Starting phenix.real_space_refine on Tue Mar 3 23:30:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7shm_25130/03_2026/7shm_25130.cif Found real_map, /net/cci-nas-00/data/ceres_data/7shm_25130/03_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_25130/03_2026/7shm_25130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7shm_25130/03_2026/7shm_25130.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7shm_25130/03_2026/7shm_25130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7shm_25130/03_2026/7shm_25130.map" } 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-5986/lib/python3.9/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: 2.10, 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: 0.56 Conformation dependent library (CDL) restraints added in 332.1 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: 0.30 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: 1.56 Time building geometry restraints manager: 0.79 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: 4933 18.09 - 36.18: 575 36.18 - 54.27: 89 54.27 - 72.36: 22 72.36 - 90.46: 8 Dihedral angle restraints: 5627 sinusoidal: 2311 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 5624 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: 1.800 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.540 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 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 : 15.732 90.455 3495 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 covalent geometry : bond 0.00624 ( 9392) covalent geometry : angle 1.16681 (12731) hydrogen bonds : bond 0.30004 ( 488) hydrogen bonds : angle 10.98266 ( 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 : 0.252 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: 0.1174 time to fit residues: 28.3618 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 : 0.321 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 157 GLN A 177 GLN A 299 HIS 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 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.196375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.150534 restraints weight = 10012.356| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.81 r_work: 0.3597 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9392 Z= 0.155 Angle : 0.648 7.590 12731 Z= 0.341 Chirality : 0.040 0.150 1416 Planarity : 0.006 0.062 1601 Dihedral : 9.155 87.910 1348 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.98 % Allowed : 11.23 % Favored : 86.80 % 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: -3.79 (0.20), residues: 1130 helix: -2.28 (0.14), residues: 757 sheet: -2.14 (0.51), residues: 88 loop : -2.61 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 401 TYR 0.018 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 669 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9392) covalent geometry : angle 0.64804 (12731) hydrogen bonds : bond 0.05469 ( 488) hydrogen bonds : angle 5.34775 ( 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 162 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.313 Fit side-chains REVERT: A 68 ASN cc_start: 0.7153 (t0) cc_final: 0.6917 (t0) REVERT: A 114 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6794 (tp) REVERT: A 140 ILE cc_start: 0.8345 (tp) cc_final: 0.8036 (tt) REVERT: A 179 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8453 (p) REVERT: A 477 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7841 (mt-10) REVERT: A 513 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7963 (mtpp) REVERT: A 592 GLU cc_start: 0.7235 (tt0) cc_final: 0.6858 (tm-30) REVERT: B 68 ASN cc_start: 0.7060 (t0) cc_final: 0.6798 (t0) REVERT: B 72 LEU cc_start: 0.8238 (mt) cc_final: 0.8020 (tp) REVERT: B 140 ILE cc_start: 0.8345 (tp) cc_final: 0.8033 (tt) REVERT: B 501 MET cc_start: 0.8719 (ptp) cc_final: 0.8471 (ttp) REVERT: B 513 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8040 (mtpp) REVERT: B 565 ASP cc_start: 0.7266 (t0) cc_final: 0.6952 (t0) outliers start: 19 outliers final: 7 residues processed: 155 average time/residue: 0.1097 time to fit residues: 22.8113 Evaluate side-chains 138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU 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 224 VAL 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: 3.9990 chunk 71 optimal weight: 0.5980 chunk 74 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 192 ASN B 133 GLN B 192 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.195783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.152991 