Starting phenix.real_space_refine on Thu Jul 2 16:20:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7shm_25130/07_2026/7shm_25130.cif Found real_map, /net/cci-nas-00/data/ceres_data/7shm_25130/07_2026/7shm_25130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7shm_25130/07_2026/7shm_25130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7shm_25130/07_2026/7shm_25130.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7shm_25130/07_2026/7shm_25130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7shm_25130/07_2026/7shm_25130.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7shm_25130/07_2026/7shm_25130.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7shm_25130/07_2026/7shm_25130.cif" } resolution = 3.14 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= 0.006 sd= 0.092 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 6 5.49 5 S 44 5.16 5 C 5885 2.51 5 N 1623 2.21 5 O 1628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9186 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4553 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 20, 'TRANS': 549} Chain breaks: 2 Chain: "B" Number of atoms: 4571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4571 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 20, 'TRANS': 551} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.13, per 1000 atoms: 0.23 Number of scatterers: 9186 At special positions: 0 Unit cell: (81.868, 73.428, 135.884, 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 44 16.00 P 6 15.00 O 1628 8.00 N 1623 7.00 C 5885 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: 0.84 Conformation dependent library (CDL) restraints added in 338.1 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 68.0% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 68 through 83 removed outlier: 3.587A pdb=" N LEU A 72 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 81 " --> pdb=" O TRP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 122 removed outlier: 3.664A pdb=" N GLY A 92 " --> pdb=" O CYS A 88 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 149 removed outlier: 3.594A pdb=" N TRP A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 152 through 175 removed outlier: 3.594A pdb=" N LEU A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.636A pdb=" N SER A 184 " --> pdb=" O TYR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.867A pdb=" N SER A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 234 removed outlier: 3.706A pdb=" N VAL A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Proline residue: A 218 - end of helix removed outlier: 3.645A pdb=" N ALA A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 261 removed outlier: 4.231A pdb=" N ILE A 246 " --> pdb=" O TRP A 242 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 289 removed outlier: 3.559A pdb=" N ALA A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 removed outlier: 3.729A pdb=" N TYR A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 324 removed outlier: 3.504A pdb=" N LEU A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.562A pdb=" N VAL A 328 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 352 removed outlier: 3.523A pdb=" N SER A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 378 through 404 removed outlier: 3.527A pdb=" N GLU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 431 removed outlier: 3.613A pdb=" N LEU A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 521 Processing helix chain 'A' and resid 553 through 558 removed outlier: 3.689A pdb=" N VAL A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 570 removed outlier: 3.751A pdb=" N GLN A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 583 removed outlier: 3.805A pdb=" N ALA A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 606 through 621 removed outlier: 3.527A pdb=" N GLY A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A 615 " --> pdb=" O GLN A 611 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET A 618 " --> pdb=" O GLY A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 644 removed outlier: 4.076A pdb=" N LYS A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 651 Processing helix chain 'A' and resid 663 through 667 removed outlier: 3.936A pdb=" N HIS A 667 " --> pdb=" O TRP A 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 83 removed outlier: 3.586A pdb=" N LEU B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 122 removed outlier: 3.664A pdb=" N GLY B 92 " --> pdb=" O CYS B 88 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR B 110 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 117 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 