Starting phenix.real_space_refine on Sat Dec 28 22:47:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7shm_25130/12_2024/7shm_25130.cif Found real_map, /net/cci-nas-00/data/ceres_data/7shm_25130/12_2024/7shm_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7shm_25130/12_2024/7shm_25130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7shm_25130/12_2024/7shm_25130.map" model { file = "/net/cci-nas-00/data/ceres_data/7shm_25130/12_2024/7shm_25130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7shm_25130/12_2024/7shm_25130.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 5.93, per 1000 atoms: 0.65 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.94 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: 2.67 Time building geometry restraints manager: 2.62 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 683 or resid 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.800 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.180 ------------------------------------------------------------------------------- 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= 0.404 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 : 5.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP A 326 HIS 0.008 0.002 HIS B 283 PHE 0.019 0.002 PHE B 146 TYR 0.015 0.002 TYR A 559 ARG 0.008 0.001 ARG A 617 *********************** 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 : 1.021 Fit side-chains REVERT: A 477 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7440 (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: 0.2935 time to fit residues: 71.0081 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 : 1.027 ------------------------------------------------------------------------------- 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 96 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN B 433 HIS B 502 HIS B 544 GLN B 556 GLN B 669 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2068 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= 0.238 Angle : 0.652 7.902 12731 Z= 0.342 Chirality : 0.041 0.152 1416 Planarity : 0.006 0.061 1601 Dihedral : 9.087 87.975 1348 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.77 % Allowed : 11.75 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.20), residues: 1130 helix: -2.26 (0.14), residues: 757 sheet: -2.02 (0.52), residues: 88 loop : -2.59 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 326 HIS 0.005 0.001 HIS A 669 PHE 0.019 0.002 PHE A 252 TYR 0.018 0.002 TYR A 406 ARG 0.004 0.000 ARG B 401 *********************** 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 163 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.106 Fit side-chains REVERT: A 140 ILE cc_start: 0.8387 (tp) cc_final: 0.8146 (tt) REVERT: A 179 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8249 (p) REVERT: A 477 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7455 (mt-10) REVERT: A 513 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7993 (mtpp) REVERT: A 642 LYS cc_start: 0.7835 (mmtp) cc_final: 0.7625 (mttp) REVERT: B 140 ILE cc_start: 0.8411 (tp) cc_final: 0.8137 (tt) REVERT: B 179 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8274 (p) REVERT: B 513 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8073 (mtpp) REVERT: B 565 ASP cc_start: 0.7155 (t0) cc_final: 0.6922 (t0) outliers start: 17 outliers final: 9 residues processed: 158 average time/residue: 0.2919 time to fit residues: 61.7016 Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 513 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 103 optimal weight: 0.0010 chunk 112 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 133 GLN A 192 ASN B 97 HIS B 133 GLN B 192 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9392 Z= 0.310 Angle : 0.635 10.502 12731 Z= 0.329 Chirality : 0.043 0.145 1416 Planarity : 0.005 0.052 1601 Dihedral : 8.694 88.303 1344 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.01 % Allowed : 13.31 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.23), residues: 1130 helix: -1.06 (0.17), residues: 764 sheet: -1.28 (0.56), residues: 86 loop : -2.21 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 595 HIS 0.004 0.001 HIS B 299 PHE 0.014 0.002 PHE B 252 TYR 0.032 0.002 TYR B 620 ARG 0.004 0.000 ARG A 496 *********************** 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 166 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.065 Fit side-chains REVERT: A 140 ILE cc_start: 0.8308 (tp) cc_final: 0.8049 (tt) REVERT: A 179 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8340 (p) REVERT: A 406 TYR cc_start: 0.8607 (t80) cc_final: 0.8386 (t80) REVERT: A 477 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 580 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7153 (mp) REVERT: A 584 HIS cc_start: 0.8503 (m-70) cc_final: 0.8171 (m170) REVERT: B 140 ILE cc_start: 0.8394 (tp) cc_final: 0.8125 (tt) REVERT: B 477 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7448 (mt-10) REVERT: B 532 TYR cc_start: 0.8281 (m-80) cc_final: 