REVERT: A 230 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7946 (mm-30) REVERT: A 410 GLN cc_start: 0.6134 (OUTLIER) cc_final: 0.4909 (tm-30) REVERT: A 424 MET cc_start: 0.8929 (ptp) cc_final: 0.8377 (tmt) REVERT: A 616 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7880 (mmmm) REVERT: B 164 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: B 282 GLU cc_start: 0.8275 (pp20) cc_final: 0.7896 (pp20) REVERT: B 311 GLU cc_start: 0.8069 (tp30) cc_final: 0.7700 (tp30) REVERT: B 315 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8416 (tmmm) REVERT: B 547 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8764 (tp) REVERT: C 105 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8272 (mmtp) REVERT: C 352 VAL cc_start: 0.8179 (t) cc_final: 0.7949 (p) REVERT: C 410 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6937 (tp40) REVERT: C 415 ILE cc_start: 0.7733 (mt) cc_final: 0.7495 (mp) REVERT: C 617 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7861 (ttm170) REVERT: C 632 GLN cc_start: 0.7510 (tm-30) cc_final: 0.7279 (tm-30) REVERT: C 645 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6770 (mm-30) outliers start: 42 outliers final: 22 residues processed: 143 average time/residue: 0.5221 time to fit residues: 82.9416 Evaluate side-chains 134 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 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 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 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 379 THR Chi-restraints excluded: chain C residue 394 LEU 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 609 THR Chi-restraints excluded: chain C residue 617 ARG 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: 0.7980 chunk 89 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.0050 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.114609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.090062 restraints weight = 21939.466| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.15 r_work: 0.3142 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1442 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= 0.126 Angle : 0.498 8.053 19985 Z= 0.269 Chirality : 0.044 0.162 2344 Planarity : 0.004 0.039 2567 Dihedral : 8.326 177.319 2110 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.48 % Rotamer: Outliers : 2.64 % Allowed : 20.96 % 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: 2.32 (0.20), residues: 1865 helix: 2.46 (0.18), residues: 747 sheet: 1.79 (0.25), residues: 430 loop : 0.39 (0.26), residues: 688 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 0.007 0.001 TRP A 184 HIS 0.002 0.000 HIS C 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (14738) covalent geometry : angle 0.49818 / 0.27 (19985) hydrogen bonds : bond 0.04627 / 3.06 ( 847) hydrogen bonds : angle 4.77987 / 3.43 ( 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 148 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 106 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7986 (mp) REVERT: A 112 ILE cc_start: 0.5034 (OUTLIER) cc_final: 0.4765 (tp) REVERT: A 223 LYS cc_start: 0.8948 (mttp) cc_final: 0.8596 (mtmm) REVERT: A 230 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7907 (mm-30) REVERT: A 282 GLU cc_start: 0.7570 (pm20) cc_final: 0.6755 (tp30) REVERT: A 410 GLN cc_start: 0.6110 (OUTLIER) cc_final: 0.4873 (tm-30) REVERT: A 424 MET cc_start: 0.8884 (ptp) cc_final: 0.8394 (tmt) REVERT: A 616 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7889 (mmmm) REVERT: B 164 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8528 (mp0) REVERT: B 282 GLU cc_start: 0.8240 (pp20) cc_final: 0.7917 (pp20) REVERT: B 311 GLU cc_start: 0.8083 (tp30) cc_final: 0.7698 (tp30) REVERT: B 315 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8436 (tmmm) REVERT: B 547 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8754 (tp) REVERT: C 105 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8307 (mmtp) REVERT: C 346 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: C 352 VAL cc_start: 0.8180 (t) cc_final: 0.7957 (p) REVERT: C 410 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6913 (tp40) REVERT: C 415 ILE cc_start: 0.7758 (mt) cc_final: 0.7519 (mp) REVERT: C 617 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7996 (ttm170) REVERT: C 645 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6786 (mm-30) outliers start: 42 outliers final: 21 residues processed: 141 average time/residue: 0.5966 time to fit residues: 93.0780 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 : 0.597 ------------------------------------------------------------------------------- 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 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 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 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 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 609 THR Chi-restraints excluded: chain C residue 617 ARG 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: 0.9990 chunk 156 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 225 GLN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.110465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.085739 restraints weight = 22254.366| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.16 r_work: 0.3063 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 14738 Z= 0.314 Angle : 0.620 7.155 19985 Z= 0.336 Chirality : 0.049 0.229 2344 Planarity : 0.005 0.062 2567 Dihedral : 8.578 171.644 2110 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.16 % Rotamer: Outliers : 2.45 % Allowed : 20.96 % Favored : 76.59 % 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: 1.93 (0.20), residues: 1865 helix: 2.08 (0.18), residues: 740 sheet: 1.69 (0.25), residues: 432 loop : 0.19 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 111 TYR 0.019 0.002 TYR C 427 PHE 0.021 0.002 PHE A 545 TRP 0.007 0.002 TRP C 184 HIS 0.005 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.31 (14738) covalent geometry : angle 0.61984 / 0.34 (19985) hydrogen bonds : bond 0.06192 / 4.07 ( 847) hydrogen bonds : angle 5.21338 / 3.75 ( 2412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4322.70 seconds wall clock time: 74 minutes 36.39 seconds (4476.39 seconds total)