149 removed outlier: 3.595A pdb=" N TRP B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Proline residue: B 143 - end of helix Processing helix chain 'B' and resid 152 through 175 removed outlier: 3.595A pdb=" N LEU B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.635A pdb=" N SER B 184 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 removed outlier: 3.866A pdb=" N SER B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 234 removed outlier: 3.705A pdb=" N VAL B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Proline residue: B 218 - end of helix removed outlier: 3.646A pdb=" N ALA B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 261 removed outlier: 4.232A pdb=" N ILE B 246 " --> pdb=" O TRP B 242 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 289 removed outlier: 3.559A pdb=" N ALA B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.729A pdb=" N TYR B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 324 removed outlier: 3.504A pdb=" N LEU B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 334 removed outlier: 3.562A pdb=" N VAL B 328 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 352 removed outlier: 3.522A pdb=" N SER B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 377 through 404 removed outlier: 3.526A pdb=" N GLU B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 431 removed outlier: 3.614A pdb=" N LEU B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B 418 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'B' and resid 553 through 558 removed outlier: 3.689A pdb=" N VAL B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 570 removed outlier: 3.751A pdb=" N GLN B 567 " --> pdb=" O VAL B 563 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 570 " --> pdb=" O MET B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.805A pdb=" N ALA B 578 " --> pdb=" O GLN B 574 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 579 " --> pdb=" O ASP B 575 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 606 through 621 removed outlier: 3.527A pdb=" N GLY B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 615 " --> pdb=" O GLN B 611 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 644 removed outlier: 4.076A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 651 Processing helix chain 'B' and resid 663 through 667 removed outlier: 3.937A pdb=" N HIS B 667 " --> pdb=" O TRP B 664 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 469 removed outlier: 3.666A pdb=" N ILE A 474 " --> pdb=" O VAL A 497 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 479 through 482 removed outlier: 6.708A pdb=" N ILE A 481 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ALA A 491 " --> pdb=" O ILE A 481 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 539 through 542 removed outlier: 6.368A pdb=" N PHE A 540 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASP A 629 " --> pdb=" O PHE A 540 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE A 542 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 503 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU A 504 " --> pdb=" O LEU A 671 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 466 through 469 removed outlier: 3.667A pdb=" N ILE B 474 " --> pdb=" O VAL B 497 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 479 through 482 removed outlier: 6.708A pdb=" N ILE B 481 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ALA B 491 " --> pdb=" O ILE B 481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 539 through 542 removed outlier: 6.363A pdb=" N PHE B 540 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASP B 629 " --> pdb=" O PHE B 540 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE B 542 " --> pdb=" O ASP B 629 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 503 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU B 504 " --> pdb=" O LEU B 671 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1440 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: 1.53 Time building geometry restraints manager: 1.11 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: 2940 1.34 - 1.46: 1471 1.46 - 1.57: 4897 1.57 - 1.69: 10 1.69 - 1.81: 74 Bond restraints: 9392 Sorted by residual: bond pdb=" C ASP A 397 " pdb=" N ALA A 398 " ideal model delta sigma weight residual 1.334 1.225 0.109 1.43e-02 4.89e+03 5.82e+01 bond pdb=" C MET B 539 " pdb=" N PHE B 540 " ideal model delta sigma weight residual 1.331 1.414 -0.084 1.32e-02 5.74e+03 4.00e+01 bond pdb=" C MET A 539 " pdb=" N PHE A 540 " ideal model delta sigma weight residual 1.331 1.408 -0.077 1.32e-02 5.74e+03 3.40e+01 bond