restraints weight = 9911.937| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.71 r_work: 0.3571 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9392 Z= 0.142 Angle : 0.582 8.464 12731 Z= 0.301 Chirality : 0.040 0.148 1416 Planarity : 0.005 0.053 1601 Dihedral : 8.622 87.365 1344 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.39 % Allowed : 13.62 % Favored : 83.99 % 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: -2.14 (0.23), residues: 1130 helix: -0.96 (0.17), residues: 762 sheet: -1.43 (0.54), residues: 88 loop : -2.24 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 496 TYR 0.033 0.002 TYR B 620 PHE 0.016 0.001 PHE A 252 TRP 0.006 0.001 TRP B 326 HIS 0.002 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9392) covalent geometry : angle 0.58184 (12731) hydrogen bonds : bond 0.04234 ( 488) hydrogen bonds : angle 4.65829 ( 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 164 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.350 Fit side-chains REVERT: A 69 ARG cc_start: 0.7467 (tpt90) cc_final: 0.7197 (mmm-85) REVERT: A 114 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6761 (tp) REVERT: A 140 ILE cc_start: 0.8231 (tp) cc_final: 0.7964 (tt) REVERT: A 179 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8443 (p) REVERT: A 477 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7821 (mt-10) REVERT: A 580 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.6876 (mp) REVERT: A 584 HIS cc_start: 0.8730 (m-70) cc_final: 0.8326 (m170) REVERT: B 68 ASN cc_start: 0.6907 (t0) cc_final: 0.6679 (t0) REVERT: B 140 ILE cc_start: 0.8178 (tp) cc_final: 0.7885 (tt) REVERT: B 501 MET cc_start: 0.8569 (ptp) cc_final: 0.8296 (ttp) REVERT: B 513 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8028 (mtpp) REVERT: B 532 TYR cc_start: 0.8401 (m-80) cc_final: 0.8018 (m-80) REVERT: B 580 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.6812 (mp) outliers start: 23 outliers final: 11 residues processed: 157 average time/residue: 0.1043 time to fit residues: 22.0589 Evaluate side-chains 144 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 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 B residue 138 LEU Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 402 ILE 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 513 LYS Chi-restraints excluded: chain B residue 580 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 chunk 71 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN B 97 HIS B 192 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.197156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.150139 restraints weight = 10158.573| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.84 r_work: 0.3572 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9392 Z= 0.166 Angle : 0.599 7.891 12731 Z= 0.304 Chirality : 0.041 0.151 1416 Planarity : 0.004 0.048 1601 Dihedral : 8.424 86.909 1344 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.81 % Allowed : 14.76 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.33 (0.24), residues: 1130 helix: -0.34 (0.18), residues: 762 sheet: -1.14 (0.60), residues: 76 loop : -1.94 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 496 TYR 0.019 0.002 TYR A 620 PHE 0.014 0.001 PHE A 83 TRP 0.005 0.001 TRP A 326 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9392) covalent geometry : angle 0.59872 (12731) hydrogen bonds : bond 0.04063 ( 488) hydrogen bonds : angle 4.52475 ( 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 158 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.306 Fit side-chains REVERT: A 69 ARG cc_start: 0.7414 (tpt90) cc_final: 0.6590 (mtm-85) REVERT: A 114 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6827 (tp) REVERT: A 140 ILE cc_start: 0.8079 (tp) cc_final: 0.7805 (tt) REVERT: A 477 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7868 (mt-10) REVERT: A 580 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.6884 (mp) REVERT: A 584 HIS cc_start: 0.8703 (m-70) cc_final: 0.8327 (m170) REVERT: B 67 MET cc_start: 0.8145 (ttt) cc_final: 0.7539 (ttt) REVERT: B 140 ILE cc_start: 0.8192 (tp) cc_final: 0.7902 (tt) REVERT: B 477 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7782 (mt-10) REVERT: B 513 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8058 (mtpp) REVERT: B 532 TYR cc_start: 0.8427 (m-80) cc_final: 0.8088 (m-80) REVERT: B 565 ASP cc_start: 0.7464 (t0) cc_final: 0.6836 (t0) REVERT: B 580 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.6818 (mp) outliers start: 27 outliers final: 17 residues processed: 151 average time/residue: 0.1121 time to fit residues: 22.4032 Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU 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 580 LEU Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 192 ASN 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 513 LYS Chi-restraints excluded: chain B residue 580 LEU 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: 2.9990 chunk 62 optimal weight: 8.9990 chunk 12 optimal weight: 0.3980 chunk 104 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4204 r_free = 0.4204 target = 0.196297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.149094 restraints weight = 10164.703| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.85 r_work: 0.3540 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9392 Z= 0.174 Angle : 0.597 7.983 12731 Z= 0.303 Chirality : 0.041 0.142 1416 Planarity : 0.004 0.046 1601 Dihedral : 8.284 85.923 1344 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.22 % Allowed : 14.45 % Favored : 82.33 % 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: -0.83 (0.25), residues: 1130 helix: 0.05 (0.18), residues: 763 sheet: -1.27 (0.64), residues: 66 loop : -1.68 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 496 TYR 0.014 0.002 TYR A 310 PHE 0.013 0.001 PHE A 252 TRP 0.006 0.001 TRP A 326 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9392) covalent geometry : angle 0.59674 (12731) hydrogen bonds : bond 0.03964 ( 488) hydrogen bonds : angle 4.45848 ( 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 163 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.223 Fit side-chains REVERT: A 114 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.7015 (tt) REVERT: A 140 ILE cc_start: 0.8066 (tp) cc_final: 0.7783 (tt) REVERT: A 469 ASP cc_start: 0.7494 (m-30) cc_final: 0.7207 (t70) REVERT: A 477 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7836 (mt-10) REVERT: A 580 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.6846 (mp) REVERT: A 584 HIS cc_start: 0.8668 (m-70) cc_final: 0.8259 (m170) REVERT: A 642 LYS cc_start: 0.7621 (mmtp) cc_final: 0.7293 (mttt) REVERT: B 140 ILE cc_start: 0.8116 (tp) cc_final: 0.7807 (tt) REVERT: B 513 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8081 (mtpp) REVERT: B 565 ASP cc_start: 0.7440 (t0) cc_final: 0.6790 (t0) REVERT: B 580 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.6759 (mp) REVERT: B 584 HIS cc_start: 0.8679 (m-70) cc_final: 0.8308 (m170) outliers start: 31 outliers final: 19 residues processed: 156 average time/residue: 0.1078 time to fit residues: 22.7164 Evaluate side-chains 148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 138 LEU 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 652 ILE Chi-restraints excluded: chain B residue 179 THR 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 429 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 530 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: 3.9990 chunk 21 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 92 optimal weight: 0.0970 chunk 70 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4219 r_free = 0.4219 target = 0.197574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.151087 restraints weight = 10100.000| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.89 r_work: 0.3584 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9392 Z= 0.132 Angle : 0.565 8.055 12731 Z= 0.286 Chirality : 0.040 0.144 1416 Planarity : 0.004 0.045 1601 Dihedral : 8.100 84.168 1344 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.91 % Allowed : 15.38 % Favored : 81.70 % 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: -0.38 (0.25), residues: 1130 helix: 0.44 (0.18), residues: 759 sheet: -1.10 (0.65), residues: 66 loop : -1.62 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 496 TYR 0.012 0.001 TYR B 212 PHE 0.019 0.001 PHE B 83 TRP 0.006 0.001 TRP A 326 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9392) covalent geometry : angle 0.56495 (12731) hydrogen bonds : bond 0.03773 ( 488) hydrogen bonds : angle 4.34604 ( 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 161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.269 Fit side-chains REVERT: A 114 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6849 (tp) REVERT: A 140 ILE cc_start: 0.8004 (tp) cc_final: 0.7746 (tt) REVERT: A 400 GLU cc_start: 0.8345 (tp30) cc_final: 0.8129 (tp30) REVERT: A 469 ASP cc_start: 0.7434 (m-30) cc_final: 0.7199 (t70) REVERT: A 477 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7880 (mt-10) REVERT: A 580 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.6849 (mp) REVERT: A 584 HIS cc_start: 0.8665 (m-70) cc_final: 0.8259 (m170) REVERT: B 67 MET cc_start: 0.8102 (ttt) cc_final: 0.7646 (ttt) REVERT: B 140 ILE cc_start: 0.8046 (tp) cc_final: 0.7768 (tt) REVERT: B 513 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8062 (mtpp) REVERT: B 565 ASP cc_start: 0.7484 (t0) cc_final: 0.7258 (t0) REVERT: B 580 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.6751 (mp) REVERT: B 584 HIS cc_start: 0.8688 (m-70) cc_final: 0.8297 (m170) REVERT: B 642 LYS cc_start: 0.7528 (mmtp) cc_final: 0.7236 (mttt) outliers start: 28 outliers final: 17 residues processed: 152 average time/residue: 0.1116 time to fit residues: 22.7545 Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU 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 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 179 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 402 ILE 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 513 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.195662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.153258 restraints weight = 10060.187| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.73 r_work: 0.3604 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3213 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= 0.140 Angle : 0.575 9.472 12731 Z= 0.289 Chirality : 0.040 0.146 1416 Planarity : 0.004 0.044 1601 Dihedral : 7.921 86.352 1344 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.01 % Allowed : 15.90 % Favored : 81.08 % 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: -0.01 (0.25), residues: 1130 helix: 0.74 (0.19), residues: 759 sheet: -0.96 (0.67), residues: 66 loop : -1.56 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 496 TYR 0.012 0.002 TYR A 337 PHE 0.016 0.001 PHE B 83 TRP 0.006 0.001 TRP A 326 HIS 0.003 0.001 HIS B 669 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9392) covalent geometry : angle 0.57470 (12731) hydrogen bonds : bond 0.03702 ( 488) hydrogen bonds : angle 4.27715 ( 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 159 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.340 Fit side-chains REVERT: A 114 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6840 (tp) REVERT: A 140 ILE cc_start: 0.8053 (tp) cc_final: 0.7807 (tt) REVERT: A 400 GLU cc_start: 0.8130 (tp30) cc_final: 0.7920 (tp30) REVERT: A 469 ASP cc_start: 0.7372 (m-30) cc_final: 0.7086 (t0) REVERT: A 477 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7881 (mt-10) REVERT: A 580 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.6858 (mp) REVERT: A 584 HIS cc_start: 0.8666 (m-70) cc_final: 0.8252 (m170) REVERT: B 67 MET cc_start: 0.8130 (ttt) cc_final: 0.7647 (ttt) REVERT: B 140 ILE cc_start: 0.8139 (tp) cc_final: 0.7848 (tt) REVERT: B 501 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7987 (ttt) REVERT: B 513 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8155 (mtpp) REVERT: B 533 LYS cc_start: 0.6305 (OUTLIER) cc_final: 0.5481 (ttmt) REVERT: B 580 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6822 (mp) REVERT: B 584 HIS cc_start: 0.8680 (m-70) cc_final: 0.8282 (m170) REVERT: B 642 LYS cc_start: 0.7544 (mmtp) cc_final: 0.7314 (mttt) outliers start: 29 outliers final: 18 residues processed: 152 average time/residue: 0.1183 time to fit residues: 24.1398 Evaluate side-chains 146 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU 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 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 179 THR 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 501 MET Chi-restraints excluded: chain B residue 513 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 30.0000 chunk 32 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.195462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149007 restraints weight = 10095.491| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.83 r_work: 0.3562 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9392 Z= 0.182 Angle : 0.606 8.503 12731 Z= 0.306 Chirality : 0.042 0.149 1416 Planarity : 0.004 0.044 1601 Dihedral : 7.907 88.831 1344 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.22 % Allowed : 16.42 % 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: 0.04 (0.25), residues: 1130 helix: 0.81 (0.19), residues: 762 sheet: -0.61 (0.63), residues: 76 loop : -1.76 