0.7962 (m-80) REVERT: B 565 ASP cc_start: 0.7311 (t0) cc_final: 0.6874 (t0) REVERT: B 580 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7099 (mp) outliers start: 29 outliers final: 18 residues processed: 158 average time/residue: 0.2557 time to fit residues: 54.4154 Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 224 VAL 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 580 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9392 Z= 0.303 Angle : 0.629 8.739 12731 Z= 0.323 Chirality : 0.042 0.144 1416 Planarity : 0.005 0.047 1601 Dihedral : 8.581 87.446 1344 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.74 % Allowed : 15.38 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.24), residues: 1130 helix: -0.40 (0.18), residues: 756 sheet: -1.17 (0.59), residues: 76 loop : -1.94 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.004 0.001 HIS B 283 PHE 0.014 0.001 PHE B 252 TYR 0.015 0.002 TYR B 310 ARG 0.005 0.000 ARG A 496 *********************** 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 165 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 1.066 Fit side-chains REVERT: A 140 ILE cc_start: 0.8211 (tp) cc_final: 0.7966 (tt) REVERT: A 477 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7500 (mt-10) REVERT: A 513 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8254 (mtpp) REVERT: A 580 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7152 (mp) REVERT: B 67 MET cc_start: 0.7444 (ttt) cc_final: 0.6978 (ttt) REVERT: B 140 ILE cc_start: 0.8321 (tp) cc_final: 0.8037 (tt) REVERT: B 312 ASP cc_start: 0.7617 (m-30) cc_final: 0.7090 (m-30) REVERT: B 513 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8196 (mtpp) REVERT: B 565 ASP cc_start: 0.7323 (t0) cc_final: 0.6837 (t0) REVERT: B 580 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7091 (mp) outliers start: 36 outliers final: 24 residues processed: 154 average time/residue: 0.2703 time to fit residues: 55.7886 Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 479 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 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 604 VAL Chi-restraints excluded: chain B residue 644 PHE 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 91 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN A 509 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9392 Z= 0.264 Angle : 0.599 7.811 12731 Z= 0.305 Chirality : 0.041 0.144 1416 Planarity : 0.004 0.045 1601 Dihedral : 8.408 86.325 1344 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.53 % Allowed : 16.42 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.25), residues: 1130 helix: 0.01 (0.18), residues: 756 sheet: -0.86 (0.61), residues: 76 loop : -1.87 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.004 0.001 HIS A 283 PHE 0.016 0.001 PHE B 252 TYR 0.014 0.002 TYR A 310 ARG 0.004 0.000 ARG A 496 *********************** 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 168 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.826 Fit side-chains REVERT: A 67 MET cc_start: 0.7402 (ttt) cc_final: 0.6922 (ttt) REVERT: A 140 ILE cc_start: 0.8198 (tp) cc_final: 0.7939 (tt) REVERT: A 477 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7499 (mt-10) REVERT: A 580 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7122 (mp) REVERT: B 67 MET cc_start: 0.7410 (ttt) cc_final: 0.6978 (ttt) REVERT: B 140 ILE cc_start: 0.8296 (tp) cc_final: 0.7991 (tt) REVERT: B 312 ASP cc_start: 0.7610 (m-30) cc_final: 0.7069 (m-30) REVERT: B 501 MET cc_start: 0.8368 (ttt) cc_final: 0.7864 (ttt) REVERT: B 513 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8209 (mtpp) REVERT: B 532 TYR cc_start: 0.8318 (m-80) cc_final: 0.8001 (m-80) REVERT: B 565 ASP cc_start: 0.7293 (t0) cc_final: 0.6774 (t0) REVERT: B 580 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7053 (mp) REVERT: B 584 HIS cc_start: 0.8504 (m-70) cc_final: 0.8169 (m170) outliers start: 34 outliers final: 23 residues processed: 158 average time/residue: 0.2564 time to fit residues: 54.2412 Evaluate side-chains 149 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 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 530 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 644 PHE Chi-restraints excluded: chain 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 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 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 37 optimal weight: 0.0570 chunk 99 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN B 192 ASN B 316 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9392 Z= 0.226 Angle : 0.590 8.089 12731 Z= 0.298 Chirality : 0.040 0.145 1416 Planarity : 0.004 0.044 1601 Dihedral : 8.251 87.374 1344 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.64 % Allowed : 17.15 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1130 helix: 0.32 (0.19), residues: 760 sheet: -0.70 (0.62), residues: 76 loop : -1.84 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.004 0.001 HIS A 283 PHE 0.019 0.001 PHE B 252 TYR 