pdb=" C6 ATP A 801 " pdb=" N6 ATP A 801 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.10e-02 8.26e+03 1.60e+01 bond pdb=" C6 ATP B 801 " pdb=" N6 ATP B 801 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.10e-02 8.26e+03 1.57e+01 ... (remaining 9387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.23: 12654 5.23 - 10.46: 65 10.46 - 15.70: 8 15.70 - 20.93: 0 20.93 - 26.16: 4 Bond angle restraints: 12731 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 113.71 26.16 1.00e+00 1.00e+00 6.84e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 113.94 25.93 1.00e+00 1.00e+00 6.72e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 111.65 25.18 1.00e+00 1.00e+00 6.34e+02 angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 112.25 24.58 1.00e+00 1.00e+00 6.04e+02 angle pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 121.27 107.40 13.87 1.00e+00 1.00e+00 1.93e+02 ... (remaining 12726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 4921 18.09 - 36.18: 536 36.18 - 54.27: 84 54.27 - 72.36: 18 72.36 - 90.46: 6 Dihedral angle restraints: 5565 sinusoidal: 2249 harmonic: 3316 Sorted by residual: dihedral pdb=" CA GLN B 630 " pdb=" C GLN B 630 " pdb=" N CYS B 631 " pdb=" CA CYS B 631 " ideal model delta harmonic sigma weight residual 180.00 155.18 24.82 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA GLN A 630 " pdb=" C GLN A 630 " pdb=" N CYS A 631 " pdb=" CA CYS A 631 " ideal model delta harmonic sigma weight residual 180.00 155.18 24.82 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA SER A 262 " pdb=" C SER A 262 " pdb=" N PRO A 263 " pdb=" CA PRO A 263 " ideal model delta harmonic sigma weight residual -180.00 -155.30 -24.70 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 5562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1262 0.084 - 0.168: 122 0.168 - 0.251: 23 0.251 - 0.335: 6 0.335 - 0.419: 3 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CA ARG A 496 " pdb=" N ARG A 496 " pdb=" C ARG A 496 " pdb=" CB ARG A 496 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA ARG B 496 " pdb=" N ARG B 496 " pdb=" C ARG B 496 " pdb=" CB ARG B 496 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CA TRP B 595 " pdb=" N TRP B 595 " pdb=" C TRP B 595 " pdb=" CB TRP B 595 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 1413 not shown) Planarity restraints: 1601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 349 " 0.052 5.00e-02 4.00e+02 7.85e-02 9.86e+00 pdb=" N PRO B 350 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 350 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 350 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 349 " -0.052 5.00e-02 4.00e+02 7.83e-02 9.80e+00 pdb=" N PRO A 350 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 350 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 350 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 507 " 0.049 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO A 508 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 508 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 508 " 0.041 5.00e-02 4.00e+02 ... (remaining 1598 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2995 2.84 - 3.35: 8257 3.35 - 3.87: 15136 3.87 - 4.38: 18549 4.38 - 4.90: 30619 Nonbonded interactions: 75556 Sorted by model distance: nonbonded pdb=" O VAL A 286 " pdb=" OG SER A 290 " model vdw 2.322 3.040 nonbonded pdb=" O VAL B 286 " pdb=" OG SER B 290 " model vdw 2.323 3.040 nonbonded pdb=" O MET A 548 " pdb=" NH2 ARG B 285 " model vdw 2.326 3.120 nonbonded pdb=" OG SER A 164 " pdb=" OH TYR B 310 " model vdw 2.328 3.040 nonbonded pdb=" O VAL B 222 " pdb=" OG SER B 226 " model vdw 2.330 3.040 ... (remaining 75551 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' selection = (chain 'B' and (resid 64 through 352 or resid 377 through 436 or resid 463 throu \ gh 801)) } 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: 1.300 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.770 Find NCS groups from input model: 0.160 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 : 0.006 0.109 9392 Z= 0.311 Angle : 1.167 26.160 12731 Z= 0.784 Chirality : 0.061 0.419 1416 Planarity : 0.008 0.079 1601 Dihedral : 15.185 90.455 3433 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.21 % Allowed : 7.80 % Favored : 92.00 % Cbeta Deviations : 0.28 % 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: -6.33 (0.15), residues: 1130 helix: -4.45 (0.08), residues: 741 sheet: -2.39 (0.52), residues: 70 loop : -3.20 (0.28), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 617 TYR 0.015 0.002 TYR A 559 PHE 0.019 0.002 PHE B 146 TRP 0.012 0.001 TRP A 326 HIS 