Starting phenix.real_space_refine on Fri Sep 11 18:16:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qm9_4592/09_2026/6qm9_4592.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qm9_4592/09_2026/6qm9_4592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6qm9_4592/09_2026/6qm9_4592.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qm9_4592/09_2026/6qm9_4592.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qm9_4592/09_2026/6qm9_4592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qm9_4592/09_2026/6qm9_4592.map" model { file = "/net/cci-nas-00/data/ceres_data/6qm9_4592/09_2026/6qm9_4592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qm9_4592/09_2026/6qm9_4592.cif" } resolution = 3.6 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= 0.001 sd= 0.012 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 Ca 4 9.91 5 S 40 5.16 5 C 7068 2.51 5 N 1818 2.21 5 O 1948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10878 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5437 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 29, 'TRANS': 643} Chain breaks: 5 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 5.32, per 1000 atoms: 0.49 Number of scatterers: 10878 At special positions: 0 Unit cell: (120.428, 110.308, 110.308, 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) Ca 4 19.99 S 40 16.00 O 1948 8.00 N 1818 7.00 C 7068 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: 0.92 Conformation dependent library (CDL) restraints added in 416.4 milliseconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2552 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 71.2% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 32 through 48 Processing helix chain 'A' and resid 72 through 90 removed outlier: 3.646A pdb=" N GLN A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 111 through 124 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 152 through 166 Processing helix chain 'A' and resid 170 through 198 removed outlier: 3.693A pdb=" N ILE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLU A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N SER A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 removed outlier: 3.599A pdb=" N PHE A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 246 removed outlier: 3.777A pdb=" N VAL A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.735A pdb=" N ARG A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.751A pdb=" N ALA A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.534A pdb=" N GLU A 313 " --> pdb=" O CYS A 309 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 359 removed outlier: 3.813A pdb=" N ILE A 338 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Proline residue: A 341 - end of helix removed outlier: 3.558A pdb=" N SER A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 3.543A pdb=" N LYS A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 392 removed outlier: 3.728A pdb=" N THR A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 412 removed outlier: 3.581A pdb=" N ALA A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN A 412 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 453 removed outlier: 3.563A pdb=" N VAL A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLN A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 471 removed outlier: 3.618A pdb=" N LYS A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 494 removed outlier: 4.243A pdb=" N PHE A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 518 removed outlier: 3.902A pdb=" N GLU A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 546 removed outlier: 3.718A pdb=" N VAL A 530 " --> pdb=" O CYS A 526 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 584 removed outlier: 3.581A pdb=" N ILE A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 581 " --> pdb=" O SER A 577 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 627 removed outlier: 3.697A pdb=" N LEU A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 649 removed outlier: 3.556A pdb=" N GLN A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 635 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 649 " --> pdb=" O ARG A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 682 removed outlier: 3.825A pdb=" N ILE A 670 " --> pdb=" O HIS A 666 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN A 681 " --> pdb=" O GLU A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 696 removed outlier: 3.922A pdb=" N TRP A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 718 removed outlier: 3.729A pdb=" N ALA A 718 " --> pdb=" O GLN A 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 48 Processing helix chain 'B' and resid 72 through 90 removed outlier: 3.646A pdb=" N GLN B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 111 through 