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 496 TYR 0.014 0.002 TYR A 310 PHE 0.016 0.001 PHE A 252 TRP 0.011 0.001 TRP A 339 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 9392) covalent geometry : angle 0.60632 (12731) hydrogen bonds : bond 0.03869 ( 488) hydrogen bonds : angle 4.34770 ( 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 164 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.351 Fit side-chains REVERT: A 67 MET cc_start: 0.8174 (ttt) cc_final: 0.7673 (ttt) REVERT: A 140 ILE cc_start: 0.7967 (tp) cc_final: 0.7762 (tt) REVERT: A 312 ASP cc_start: 0.8132 (m-30) cc_final: 0.7567 (m-30) REVERT: A 400 GLU cc_start: 0.8131 (tp30) cc_final: 0.7846 (tp30) REVERT: A 477 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7921 (mt-10) REVERT: A 580 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.6894 (mp) REVERT: A 584 HIS cc_start: 0.8666 (m-70) cc_final: 0.8238 (m170) REVERT: B 67 MET cc_start: 0.8221 (ttt) cc_final: 0.7766 (ttt) REVERT: B 140 ILE cc_start: 0.8083 (tp) cc_final: 0.7803 (tt) REVERT: B 312 ASP cc_start: 0.8146 (m-30) cc_final: 0.7592 (m-30) REVERT: B 462 LYS cc_start: 0.4539 (OUTLIER) cc_final: 0.4312 (ptpp) REVERT: B 469 ASP cc_start: 0.7411 (m-30) cc_final: 0.7030 (t0) REVERT: B 501 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7943 (ttt) REVERT: B 513 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8231 (mtpp) REVERT: B 533 LYS cc_start: 0.6368 (OUTLIER) cc_final: 0.5403 (ttmt) REVERT: B 565 ASP cc_start: 0.7563 (t0) cc_final: 0.7167 (t0) REVERT: B 580 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.6920 (mp) REVERT: B 584 HIS cc_start: 0.8709 (m-70) cc_final: 0.8292 (m170) REVERT: B 644 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.6257 (t80) outliers start: 31 outliers final: 19 residues processed: 155 average time/residue: 0.1128 time to fit residues: 23.5797 Evaluate side-chains 153 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 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 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 462 LYS 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 501 MET Chi-restraints excluded: chain B residue 513 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 0.0870 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.195985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.150034 restraints weight = 10025.123| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.82 r_work: 0.3575 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9392 Z= 0.158 Angle : 0.598 9.068 12731 Z= 0.302 Chirality : 0.041 0.144 1416 Planarity : 0.004 0.043 1601 Dihedral : 7.801 85.771 1344 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.22 % Allowed : 16.84 % Favored : 79.94 % 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: 0.19 (0.25), residues: 1130 helix: 0.93 (0.19), residues: 760 sheet: -0.59 (0.63), residues: 76 loop : -1.70 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 496 TYR 0.013 0.002 TYR A 310 PHE 0.018 0.001 PHE A 252 TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9392) covalent geometry : angle 0.59841 (12731) hydrogen bonds : bond 0.03762 ( 488) hydrogen bonds : angle 4.27075 ( 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 160 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.314 Fit side-chains REVERT: A 67 MET cc_start: 0.8146 (ttt) cc_final: 0.7690 (ttt) REVERT: A 312 ASP cc_start: 0.8110 (m-30) cc_final: 0.7539 (m-30) REVERT: A 400 GLU cc_start: 0.8116 (tp30) cc_final: 0.7819 (tp30) REVERT: A 477 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7866 (mt-10) REVERT: A 580 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.6817 (mp) REVERT: A 584 HIS cc_start: 0.8670 (m-70) cc_final: 0.8244 (m170) REVERT: B 67 MET cc_start: 0.8242 (ttt) cc_final: 0.7807 (ttt) REVERT: B 140 ILE cc_start: 0.8035 (tp) cc_final: 0.7773 (tt) REVERT: B 191 ARG cc_start: 0.7795 (mmp80) cc_final: 0.7271 (mmm160) REVERT: B 312 ASP cc_start: 0.8091 (m-30) cc_final: 0.7547 (m-30) REVERT: B 462 LYS cc_start: 0.4572 (OUTLIER) cc_final: 0.4301 (ptpp) REVERT: B 469 ASP cc_start: 0.7373 (m-30) cc_final: 0.7041 (t0) REVERT: B 513 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8192 (mtpp) REVERT: B 533 LYS cc_start: 0.6294 (OUTLIER) cc_final: 0.5386 (ttmt) REVERT: B 580 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.6834 (mp) REVERT: B 584 HIS cc_start: 0.8683 (m-70) cc_final: 0.8254 (m170) REVERT: B 644 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.6205 (t80) outliers start: 31 outliers final: 21 residues