0.008 0.002 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.31 ( 9392) covalent geometry : angle 1.16681 / 0.78 (12731) hydrogen bonds : bond 0.30004 / 19.82 ( 488) hydrogen bonds : angle 10.98266 / 7.69 ( 1440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 0.340 Fit side-chains REVERT: A 477 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7439 (mt-10) REVERT: A 565 ASP cc_start: 0.7856 (m-30) cc_final: 0.7525 (t0) REVERT: B 592 GLU cc_start: 0.6537 (tt0) cc_final: 0.6218 (pt0) REVERT: B 638 ASP cc_start: 0.7651 (p0) cc_final: 0.7381 (p0) outliers start: 2 outliers final: 2 residues processed: 185 average time/residue: 0.1231 time to fit residues: 29.9736 Evaluate side-chains 126 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 118 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN A 157 GLN A 177 GLN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN A 430 GLN A 433 HIS A 502 HIS A 544 GLN A 556 GLN A 587 HIS B 136 GLN B 157 GLN B 177 GLN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN B 433 HIS B 502 HIS B 544 GLN B 556 GLN B 669 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.198180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.151662 restraints weight = 10010.409| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.85 r_work: 0.3570 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9392 Z= 0.157 Angle : 0.651 7.916 12731 Z= 0.340 Chirality : 0.041 0.154 1416 Planarity : 0.006 0.061 1601 Dihedral : 6.810 89.687 1286 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.98 % Allowed : 11.43 % Favored : 86.59 % 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: -3.74 (0.20), residues: 1130 helix: -2.25 (0.14), residues: 757 sheet: -2.04 (0.52), residues: 88 loop : -2.58 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 104 TYR 0.019 0.002 TYR A 406 PHE 0.019 0.001 PHE A 252 TRP 0.009 0.001 TRP A 326 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 9392) covalent geometry : angle 0.65106 / 0.34 (12731) hydrogen bonds : bond 0.05182 / 3.43 ( 488) hydrogen bonds : angle 5.25140 / 3.68 ( 1440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.344 Fit side-chains REVERT: A 68 ASN cc_start: 0.7052 (t0) cc_final: 0.6816 (t0) REVERT: A 72 LEU cc_start: 0.8190 (mt) cc_final: 0.7971 (tp) REVERT: A 140 ILE cc_start: 0.8279 (tp) cc_final: 0.7988 (tt) REVERT: A 179 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8485 (p) REVERT: A 477 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7858 (mt-10) REVERT: A 513 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7980 (mtpp) REVERT: A 592 GLU cc_start: 0.7219 (tt0) cc_final: 0.6807 (tm-30) REVERT: B 68 ASN cc_start: 0.6939 (t0) cc_final: 0.6687 (t0) REVERT: B 72 LEU cc_start: 0.8208 (mt) cc_final: 0.7969 (tp) REVERT: B 140 ILE cc_start: 0.8313 (tp) cc_final: 0.8005 (tt) REVERT: B 179 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8479 (p) REVERT: B 501 MET cc_start: 0.8699 (ptp) cc_final: 0.8444 (ttp) REVERT: B 513 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7865 (mtpp) REVERT: B 532 TYR cc_start: 0.8418 (m-80) cc_final: 0.8026 (m-80) REVERT: B 565 ASP cc_start: 0.7200 (t0) cc_final: 0.6845 (t0) REVERT: B 620 TYR cc_start: 0.8409 (t80) cc_final: 0.8191 (t80) outliers start: 19 outliers final: 8 residues processed: 159 average time/residue: 0.1150 time to fit residues: 24.6392 Evaluate side-chains 140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 513 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 64 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 30.0000 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 67 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 HIS A 133 GLN A 192 ASN A 299 HIS B 97 HIS B 133 GLN B 192 ASN B 299 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.194975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.152290 restraints weight = 9935.942| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.69 r_work: 0.3571 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9392 Z= 0.156 Angle : 0.587 9.027 12731 Z= 0.303 Chirality : 0.041 0.147 1416 Planarity : 0.005 0.052 1601 Dihedral : 6.290 84.692 1282 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.81 % Allowed : 13.62 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.23), residues: 1130 helix: -0.99 (0.17), residues: 760 sheet: -1.28 (0.55), residues: 87 loop : -2.25 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 496 TYR 0.021 0.002 TYR A 620 PHE 0.015 0.001 PHE B 252 TRP 0.006 0.001 TRP B 326 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 9392) covalent geometry : angle 0.58742 / 0.30 (12731) hydrogen bonds : bond 0.04278 / 2.84 ( 488) hydrogen bonds : angle 4.66758 / 3.28 ( 1440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.350 Fit side-chains REVERT: A 69 ARG cc_start: 0.7450 (tpt90) cc_final: 0.7169 (mmm-85) REVERT: A 140 ILE cc_start: 0.8184 (tp) cc_final: 0.7911 (tt) REVERT: A 179 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8438 (p) REVERT: A 406 TYR cc_start: 0.8687 (t80) cc_final: 0.8398 (t80) REVERT: A 477 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7838 (mt-10) REVERT: A 580 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.6861 (mp) REVERT: A 584 HIS cc_start: 0.8722 (m-70) cc_final: 0.8339 (m170) REVERT: A 591 ARG cc_start: 0.7389 (mmt90) cc_final: 0.7062 (mmt90) REVERT: B 140 ILE cc_start: 0.8211 (tp) cc_final: 0.7923 (tt) REVERT: B 477 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7770 (mt-10) outliers start: 27 outliers final: 18 residues processed: 161 average time/residue: 0.1154 time to fit residues: 25.0783 Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 602 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 ASN A 478 ASN B 192 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.198042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151278 restraints weight = 10154.312| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.85 r_work: 0.3558 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9392 Z= 0.142 Angle : 0.574 7.085 12731 Z= 0.293 Chirality : 0.040 0.146 1416 Planarity : 0.004 0.047 1601 Dihedral : 6.099 81.497 1282 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.81 % Allowed : 14.97 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.24), residues: 1130 helix: -0.31 (0.18), residues: 760 sheet: -1.09 (0.60), residues: 76 loop : -1.95 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 496 TYR 0.013 0.002 TYR A 310 PHE 0.013 0.001 PHE B 252 TRP 0.006 0.001 TRP A 326 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9392) covalent geometry : angle 0.57417 / 0.29 (12731) hydrogen bonds : bond 0.03951 / 2.61 ( 488) hydrogen bonds : angle 4.47653 / 3.15 ( 1440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.314 Fit side-chains REVERT: A 140 ILE cc_start: 0.8003 (tp) cc_final: 0.7715 (tt) REVERT: A 179 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8421 (p) REVERT: A 477 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7848 (mt-10) REVERT: A 580 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6717 (mp) REVERT: A 584 HIS cc_start: 0.8690 (m-70) cc_final: 0.8302 (m170) REVERT: A 591 ARG cc_start: 0.7361 (mmt90) cc_final: 0.7033 (mmt90) REVERT: B 67 MET cc_start: 0.8133 (ttt) cc_final: 0.7634 (ttt) REVERT: B 140 ILE cc_start: 0.8122 (tp) cc_final: 0.7826 (tt) REVERT: B 565 ASP cc_start: 0.7371 (t0) cc_final: 0.6713 (t0) REVERT: B 580 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.6693 (mp) outliers start: 27 outliers final: 18 residues processed: 152 average time/residue: 0.1191 time to fit residues: 24.1737 Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 652 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 2 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 12 optimal weight: 0.0470 chunk 104 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.196411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.154069 restraints weight = 10076.513| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.71 r_work: 0.3590 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9392 Z= 0.128 Angle : 0.562 7.212 12731 Z= 0.284 Chirality : 0.040 0.145 1416 Planarity : 0.004 0.045 1601 Dihedral : 5.892 77.825 1282 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.81 % Allowed : 15.38 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.67 (0.25), residues: 1130 helix: 0.21 (0.18), residues: 759 sheet: -1.18 (0.64), residues: 66 loop : -1.73 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 496 TYR 0.011 0.001 TYR A 310 PHE 0.014 0.001 PHE B 252 TRP 0.006 0.001 TRP A 326 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 9392) covalent geometry : angle 0.56159 / 0.28 (12731) hydrogen bonds : bond 0.03775 / 2.49 ( 488) hydrogen bonds : angle 4.34816 / 3.06 ( 1440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.353 Fit side-chains REVERT: A 140 ILE cc_start: 0.7982 (tp) cc_final: 0.7719 (tt) REVERT: A 477 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7835 (mt-10) REVERT: A 580 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.6788 (mp) REVERT: A 584 HIS cc_start: 0.8670 (m-70) cc_final: 0.8286 (m170) REVERT: A 642 LYS cc_start: 0.7635 (mmtp) cc_final: 0.7401 (mttt) REVERT: B 67 MET cc_start: 0.8132 (ttt) cc_final: 0.7617 (ttt) REVERT: B 140 