Starting phenix.real_space_refine on Thu Feb 5 03:46:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xyi_72335/02_2026/9xyi_72335.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xyi_72335/02_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_72335/02_2026/9xyi_72335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xyi_72335/02_2026/9xyi_72335.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xyi_72335/02_2026/9xyi_72335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xyi_72335/02_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-2.0-5952/lib/python3.9/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: 3.83, per 1000 atoms: 0.26 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: 1.52 Conformation dependent library (CDL) restraints added in 792.0 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: 0.60 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: 2.92 Time building geometry restraints manager: 1.92 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=" 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 bond pdb=" CB LYS B 126 " pdb=" CG LYS B 126 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.02e-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=" N VAL C 162 " pdb=" CA VAL C 162 " pdb=" C VAL C 162 " ideal model delta sigma weight residual 111.62 109.08 2.54 7.90e-01 1.60e+00 1.04e+01 angle pdb=" CA GLU C 293 " pdb=" CB GLU C 293 " pdb=" CG GLU C 293 " ideal model delta sigma weight residual 114.10 120.09 -5.99 2.00e+00 2.50e-01 8.97e+00 angle pdb=" CB GLU C 293 " pdb=" CG GLU C 293 " pdb=" CD GLU C 293 " ideal model delta sigma weight residual 112.60 117.65 -5.05 1.70e+00 3.46e-01 8.84e+00 angle pdb=" C ARG B 464 " pdb=" N ASP B 465 " pdb=" CA ASP B 465 " ideal model delta sigma weight residual 121.54 127.04 -5.50 1.91e+00 2.74e-01 8.30e+00 angle pdb=" CB GLU C 330 " pdb=" CG GLU C 330 " pdb=" CD GLU C 330 " ideal model delta sigma weight residual 112.60 117.38 -4.78 1.70e+00 3.46e-01 7.92e+00 ... (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: 3.960 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: 0.040 Set scattering table: 0.050 Process input model: 15.950 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:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 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= 0.108 Angle : 0.468 7.312 19985 Z= 0.249 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 covalent geometry : bond 0.00239 (14738) covalent geometry : angle 0.46797 (19985) hydrogen bonds : bond 0.21473 ( 847) hydrogen bonds : angle 7.89597 ( 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 : 0.612 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: 0.6940 time to fit residues: 99.5599 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 : 0.542 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN B 155 ASN C 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.110695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.085347 restraints weight = 21413.335| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.19 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: 0.8633 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14738 Z= 0.219 Angle : 0.545 6.614 19985 Z= 0.300 Chirality : 0.046 0.211 2344 Planarity : 0.004 0.040 2567 Dihedral : 8.732 171.802 2129 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.09 % Allowed : 17.94 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.87 (0.18), residues: 739 sheet: 1.78 (0.25), residues: 424 loop : 0.34 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 111 TYR 0.016 0.002 TYR A 334 PHE 0.018 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 covalent geometry : bond 0.00482 (14738) covalent geometry : angle 0.54493 (19985) hydrogen bonds : bond 0.06812 ( 847) hydrogen bonds : angle 5.63106 ( 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 173 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 108 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 112 ILE cc_start: 0.5258 (OUTLIER) cc_final: 0.4966 (tp) REVERT: A 223 LYS cc_start: 0.9035 (mttp) cc_final: 0.8658 (mtmm) REVERT: A 230 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8028 (mm-30) REVERT: A 282 GLU cc_start: 0.7765 (pm20) cc_final: 0.7075 (tp30) REVERT: A 424 MET cc_start: 0.8987 (ptp) cc_final: 0.8443 (tmt) REVERT: A 616 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7883 (mmmm) REVERT: A 617 ARG cc_start: 0.8114 (mtp85) cc_final: 0.7235 (tpt90) REVERT: B 81 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8746 (ttm) REVERT: B 164 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: B 311 GLU cc_start: 0.8029 (tp30) cc_final: 0.7713 (tp30) REVERT: B 315 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8358 (tmmm) REVERT: B 547 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8692 (tp) REVERT: B 606 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8751 (m) REVERT: B 664 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7727 (mp) REVERT: C 346 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: C 632 GLN cc_start: 0.7568 (tm-30) cc_final: 0.6907 (mt0) outliers start: 65 outliers final: 25 residues processed: 162 average time/residue: 0.6533 time to fit residues: 115.8459 Evaluate side-chains 135 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 A residue 616 LYS 