processed: 150 average time/residue: 0.1077 time to fit residues: 21.8529 Evaluate side-chains 152 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 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 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 462 LYS 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 513 LYS 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: 0.0570 chunk 27 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.196997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.150676 restraints weight = 10086.940| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.83 r_work: 0.3573 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.288 9392 Z= 0.196 Angle : 0.899 59.189 12731 Z= 0.509 Chirality : 0.041 0.311 1416 Planarity : 0.005 0.066 1601 Dihedral : 7.846 85.716 1344 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.22 % Allowed : 17.15 % Favored : 79.63 % 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: 0.21 (0.25), residues: 1130 helix: 0.95 (0.19), residues: 760 sheet: -0.58 (0.63), residues: 76 loop : -1.70 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 496 TYR 0.013 0.002 TYR A 310 PHE 0.017 0.001 PHE A 252 TRP 0.008 0.001 TRP A 339 HIS 0.008 0.001 HIS B 669 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 9392) covalent geometry : angle 0.89909 (12731) hydrogen bonds : bond 0.03753 ( 488) hydrogen bonds : angle 4.26906 ( 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 156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.364 Fit side-chains REVERT: A 67 MET cc_start: 0.8158 (ttt) cc_final: 0.7705 (ttt) REVERT: A 312 ASP cc_start: 0.8118 (m-30) cc_final: 0.7548 (m-30) REVERT: A 400 GLU cc_start: 0.8120 (tp30) cc_final: 0.7813 (tp30) REVERT: A 477 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7868 (mt-10) REVERT: A 532 TYR cc_start: 0.8344 (m-80) cc_final: 0.8129 (m-80) REVERT: A 580 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.6813 (mp) REVERT: A 584 HIS cc_start: 0.8669 (m-70) cc_final: 0.8243 (m170) REVERT: B 67 MET cc_start: 0.8236 (ttt) cc_final: 0.7803 (ttt) REVERT: B 140 ILE cc_start: 0.8015 (tp) cc_final: 0.7761 (tt) REVERT: B 191 ARG cc_start: 0.7787 (mmp80) cc_final: 0.7261 (mmm160) REVERT: B 312 ASP cc_start: 0.8080 (m-30) cc_final: 0.7531 (m-30) REVERT: B 462 LYS cc_start: 0.4566 (OUTLIER) cc_final: 0.4297 (ptpp) REVERT: B 469 ASP cc_start: 0.7381 (m-30) cc_final: 0.7045 (t0) REVERT: B 513 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8184 (mtpp) REVERT: B 533 LYS cc_start: 0.6310 (OUTLIER) cc_final: 0.5376 (ttmt) REVERT: B 580 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.6831 (mp) REVERT: B 584 HIS cc_start: 0.8684 (m-70) cc_final: 0.8254 (m170) REVERT: B 644 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.6197 (t80) outliers start: 31 outliers final: 22 residues processed: 145 average time/residue: 0.1129 time to fit residues: 22.3218 Evaluate side-chains 151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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 138 LEU 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 462 LYS 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 513 LYS 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: 1.9990 chunk 20 optimal weight: 0.0030 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 ASN ** 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 = 0.4210 r_free = 0.4210 target = 0.197019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.150672 restraints weight = 10027.058| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.83 r_work: 0.3574 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.288 9392 Z= 0.223 Angle : 0.721 25.206 12731 Z= 0.416 Chirality : 0.040 0.143 1416 Planarity : 0.005 0.093 1601 Dihedral : 7.846 85.716 1344 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.91 % Allowed : 17.46 % Favored : 79.63 % 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: 0.21 (0.25), residues: 1130 helix: 0.95 (0.19), residues: 760 sheet: -0.58 (0.63), residues: 76 loop : -1.70 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 496 TYR 0.013 0.002 TYR A 310 PHE 0.017 0.001 PHE A 252 TRP 0.008 0.001 TRP A 339 HIS 0.008 0.001 HIS B 669 Details of bonding type rmsd covalent geometry : bond 0.00540 ( 9392) covalent geometry : angle 0.72132 (12731) hydrogen bonds : bond 0.03753 ( 488) hydrogen bonds : angle 4.26906 ( 1440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2502.59 seconds wall clock time: 43 minutes 24.75 seconds (2604.75 seconds total)