ILE cc_start: 0.8075 (tp) cc_final: 0.7772 (tt) REVERT: B 501 MET cc_start: 0.8574 (ptp) cc_final: 0.8290 (ttp) REVERT: B 565 ASP cc_start: 0.7343 (t0) cc_final: 0.7139 (t0) REVERT: B 580 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.6724 (mp) REVERT: B 584 HIS cc_start: 0.8647 (m-70) cc_final: 0.8278 (m170) outliers start: 27 outliers final: 14 residues processed: 151 average time/residue: 0.1108 time to fit residues: 22.7643 Evaluate side-chains 136 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 644 PHE Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 644 PHE Chi-restraints excluded: chain B residue 652 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 107 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 52 optimal weight: 0.0000 chunk 40 optimal weight: 0.9990 chunk 86 optimal weight: 0.0770 chunk 92 optimal weight: 10.0000 chunk 70 optimal weight: 0.1980 chunk 73 optimal weight: 8.9990 overall best weight: 0.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 ASN B 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.202744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.155628 restraints weight = 10139.384| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.91 r_work: 0.3626 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9392 Z= 0.110 Angle : 0.534 7.695 12731 Z= 0.270 Chirality : 0.039 0.143 1416 Planarity : 0.004 0.044 1601 Dihedral : 5.587 70.597 1282 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.49 % Allowed : 15.70 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.06 (0.25), residues: 1130 helix: 0.72 (0.19), residues: 759 sheet: -0.97 (0.66), residues: 66 loop : -1.63 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 285 TYR 0.013 0.001 TYR A 337 PHE 0.016 0.001 PHE B 252 TRP 0.006 0.001 TRP A 326 HIS 0.002 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9392) covalent geometry : angle 0.53449 / 0.27 (12731) hydrogen bonds : bond 0.03559 / 2.35 ( 488) hydrogen bonds : angle 4.18274 / 2.94 ( 1440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.290 Fit side-chains REVERT: A 140 ILE cc_start: 0.8014 (tp) cc_final: 0.7772 (tt) REVERT: A 292 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7666 (mp0) REVERT: A 477 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7859 (mt-10) REVERT: A 580 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.6761 (mp) REVERT: A 584 HIS cc_start: 0.8654 (m-70) cc_final: 0.8245 (m170) REVERT: B 67 MET cc_start: 0.8141 (ttt) cc_final: 0.7664 (ttt) REVERT: B 140 ILE cc_start: 0.8042 (tp) cc_final: 0.7772 (tt) REVERT: B 403 MET cc_start: 0.8280 (mtp) cc_final: 0.8070 (ttm) REVERT: B 501 MET cc_start: 0.8588 (ptp) cc_final: 0.8345 (ttp) REVERT: B 580 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.6717 (mp) REVERT: B 584 HIS cc_start: 0.8679 (m-70) cc_final: 0.8291 (m170) outliers start: 24 outliers final: 15 residues processed: 162 average time/residue: 0.0894 time to fit residues: 20.0183 Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 644 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 644 PHE Chi-restraints excluded: chain B residue 652 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 ASN A 478 ASN B 192 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.198466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.151462 restraints weight = 10186.613| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.91 r_work: 0.3560 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9392 Z= 0.156 Angle : 0.578 9.114 12731 Z= 0.289 Chirality : 0.040 0.143 1416 Planarity : 0.004 0.044 1601 Dihedral : 5.665 72.807 1282 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.22 % Allowed : 16.01 % Favored : 80.77 % 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: 0.11 (0.25), residues: 1130 helix: 0.86 (0.19), residues: 761 sheet: -0.89 (0.66), residues: 66 loop : -1.59 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 496 TYR 0.012 0.001 TYR A 310 PHE 0.015 0.001 PHE B 252 TRP 0.005 0.001 TRP A 326 HIS 0.005 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 9392) covalent geometry : angle 0.57788 / 0.29 (12731) hydrogen bonds : bond 0.03678 / 2.43 ( 488) hydrogen bonds : angle 4.24354 / 2.97 ( 1440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.332 Fit side-chains REVERT: A 140 ILE cc_start: 0.8024 (tp) cc_final: 0.7774 (tt) REVERT: A 477 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7827 (mt-10) REVERT: A 584 HIS cc_start: 0.8619 (m-70) cc_final: 0.8192 (m170) REVERT: B 67 MET cc_start: 0.8244 (ttt) cc_final: 0.7811 (ttt) REVERT: B 140 ILE cc_start: 0.8045 (tp) cc_final: 0.7754 (tt) REVERT: B 501 MET cc_start: 