124 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 152 through 166 Processing helix chain 'B' and resid 170 through 198 removed outlier: 3.693A pdb=" N ILE B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLU B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N SER B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL B 185 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.599A pdb=" N PHE B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 246 removed outlier: 3.777A pdb=" N VAL B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.735A pdb=" N ARG B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 302 removed outlier: 3.751A pdb=" N ALA B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 317 removed outlier: 3.534A pdb=" N GLU B 313 " --> pdb=" O CYS B 309 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 359 removed outlier: 3.813A pdb=" N ILE B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.558A pdb=" N SER B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 381 removed outlier: 3.543A pdb=" N LYS B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL B 376 " --> pdb=" O GLN B 372 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 392 removed outlier: 3.729A pdb=" N THR B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 412 removed outlier: 3.581A pdb=" N ALA B 409 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 412 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 453 removed outlier: 3.564A pdb=" N VAL B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN B 445 " --> pdb=" O THR B 441 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 471 removed outlier: 3.617A pdb=" N LYS B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 470 " --> pdb=" O ALA B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 494 removed outlier: 4.243A pdb=" N PHE B 485 " --> pdb=" O GLU B 481 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR B 494 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 518 removed outlier: 3.902A pdb=" N GLU B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 546 removed outlier: 3.718A pdb=" N VAL B 530 " --> pdb=" O CYS B 526 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 584 removed outlier: 3.581A pdb=" N ILE B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 627 removed outlier: 3.697A pdb=" N LEU B 602 " --> pdb=" O LYS B 598 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 649 removed outlier: 3.556A pdb=" N GLN B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS B 634 " --> pdb=" O PRO B 630 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU B 635 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 643 " --> pdb=" O ARG B 639 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 646 " --> pdb=" O THR B 642 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU B 649 " --> pdb=" O ARG B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 682 removed outlier: 3.825A pdb=" N ILE B 670 " --> pdb=" O HIS B 666 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN B 681 " --> pdb=" O GLU B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 696 removed outlier: 3.921A pdb=" N TRP B 695 " --> pdb=" O GLU B 691 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 718 removed outlier: 3.729A pdb=" N ALA B 718 " --> pdb=" O GLN B 714 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 268 removed outlier: 4.038A pdb=" N HIS A 265 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 278 " --> pdb=" O HIS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 58 Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 268 removed outlier: 4.039A pdb=" N HIS B 265 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 278 " --> pdb=" O HIS B 265 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1884 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: 1.67 Time building geometry restraints manager: 1.27 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: 3438 1.34 - 1.46: 1962 1.46 - 1.57: 5686 1.57 - 1.69: 2 1.69 - 1.81: 66 Bond restraints: 11154 Sorted by residual: bond pdb=" N PRO B 126 " pdb=" CD PRO B 126 " ideal model delta sigma weight residual 1.473 1.613 -0.140 1.40e-02 5.10e+03 1.00e+02 bond pdb=" N PRO A 126 " pdb=" CD PRO A 126 " ideal model delta sigma weight residual 1.473 1.613 -0.140 1.40e-02 5.10e+03 9.93e+01 bond pdb=" C LEU A 331 " pdb=" N PRO A 332 " ideal model delta sigma weight residual 1.336 1.380 -0.045 1.23e-02 6.61e+03 1.33e+01 bond pdb=" C LEU B 331 " pdb=" N PRO B 332 " ideal model delta sigma weight residual 1.336 1.380 -0.045 1.23e-02 6.61e+03 1.33e+01 bond pdb=" C SER A 595 " pdb=" N PRO A 596 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.51e+00 ... (remaining 11149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 14538 1.95 - 3.91: 495 3.91 - 5.86: 71 5.86 - 7.82: 