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 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 394 LEU 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: 0.0170 chunk 44 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3614 r_free = 0.3614 target = 0.112328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.087566 restraints weight = 21379.071| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.15 r_work: 0.3071 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14738 Z= 0.143 Angle : 0.492 6.486 19985 Z= 0.267 Chirality : 0.044 0.184 2344 Planarity : 0.004 0.054 2567 Dihedral : 8.429 173.240 2112 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.78 % Allowed : 18.44 % Favored : 77.78 % 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: 2.13 (0.20), residues: 1865 helix: 2.19 (0.18), residues: 741 sheet: 1.76 (0.25), residues: 430 loop : 0.39 (0.26), residues: 694 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 0.025 0.001 PHE B 663 TRP 0.006 0.001 TRP A 184 HIS 0.002 0.000 HIS C 304 Details of bonding type rmsd covalent geometry : bond 0.00299 (14738) covalent geometry : angle 0.49176 (19985) hydrogen bonds : bond 0.05632 ( 847) hydrogen bonds : angle 5.20857 ( 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 175 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 115 time to evaluate : 0.624 Fit side-chains REVERT: A 112 ILE cc_start: 0.5186 (OUTLIER) cc_final: 0.4925 (tp) REVERT: A 223 LYS cc_start: 0.9016 (mttp) cc_final: 0.8639 (mtmm) REVERT: A 230 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7967 (mm-30) REVERT: A 282 GLU cc_start: 0.7709 (pm20) cc_final: 0.6925 (tp30) REVERT: A 394 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8698 (tm) REVERT: A 424 MET cc_start: 0.8986 (ptp) cc_final: 0.8416 (tmt) REVERT: A 428 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8517 (mp0) REVERT: A 616 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.7920 (mmmm) REVERT: A 617 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7441 (tpt90) REVERT: B 164 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8561 (mp0) REVERT: B 311 GLU cc_start: 0.8042 (tp30) cc_final: 0.7708 (tp30) REVERT: B 315 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8363 (tmmm) REVERT: B 547 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8729 (tp) REVERT: B 606 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8717 (m) REVERT: B 664 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7771 (mp) REVERT: C 96 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8113 (tmm) REVERT: C 105 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8415 (mmtp) REVERT: C 346 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: C 415 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7358 (mp) REVERT: C 632 GLN cc_start: 0.7529 (tm-30) cc_final: 0.7292 (tm-30) outliers start: 60 outliers final: 27 residues processed: 162 average time/residue: 0.6283 time to fit residues: 111.6008 Evaluate side-chains 143 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 103 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 206 ARG Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 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 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 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 379 THR Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 610 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 131 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 73 optimal weight: 0.3980 chunk 88 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 133 optimal weight: 0.1980 chunk 28 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 122 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3597 r_free = 0.3597 target = 0.111198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.086421 restraints weight = 21438.081| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.15 r_work: 0.3044 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14738 Z= 0.189 Angle : 0.515 6.549 19985 Z= 0.279 Chirality : 0.045 0.198 2344 Planarity : 0.004 0.046 2567 Dihedral : 8.469 172.033 2111 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.47 % Allowed : 18.19 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.20), residues: 1865 helix: 2.23 (0.18), residues: 742 sheet: 1.73 (0.25), residues: 430 loop : 0.33 (0.26), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 118 TYR 0.016 0.002 TYR C 334 PHE 0.019 0.001 PHE B 663 TRP 0.006 0.001 TRP C 184 HIS 0.003 0.001 HIS C 304 Details of bonding type rmsd covalent geometry : bond 0.00419 (14738) covalent geometry : angle 0.51488 (19985) hydrogen bonds : bond 0.05678 ( 847) hydrogen bonds : angle 5.15723 ( 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 176 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 105 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.5265 (OUTLIER) cc_final: 0.4995 (tp) REVERT: A 223 LYS cc_start: 0.9021 (mttp) cc_final: 0.8630 (mtmm) REVERT: A 230 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7986 (mm-30) REVERT: A 282 GLU cc_start: 0.7723 (pm20) cc_final: 0.7007 (tp30) REVERT: A 410 GLN cc_start: 0.5872 (OUTLIER) cc_final: 0.4878 (tm-30) REVERT: A 424 MET cc_start: 0.8979 (ptp) cc_final: 0.8422 (tmt) REVERT: A 428 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8483 (mp0) REVERT: A 617 