0.8539 (ptp) cc_final: 0.8273 (ttp) REVERT: B 533 LYS cc_start: 0.6109 (OUTLIER) cc_final: 0.5374 (ttmt) REVERT: B 565 ASP cc_start: 0.7448 (t0) cc_final: 0.7050 (t0) REVERT: B 580 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.6757 (mp) REVERT: B 584 HIS cc_start: 0.8671 (m-70) cc_final: 0.8262 (m170) outliers start: 31 outliers final: 24 residues processed: 151 average time/residue: 0.1089 time to fit residues: 22.2407 Evaluate side-chains 149 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 644 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 644 PHE Chi-restraints excluded: chain B residue 652 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 ASN A 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.197644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151106 restraints weight = 10131.098| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.85 r_work: 0.3587 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9392 Z= 0.159 Angle : 0.587 9.534 12731 Z= 0.292 Chirality : 0.040 0.155 1416 Planarity : 0.004 0.043 1601 Dihedral : 5.700 73.600 1282 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.64 % Allowed : 15.59 % Favored : 80.77 % 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: 0.26 (0.25), residues: 1130 helix: 0.98 (0.19), residues: 759 sheet: -0.90 (0.66), residues: 66 loop : -1.55 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 496 TYR 0.012 0.002 TYR A 310 PHE 0.019 0.001 PHE B 252 TRP 0.005 0.001 TRP A 326 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 9392) covalent geometry : angle 0.58748 / 0.29 (12731) hydrogen bonds : bond 0.03715 / 2.44 ( 488) hydrogen bonds : angle 4.25728 / 2.98 ( 1440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.332 Fit side-chains REVERT: A 140 ILE cc_start: 0.7958 (tp) cc_final: 0.7739 (tt) REVERT: A 477 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7857 (mt-10) REVERT: A 580 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.6863 (mp) REVERT: A 584 HIS cc_start: 0.8659 (m-70) cc_final: 0.8243 (m170) REVERT: B 67 MET cc_start: 0.8298 (ttt) cc_final: 0.7884 (ttt) REVERT: B 140 ILE cc_start: 0.8066 (tp) cc_final: 0.7780 (tt) REVERT: B 501 MET cc_start: 0.8612 (ptp) cc_final: 0.8342 (ttp) REVERT: B 533 LYS cc_start: 0.6296 (OUTLIER) cc_final: 0.5502 (ttmt) REVERT: B 565 ASP cc_start: 0.7528 (t0) cc_final: 0.7111 (t0) REVERT: B 580 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.6874 (mp) REVERT: B 584 HIS cc_start: 0.8699 (m-70) cc_final: 0.8296 (m170) outliers start: 35 outliers final: 27 residues processed: 148 average time/residue: 0.1057 time to fit residues: 21.0259 Evaluate side-chains 154 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 644 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 602 LYS Chi-restraints excluded: chain B residue 644 PHE Chi-restraints excluded: chain B residue 652 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 GLN A 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.193249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.146683 restraints weight = 10106.222| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.81 r_work: 0.3533 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9392 Z= 0.229 Angle : 0.655 9.699 12731 Z= 0.327 Chirality : 0.043 0.144 1416 Planarity : 0.004 0.043 1601 Dihedral : 6.105 83.164 1282 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.85 % Allowed : 15.80 % Favored : 80.35 % 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: 0.05 (0.25), residues: 1130 helix: 0.83 (0.19), residues: 762 sheet: -0.96 (0.65), residues: 67 loop : -1.66 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 163 TYR 0.014 0.002 TYR B 310 PHE 0.020 0.001 PHE B 252 TRP 0.007 0.001 TRP B 664 HIS 0.005 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.23 ( 9392) covalent geometry : angle 0.65465 / 0.33 (12731) hydrogen bonds : bond 0.04031 / 2.64 ( 488) hydrogen bonds : angle 4.44916 / 3.11 ( 1440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.342 Fit side-chains REVERT: A 67 MET cc_start: 0.8217 (ttt) cc_final: 0.7711 (ttt) REVERT: A 140 ILE cc_start: 0.7981 (tp) cc_final: 0.7772 (tt) REVERT: A 191 ARG cc_start: 0.7814 (mmp80) cc_final: 0.7330 (mmm160) REVERT: A 477 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7894 (mt-10) REVERT: A 580 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.6902 (mp) REVERT: A 584 HIS cc_start: 0.8672 (m-70) cc_final: 0.8242 (m170) REVERT: B 67 MET cc_start: 0.8258 (ttt) cc_final: 0.7807 (ttt) REVERT: B 140 ILE cc_start: 0.8059 (tp) cc_final: 0.7807 (tt) REVERT: B 191 ARG cc_start: 0.7882 (mmp80) cc_final: 0.7335 (mmm160) REVERT: B 312 ASP