0.012 0.002 TYR B 310 ARG 0.004 0.000 ARG A 496 *********************** 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 165 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 1.045 Fit side-chains REVERT: A 140 ILE cc_start: 0.8166 (tp) cc_final: 0.7928 (tt) REVERT: A 400 GLU cc_start: 0.8050 (tp30) cc_final: 0.7765 (tm-30) REVERT: A 477 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7527 (mt-10) REVERT: A 513 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8241 (mtpp) REVERT: A 580 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7080 (mp) REVERT: B 140 ILE cc_start: 0.8255 (tp) cc_final: 0.7989 (tt) REVERT: B 312 ASP cc_start: 0.7581 (m-30) cc_final: 0.7051 (m-30) REVERT: B 501 MET cc_start: 0.8355 (ttt) cc_final: 0.7892 (ttt) REVERT: B 513 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8229 (mtpp) REVERT: B 532 TYR cc_start: 0.8303 (m-80) cc_final: 0.8039 (m-80) REVERT: B 580 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7029 (mp) REVERT: B 584 HIS cc_start: 0.8449 (m-70) cc_final: 0.8118 (m170) REVERT: B 642 LYS cc_start: 0.7541 (mmtp) cc_final: 0.7268 (mttt) REVERT: B 644 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.6392 (t80) outliers start: 35 outliers final: 25 residues processed: 159 average time/residue: 0.2618 time to fit residues: 55.5947 Evaluate side-chains 154 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 410 THR 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 513 LYS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 644 PHE Chi-restraints excluded: chain 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 186 MET Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 0.0030 chunk 80 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 68 optimal weight: 0.0050 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3262 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= 0.167 Angle : 0.567 9.344 12731 Z= 0.285 Chirality : 0.039 0.147 1416 Planarity : 0.004 0.043 1601 Dihedral : 8.004 89.693 1344 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.43 % Allowed : 17.36 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.25), residues: 1130 helix: 0.69 (0.19), residues: 760 sheet: -0.59 (0.62), residues: 76 loop : -1.74 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 326 HIS 0.003 0.001 HIS B 299 PHE 0.021 0.001 PHE B 252 TYR 0.010 0.001 TYR A 310 ARG 0.004 0.000 ARG B 285 *********************** 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 172 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 1.077 Fit side-chains REVERT: A 140 ILE cc_start: 0.8128 (tp) cc_final: 0.7924 (tt) REVERT: A 400 GLU cc_start: 0.8038 (tp30) cc_final: 0.7705 (tp30) REVERT: A 477 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7526 (mt-10) REVERT: A 513 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8200 (mtpp) REVERT: A 580 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7042 (mp) REVERT: B 140 ILE cc_start: 0.8273 (tp) cc_final: 0.8014 (tt) REVERT: B 501 MET cc_start: 0.8325 (ttt) cc_final: 0.7893 (ttt) REVERT: B 513 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8248 (mtpp) REVERT: B 532 TYR cc_start: 0.8328 (m-80) cc_final: 0.8083 (m-80) REVERT: B 565 ASP cc_start: 0.7318 (t0) cc_final: 0.7035 (t0) REVERT: B 580 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.6986 (mp) REVERT: B 584 HIS cc_start: 0.8398 (m-70) cc_final: 0.8064 (m170) outliers start: 33 outliers final: 17 residues processed: 166 average time/residue: 0.2780 time to fit residues: 60.8403 Evaluate side-chains 151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 513 LYS Chi-restraints excluded: chain A residue 530 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 410 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 99 optimal weight: 0.0040 chunk 105 optimal weight: 0.2980 overall best weight: 0.1728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN B 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9392 Z= 0.144 Angle : 0.548 9.575 12731 Z= 0.275 Chirality : 0.038 0.144 1416 Planarity : 0.004 0.045 1601 Dihedral : 7.526 84.413 1344 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.70 % Allowed : 18.19 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.25), residues: 1130 helix: 1.10 (0.19), residues: 760 sheet: -0.78 (0.69), residues: 59 loop : -1.48 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.003 0.001 HIS B 299 PHE 0.022 0.001 PHE B 252 TYR 0.012 0.001 TYR B 174 ARG 0.006 0.000 ARG B 401 *********************** 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 170 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.104 Fit side-chains REVERT: A 292 GLU cc_start: 0.7548 (mp0) cc_final: 0.6995 (mp0) REVERT: A 400 GLU cc_start: 0.8044 (tp30) cc_final: 0.7622 (tp30) REVERT: A 477 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7511 (mt-10) REVERT: A 513 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8137 (mtpp) REVERT: A 580 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.6996 (mp) REVERT: B 140 ILE cc_start: 