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7291 (tpt90) REVERT: B 164 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8220 (mp0) REVERT: B 282 GLU cc_start: 0.8254 (pp20) cc_final: 0.7959 (pp20) REVERT: B 311 GLU cc_start: 0.8043 (tp30) cc_final: 0.7704 (tp30) REVERT: B 315 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8374 (tmmm) REVERT: B 547 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8745 (tp) REVERT: C 96 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8192 (tmm) REVERT: C 346 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: C 415 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7390 (mp) REVERT: C 632 GLN cc_start: 0.7521 (tm-30) cc_final: 0.7284 (tm-30) outliers start: 71 outliers final: 34 residues processed: 158 average time/residue: 0.6469 time to fit residues: 112.1455 Evaluate side-chains 148 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 206 ARG Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 128 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 38 optimal weight: 0.0670 chunk 145 optimal weight: 2.9990 overall best weight: 1.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3589 r_free = 0.3589 target = 0.110684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.085893 restraints weight = 21421.571| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.15 r_work: 0.3034 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14738 Z= 0.211 Angle : 0.531 6.550 19985 Z= 0.287 Chirality : 0.046 0.196 2344 Planarity : 0.004 0.051 2567 Dihedral : 8.531 171.847 2111 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.34 % Allowed : 18.50 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.20), residues: 1865 helix: 2.25 (0.18), residues: 736 sheet: 1.71 (0.25), residues: 431 loop : 0.33 (0.26), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 118 TYR 0.016 0.002 TYR C 334 PHE 0.019 0.001 PHE A 545 TRP 0.006 0.001 TRP C 184 HIS 0.003 0.001 HIS C 304 Details of bonding type rmsd covalent geometry : bond 0.00471 (14738) covalent geometry : angle 0.53082 (19985) hydrogen bonds : bond 0.05754 ( 847) hydrogen bonds : angle 5.15590 ( 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 177 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 108 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.5305 (OUTLIER) cc_final: 0.5042 (tp) REVERT: A 223 LYS cc_start: 0.9020 (mttp) cc_final: 0.8641 (mtmm) REVERT: A 230 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8002 (mm-30) REVERT: A 282 GLU cc_start: 0.7712 (pm20) cc_final: 0.7010 (tp30) REVERT: A 410 GLN cc_start: 0.5850 (OUTLIER) cc_final: 0.4847 (tm-30) REVERT: A 424 MET cc_start: 0.8980 (ptp) cc_final: 0.8419 (tmt) REVERT: A 616 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7869 (mmmm) REVERT: B 123 THR cc_start: 0.7712 (OUTLIER) cc_final: 0.7494 (p) REVERT: B 164 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8234 (mp0) REVERT: B 282 GLU cc_start: 0.8281 (pp20) cc_final: 0.7959 (pp20) REVERT: B 311 GLU cc_start: 0.8060 (tp30) cc_final: 0.7709 (tp30) REVERT: B 315 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8387 (tmmm) REVERT: B 547 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8741 (tp) REVERT: C 96 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8179 (tmm) REVERT: C 105 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8523 (mmtp) REVERT: C 346 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: C 408 SER cc_start: 0.7601 (t) cc_final: 0.7206 (p) REVERT: C 415 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7321 (mp) REVERT: C 632 GLN cc_start: 0.7522 (tm-30) cc_final: 0.7294 (tm-30) outliers start: 69 outliers final: 38 residues processed: 166 average time/residue: 0.5787 time to fit residues: 106.7608 Evaluate side-chains 149 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 99 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 88 THR 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 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 638 THR 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 415 ILE Chi-restraints excluded: chain C residue 440 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 23 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3611 r_free = 0.3611 target = 0.112231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.086999 restraints weight = 21342.751| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.19 r_work: 0.3057 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14738 Z= 0.155 Angle : 0.504 7.003 19985 Z= 0.272 Chirality : 0.045 0.189 2344 Planarity : 0.004 0.050 2567 Dihedral : 8.461 172.051 2111 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.59 % Allowed : 19.57 % Favored : 76.84 % 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: 2.21 (0.20), residues: 1865 helix: 2.38 (0.18), residues: 736 sheet: 1.71 (0.25), residues: 431 loop : 0.36 (0.26), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 118 TYR 0.017 0.001 TYR C 334 PHE 0.018 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 covalent geometry : bond 0.00336 (14738) covalent geometry : angle 0.50363 (19985) hydrogen bonds : bond 0.05234 ( 847) hydrogen bonds : angle 5.00395 ( 2412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 108 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8016 (mp) REVERT: A 112 ILE cc_start: 0.5225 (OUTLIER) cc_final: 0.4940 (tp) REVERT: A 223 LYS cc_start: 0.9010 (mttp) cc_final: 0.8624 (mtmm) REVERT: A 230 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8002 (mm-30) REVERT: A 282 GLU cc_start: 0.7686 (pm20) cc_final: 0.6968 (tp30) REVERT: A 410 GLN cc_start: 0.5838 (OUTLIER) cc_final: 0.4838 (tm-30) REVERT: A 424 MET cc_start: 0.8971 (ptp) cc_final: 0.8410 (tmt) REVERT: A 428 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8575 (mp0) REVERT: A 616 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7860 (mmmm) REVERT: B 164 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: B 282 GLU cc_start: 0.8284 (pp20) cc_final: 0.8004 (pp20) REVERT: B 311 GLU cc_start: 0.8054 (tp30) cc_final: 0.7692 (tp30) REVERT: B 315 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8395 (tmmm) REVERT: B 547 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8746 (tp) REVERT: C 96 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8144 (tmm) REVERT: C 105 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8505 (mmtp) REVERT: C 346 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: C 415 ILE cc_start: 0.7727 (mt) cc_final: 0.7362 (mp) REVERT: C 617 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7876 (ttm170) REVERT: C 632 GLN cc_start: 0.7468 (tm-30) cc_final: 0.7255 (tm-30) REVERT: C 645 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6765 (mm-30) outliers start: 57 outliers final: 31 residues processed: 150 average time/residue: 0.5846 time to fit residues: 96.8232 Evaluate side-chains 147 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 103 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 206 ARG Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 448 LEU 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 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 410 GLN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 645 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 178 optimal weight: 0.2980 chunk 133 optimal weight: 0.0870 chunk 21 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 167 optimal weight: 0.5980 overall best weight: 0.4960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3668 r_free = 0.3668 target = 0.115383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.091025 restraints weight = 21980.118| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.16 r_work: 0.3155 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1454 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= 0.113 Angle : 0.481 8.167 19985 Z= 0.257 Chirality : 0.044 0.159 2344 Planarity : 0.004 0.047 2567 Dihedral : 8.323 176.648 2111 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.09 % Favored : 97.86 % Rotamer: Outliers : 3.15 % Allowed : 20.26 % 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: 2.35 (0.20), residues: 1865 helix: 2.51 (0.18), residues: 742 sheet: 1.77 (0.25), residues: 431 loop : 0.40 (0.26), residues: 692 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 0.017 0.001 PHE A 545 TRP 0.009 0.002 TRP A 184 HIS 0.001 0.000 HIS C 304 Details of bonding type rmsd covalent geometry : bond 0.00233 (14738) covalent geometry : angle 0.48059 (19985) hydrogen bonds : bond 0.04409 ( 847) hydrogen bonds : angle 4.73919 ( 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 169 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8031 (mp) REVERT: A 112 ILE cc_start: 0.5023 (OUTLIER) cc_final: 0.4765 (tp) REVERT: A 223 LYS cc_start: 0.8933 (mttp) cc_final: 0.8570 (mtmm) REVERT: A 230 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7878 (mm-30) REVERT: A 394 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8684 (tm) REVERT: A 410 GLN cc_start: 0.5951 (OUTLIER) cc_final: 0.4938 (tm-30) REVERT: A 424 MET cc_start: 0.8862 (ptp) cc_final: 0.8386 (tmt) REVERT: A 428 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8493 (mp0) REVERT: A 616 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.7882 (mmmm) REVERT: B 164 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: B 282 GLU cc_start: 0.8297 (pp20) cc_final: 0.8028 (pp20) REVERT: B 311 GLU cc_start: 0.8060 (tp30) cc_final: 0.7679 (tp30) REVERT: B 315 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8431 (tmmm) REVERT: B 547 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8739 (tp) REVERT: C 105 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8331 (mmtp) REVERT: C 352 VAL cc_start: 0.8135 (t) cc_final: 0.7888 (p) REVERT: C 415 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7374 (mp) REVERT: C 617 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7777 (ttm170) REVERT: C 641 GLN cc_start: 0.8780 (tp40) cc_final: 0.8287 (tm-30) REVERT: C 645 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6805 (mm-30) outliers start: 50 outliers final: 20 residues processed: 156 average time/residue: 0.6144 time to fit residues: 106.0441 Evaluate side-chains 138 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 206 ARG 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 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 610 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 645 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.0040 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 149 optimal weight: 0.4980 chunk 174 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN B 155 ASN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.112293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.087710 