cc_start: 0.8156 (m-30) cc_final: 0.7588 (m-30) REVERT: B 469 ASP cc_start: 0.7408 (m-30) cc_final: 0.7050 (t0) REVERT: B 533 LYS cc_start: 0.6341 (OUTLIER) cc_final: 0.5358 (ttmt) REVERT: B 580 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.6863 (mp) REVERT: B 584 HIS cc_start: 0.8712 (m-70) cc_final: 0.8283 (m170) REVERT: B 644 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.6256 (t80) outliers start: 37 outliers final: 26 residues processed: 156 average time/residue: 0.1002 time to fit residues: 20.9358 Evaluate side-chains 161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 644 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 644 PHE Chi-restraints excluded: chain B residue 652 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.197281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.151611 restraints weight = 10103.033| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.81 r_work: 0.3558 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9392 Z= 0.134 Angle : 0.592 11.440 12731 Z= 0.296 Chirality : 0.040 0.146 1416 Planarity : 0.004 0.043 1601 Dihedral : 5.814 76.986 1282 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.01 % Allowed : 17.15 % Favored : 79.83 % 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: 0.32 (0.25), residues: 1130 helix: 1.05 (0.19), residues: 761 sheet: -0.48 (0.63), residues: 76 loop : -1.74 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 285 TYR 0.012 0.002 TYR A 337 PHE 0.025 0.001 PHE B 252 TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9392) covalent geometry : angle 0.59211 / 0.30 (12731) hydrogen bonds : bond 0.03727 / 2.46 ( 488) hydrogen bonds : angle 4.27555 / 2.99 ( 1440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.323 Fit side-chains REVERT: A 67 MET cc_start: 0.8173 (ttt) cc_final: 0.7734 (ttt) REVERT: A 191 ARG cc_start: 0.7760 (mmp80) cc_final: 0.7241 (mmm160) REVERT: A 312 ASP cc_start: 0.8133 (m-30) cc_final: 0.7600 (m-30) REVERT: A 408 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7754 (mm-30) REVERT: A 477 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7893 (mt-10) REVERT: A 580 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.6827 (mp) REVERT: A 584 HIS cc_start: 0.8644 (m-70) cc_final: 0.8200 (m170) REVERT: B 67 MET cc_start: 0.8254 (ttt) cc_final: 0.7868 (ttt) REVERT: B 140 ILE cc_start: 0.7844 (tp) cc_final: 0.7617 (tt) REVERT: B 191 ARG cc_start: 0.7740 (mmp80) cc_final: 0.7229 (mmm160) REVERT: B 312 ASP cc_start: 0.8112 (m-30) cc_final: 0.7570 (m-30) REVERT: B 335 MET cc_start: 0.8638 (mtp) cc_final: 0.8359 (mtt) REVERT: B 469 ASP cc_start: 0.7414 (m-30) cc_final: 0.7097 (t0) REVERT: B 501 MET cc_start: 0.8624 (ptp) cc_final: 0.8277 (ttp) REVERT: B 533 LYS cc_start: 0.6274 (OUTLIER) cc_final: 0.5301 (ttmt) REVERT: B 580 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.6881 (mp) REVERT: B 584 HIS cc_start: 0.8683 (m-70) cc_final: 0.8257 (m170) REVERT: B 644 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.6204 (t80) outliers start: 29 outliers final: 21 residues processed: 152 average time/residue: 0.1016 time to fit residues: 20.7239 Evaluate side-chains 156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 644 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 644 PHE Chi-restraints excluded: chain B residue 652 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 98 optimal weight: 0.0870 chunk 17 optimal weight: 9.9990 chunk 42 optimal weight: 0.0570 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 76 optimal weight: 4.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.197107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.155023 restraints weight = 9943.333| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.69 r_work: 0.3588 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9392 Z= 0.119 Angle : 0.566 9.021 12731 Z= 0.285 Chirality : 0.039 0.144 1416 Planarity : 0.004 0.043 1601 Dihedral : 5.625 71.956 1282 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.12 % Allowed : 16.53 % Favored : 80.35 % 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: 0.51 (0.25), residues: 1130 helix: 1.22 (0.19), residues: 758 sheet: -0.47 (0.62), residues: 76 loop : -1.70 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 496 TYR 0.010 0.001 TYR A 337 PHE 0.026 0.001 PHE B 252 TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 9392) covalent geometry : angle 0.56567 / 0.29 (12731) hydrogen bonds : bond 0.03608 / 2.38 ( 488) hydrogen bonds : angle 4.17704 / 2.93 ( 1440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2499.03 seconds wall clock time: 43 minutes 27.55 seconds (2607.55 seconds total)