0.8111 (tp) cc_final: 0.7872 (tt) REVERT: B 501 MET cc_start: 0.8268 (ttt) cc_final: 0.7822 (ttt) REVERT: B 513 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8211 (mtpp) REVERT: B 565 ASP cc_start: 0.7184 (t0) cc_final: 0.6915 (t0) REVERT: B 584 HIS cc_start: 0.8427 (m-70) cc_final: 0.8092 (m170) outliers start: 26 outliers final: 15 residues processed: 163 average time/residue: 0.2521 time to fit residues: 55.0209 Evaluate side-chains 151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 530 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 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 513 LYS Chi-restraints excluded: chain B residue 530 VAL 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 96 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 92 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN B 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9392 Z= 0.187 Angle : 0.574 9.255 12731 Z= 0.285 Chirality : 0.040 0.144 1416 Planarity : 0.004 0.042 1601 Dihedral : 7.490 82.127 1344 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.18 % Allowed : 18.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1130 helix: 1.22 (0.19), residues: 762 sheet: -0.83 (0.66), residues: 66 loop : -1.56 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.003 0.001 HIS A 283 PHE 0.021 0.001 PHE B 252 TYR 0.011 0.002 TYR B 174 ARG 0.004 0.000 ARG B 285 *********************** 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 158 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.013 Fit side-chains REVERT: A 292 GLU cc_start: 0.7585 (mp0) cc_final: 0.7009 (mp0) REVERT: A 400 GLU cc_start: 0.8018 (tp30) cc_final: 0.7652 (tp30) REVERT: B 140 ILE cc_start: 0.8074 (tp) cc_final: 0.7861 (tt) REVERT: B 282 MET cc_start: 0.8325 (mmt) cc_final: 0.7862 (mmt) REVERT: B 501 MET cc_start: 0.8285 (ttt) cc_final: 0.7833 (ttt) REVERT: B 565 ASP cc_start: 0.7201 (t0) cc_final: 0.6913 (t0) REVERT: B 580 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.6967 (mp) REVERT: B 584 HIS cc_start: 0.8434 (m-70) cc_final: 0.8099 (m170) outliers start: 21 outliers final: 14 residues processed: 152 average time/residue: 0.2469 time to fit residues: 51.0821 Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 644 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 644 PHE Chi-restraints excluded: chain B residue 652 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 0.3980 chunk 104 optimal weight: 0.9980 chunk 90 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9392 Z= 0.186 Angle : 0.580 9.341 12731 Z= 0.287 Chirality : 0.040 0.148 1416 Planarity : 0.004 0.042 1601 Dihedral : 7.405 77.392 1344 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.08 % Allowed : 18.61 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1130 helix: 1.29 (0.19), residues: 759 sheet: -0.83 (0.65), residues: 66 loop : -1.53 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 326 HIS 0.003 0.001 HIS A 283 PHE 0.023 0.001 PHE B 252 TYR 0.013 0.002 TYR A 110 ARG 0.004 0.000 ARG B 285 ********************** 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: 20 poor density : 136 time to evaluate : 0.973 Fit side-chains REVERT: A 400 GLU cc_start: 0.7955 (tp30) cc_final: 0.7559 (tp30) REVERT: A 580 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7031 (mp) REVERT: B 140 ILE cc_start: 0.8076 (tp) cc_final: 0.7857 (tt) REVERT: B 282 MET cc_start: 0.8371 (mmt) cc_final: 0.8037 (mmt) REVERT: B 565 ASP cc_start: 0.7225 (t0) cc_final: 0.6934 (t0) REVERT: B 580 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.6944 (mp) outliers start: 20 outliers final: 16 residues processed: 149 average time/residue: 0.2543 time to fit residues: 51.4076 Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 530 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 186 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 644 PHE Chi-restraints excluded: chain B residue 652 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.9980 chunk 13 optimal weight: 0.0010 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 37 optimal weight: 0.0040 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.4226 r_free = 0.4226 target = 0.198451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153027 restraints weight = 10067.143| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.82 r_work: 0.3600 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9392 Z= 0.156 Angle : 0.553 9.470 12731 Z= 0.276 Chirality : 0.039 0.147 1416 Planarity : 0.004 0.042 1601 Dihedral : 7.267 74.056 1344 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.87 % Allowed : 18.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1130 helix: 1.46 (0.19), residues: 758 sheet: -0.79 (0.66), residues: 66 loop : -1.46 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.004 0.001 HIS B 669 PHE 0.025 0.001 PHE B 252 TYR 0.011 0.001 TYR B 174 ARG 0.004 0.000 ARG B 496 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2237.17 seconds wall clock time: 41 minutes 35.81 seconds (2495.81 seconds total)