restraints weight = 22204.260| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.16 r_work: 0.3093 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14738 Z= 0.203 Angle : 0.538 7.495 19985 Z= 0.289 Chirality : 0.046 0.196 2344 Planarity : 0.004 0.041 2567 Dihedral : 8.428 172.391 2110 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.36 % Favored : 97.59 % Rotamer: Outliers : 3.15 % Allowed : 20.45 % 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: 2.24 (0.20), residues: 1865 helix: 2.41 (0.18), residues: 736 sheet: 1.75 (0.25), residues: 434 loop : 0.35 (0.26), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 118 TYR 0.016 0.002 TYR A 334 PHE 0.018 0.001 PHE A 545 TRP 0.006 0.001 TRP C 184 HIS 0.003 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00457 (14738) covalent geometry : angle 0.53795 (19985) hydrogen bonds : bond 0.05400 ( 847) hydrogen bonds : angle 4.99067 ( 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 156 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 106 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8058 (mp) REVERT: A 112 ILE cc_start: 0.5047 (OUTLIER) cc_final: 0.4776 (tp) REVERT: A 223 LYS cc_start: 0.8985 (mttp) cc_final: 0.8618 (mtmm) REVERT: A 230 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7926 (mm-30) REVERT: A 282 GLU cc_start: 0.7725 (pm20) cc_final: 0.6965 (tp30) REVERT: A 410 GLN cc_start: 0.6017 (OUTLIER) cc_final: 0.4850 (tm-30) REVERT: A 424 MET cc_start: 0.9004 (ptp) cc_final: 0.8455 (tmt) REVERT: A 428 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8553 (mp0) REVERT: A 616 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7930 (mmmm) REVERT: B 123 THR cc_start: 0.7816 (m) cc_final: 0.7560 (p) REVERT: B 164 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8636 (mp0) REVERT: B 282 GLU cc_start: 0.8275 (pp20) cc_final: 0.7980 (pp20) REVERT: B 311 GLU cc_start: 0.8095 (tp30) cc_final: 0.7725 (tp30) REVERT: B 315 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8421 (tmmm) REVERT: B 547 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8751 (tp) REVERT: C 105 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8534 (mmtp) REVERT: C 346 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: C 410 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6957 (tp40) REVERT: C 415 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7401 (mp) REVERT: C 632 GLN cc_start: 0.7543 (tm-30) cc_final: 0.7287 (tm-30) REVERT: C 641 GLN cc_start: 0.8872 (tp40) cc_final: 0.8659 (tp-100) REVERT: C 645 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6904 (mm-30) outliers start: 50 outliers final: 20 residues processed: 149 average time/residue: 0.6184 time to fit residues: 102.1841 Evaluate side-chains 138 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 616 LYS 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 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 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 346 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 645 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 169 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 182 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3645 r_free = 0.3645 target = 0.113704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.089199 restraints weight = 22158.075| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.16 r_work: 0.3123 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1410 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= 0.142 Angle : 0.508 10.044 19985 Z= 0.272 Chirality : 0.044 0.159 2344 Planarity : 0.004 0.040 2567 Dihedral : 8.362 173.749 2109 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.80 % Rotamer: Outliers : 2.71 % Allowed : 20.70 % 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: 2.31 (0.20), residues: 1865 helix: 2.44 (0.18), residues: 744 sheet: 1.77 (0.25), residues: 432 loop : 0.41 (0.26), residues: 689 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 0.006 0.001 TRP A 184 HIS 0.002 0.000 HIS C 304 Details of bonding type rmsd covalent geometry : bond 0.00309 (14738) covalent geometry : angle 0.50841 (19985) hydrogen bonds : bond 0.04905 ( 847) hydrogen bonds : angle 4.86180 ( 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 149 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 106 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8065 (mp) REVERT: A 112 ILE cc_start: 0.5036 (OUTLIER) cc_final: 0.4765 (tp) REVERT: A 223 LYS cc_start: 0.8950 (mttp) cc_final: 0.8588 (mtmm) REVERT: A 230 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7909 (mm-30) REVERT: A 282 GLU cc_start: 0.7655 (pm20) cc_final: 0.6858 (tp30) REVERT: A 394 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8715 (tm) REVERT: A 410 GLN cc_start: 0.6014 (OUTLIER) cc_final: 0.4920 (tm-30) REVERT: A 424 MET cc_start: 0.9003 (ptp) cc_final: 0.8444 (tmt) REVERT: A 428 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8526 (mp0) REVERT: A 616 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7905 (mmmm) REVERT: B 164 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8623 (mp0) REVERT: B 282 GLU cc_start: 0.8270 (pp20) cc_final: 0.7963 (pp20) REVERT: B 311 GLU cc_start: 0.8070 (tp30) cc_final: 0.7688 (tp30) REVERT: B 315 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8419 (tmmm) REVERT: B 547 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8780 (tp) REVERT: C 105 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8511 (mmtp) REVERT: C 415 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7417 (mp) REVERT: C 645 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6870 (mm-30) outliers start: 43 outliers final: 24 residues processed: 141 average time/residue: 0.6681 time to fit residues: 104.0702 Evaluate side-chains 139 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 394 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 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 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 376 MET Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 645 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 133 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 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: 0.8980 chunk 165 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3652 r_free = 0.3652 target = 0.114087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.089655 restraints weight = 22072.503| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.17 r_work: 0.3127 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14738 Z= 0.135 Angle : 0.511 8.306 19985 Z= 0.273 Chirality : 0.044 0.171 2344 Planarity : 0.004 0.069 2567 Dihedral : 8.344 174.789 2109 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.53 % Rotamer: Outliers : 2.58 % Allowed : 21.08 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.20), residues: 1865 helix: 2.47 (0.18), residues: 744 sheet: 1.79 (0.25), residues: 431 loop : 0.40 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 118 TYR 0.016 0.001 TYR C 334 PHE 0.018 0.001 PHE A 545 TRP 0.006 0.001 TRP A 184 HIS 0.002 0.000 HIS C 304 Details of bonding type rmsd covalent geometry : bond 0.00292 (14738) covalent geometry : angle 0.51094 (19985) hydrogen bonds : bond 0.04756 ( 847) hydrogen bonds : angle 4.81295 ( 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 143 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 102 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8042 (mp) REVERT: A 112 ILE cc_start: 0.4959 (OUTLIER) cc_final: 0.4688 (tp) REVERT: A 223 LYS cc_start: 0.8949 (mttp) cc_final: 0.8585 (mtmm) REVERT: A 230 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7910 (mm-30) REVERT: A 282 GLU cc_start: 0.7636 (pm20) cc_final: 0.6786 (tp30) REVERT: A 394 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8708 (tm) REVERT: A 410 GLN cc_start: 0.5983 (OUTLIER) cc_final: 0.4909 (tm-30) REVERT: A 424 MET cc_start: 0.8969 (ptp) cc_final: 0.8425 (tmt) REVERT: A 428 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8534 (mp0) REVERT: A 616 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7921 (mmmm) REVERT: B 164 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8606 (mp0) REVERT: B 282 GLU cc_start: 0.8246 (pp20) cc_final: 0.7969 (pp20) REVERT: B 311 GLU cc_start: 0.8082 (tp30) cc_final: 0.7688 (tp30) REVERT: B 315 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8434 (tmmm) REVERT: B 547 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8773 (tp) REVERT: C 105 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8484 (mmtp) REVERT: C 346 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: C 410 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6931 (tp40) REVERT: C 415 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7385 (mp) REVERT: C 645 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6356 (tp30) outliers start: 41 outliers final: 24 residues processed: 138 average time/residue: 0.6341 time to fit residues: 96.8240 Evaluate side-chains 138 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 123 THR 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 610 VAL Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 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 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 346 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 645 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 114 optimal weight: 0.1980 chunk 152 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 0.1980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.112712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.088063 restraints weight = 22192.931| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.17 r_work: 0.3103 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14738 Z= 0.185 Angle : 0.542 10.695 19985 Z= 0.289 Chirality : 0.045 0.176 2344 Planarity : 0.004 0.066 2567 Dihedral : 8.407 173.005 2109 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.25 % Favored : 97.69 % Rotamer: Outliers : 2.89 % Allowed : 20.83 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.20), residues: 1865 helix: 2.38 (0.18), residues: 740 sheet: 1.75 (0.25), residues: 432 loop : 0.35 (0.26), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 118 TYR 0.016 0.002 TYR C 334 PHE 0.018 0.001 PHE A 545 TRP 0.005 0.001 TRP C 184 HIS 0.003 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00412 (14738) covalent geometry : angle 0.54167 (19985) hydrogen bonds : bond 0.05200 ( 847) hydrogen bonds : angle 4.92915 ( 2412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4599.17 seconds wall clock time: 79 minutes 27.13 seconds (4767.13 seconds total)