12 7.82 - 9.77: 10 Bond angle restraints: 15126 Sorted by residual: angle pdb=" CA GLU B 60 " pdb=" CB GLU B 60 " pdb=" CG GLU B 60 " ideal model delta sigma weight residual 114.10 123.30 -9.20 2.00e+00 2.50e-01 2.11e+01 angle pdb=" C VAL B 200 " pdb=" N ILE B 201 " pdb=" CA ILE B 201 " ideal model delta sigma weight residual 120.33 124.01 -3.68 8.00e-01 1.56e+00 2.11e+01 angle pdb=" CA GLU A 60 " pdb=" CB GLU A 60 " pdb=" CG GLU A 60 " ideal model delta sigma weight residual 114.10 123.26 -9.16 2.00e+00 2.50e-01 2.10e+01 angle pdb=" C VAL A 200 " pdb=" N ILE A 201 " pdb=" CA ILE A 201 " ideal model delta sigma weight residual 120.33 123.97 -3.64 8.00e-01 1.56e+00 2.07e+01 angle pdb=" C GLU A 452 " pdb=" N VAL A 453 " pdb=" CA VAL A 453 " ideal model delta sigma weight residual 123.08 119.17 3.91 1.01e+00 9.80e-01 1.50e+01 ... (remaining 15121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 5815 17.62 - 35.24: 598 35.24 - 52.86: 119 52.86 - 70.48: 26 70.48 - 88.10: 16 Dihedral angle restraints: 6574 sinusoidal: 2644 harmonic: 3930 Sorted by residual: dihedral pdb=" CA LYS A 140 " pdb=" C LYS A 140 " pdb=" N TRP A 141 " pdb=" CA TRP A 141 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LYS B 140 " pdb=" C LYS B 140 " pdb=" N TRP B 141 " pdb=" CA TRP B 141 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA MET A 516 " pdb=" C MET A 516 " pdb=" N PHE A 517 " pdb=" CA PHE A 517 " ideal model delta harmonic sigma weight residual -180.00 -163.16 -16.84 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 6571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1166 0.042 - 0.085: 354 0.085 - 0.127: 96 0.127 - 0.169: 38 0.169 - 0.212: 6 Chirality restraints: 1660 Sorted by residual: chirality pdb=" CA THR B 340 " pdb=" N THR B 340 " pdb=" C THR B 340 " pdb=" CB THR B 340 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA THR A 340 " pdb=" N THR A 340 " pdb=" C THR A 340 " pdb=" CB THR A 340 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL B 580 " pdb=" CA VAL B 580 " pdb=" CG1 VAL B 580 " pdb=" CG2 VAL B 580 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.26e-01 ... (remaining 1657 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 689 " 0.040 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO A 690 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 690 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 690 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 689 " -0.040 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO B 690 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 690 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 690 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 455 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO A 456 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " -0.032 5.00e-02 4.00e+02 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3179 2.80 - 3.32: 9918 3.32 - 3.85: 18042 3.85 - 4.37: 20520 4.37 - 4.90: 34868 Nonbonded interactions: 86527 Sorted by model distance: nonbonded pdb=" OH TYR B 188 " pdb=" OD2 ASP B 539 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR A 188 " pdb=" OD2 ASP A 539 " model vdw 2.275 3.040 nonbonded pdb=" O SER A 667 " pdb=" CG1 ILE A 670 " model vdw 2.277 3.440 nonbonded pdb=" O SER B 667 " pdb=" CG1 ILE B 670 " model vdw 2.277 3.440 nonbonded pdb=" O GLY B 572 " pdb=" OG SER B 576 " model vdw 2.297 3.040 ... (remaining 86522 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.350 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 0.005 0.140 11154 Z= 0.251 Angle : 0.888 9.769 15126 Z= 0.529 Chirality : 0.047 0.212 1660 Planarity : 0.006 0.060 1920 Dihedral : 15.520 88.097 4022 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % 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: -6.09 (0.14), residues: 1322 helix: -4.39 (0.07), residues: 906 sheet: -2.25 (0.57), residues: 42 loop : -2.49 (0.27), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 432 TYR 0.014 0.001 TYR A 26 PHE 0.040 0.002 PHE B 396 TRP 0.015 0.002 TRP A 235 HIS 0.004 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.25 (11154) covalent geometry : angle 0.88795 / 0.53 (15126) hydrogen bonds : bond 0.29457 / 19.68 ( 634) hydrogen bonds : angle 10.15330 / 7.13 ( 1884) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.531 Fit side-chains REVERT: A 141 TRP cc_start: 0.7509 (p90) cc_final: 0.7176 (p90) REVERT: A 313 GLU cc_start: 0.8203 (pp20) cc_final: 0.7983 (pp20) REVERT: A 338 ILE cc_start: 0.8607 (mm) cc_final: 0.8344 (mt) REVERT: A 407 TRP cc_start: 0.8506 (m100) cc_final: 0.8163 (m100) REVERT: A 673 GLU cc_start: 0.8299 (tp30) cc_final: 0.8084 (tp30) REVERT: A 691 GLU cc_start: 0.7848 (pp20) cc_final: 0.7467 (pm20) REVERT: B 141 TRP cc_start: 0.7564 (p90) cc_final: 0.7216 (p90) REVERT: B 313 GLU cc_start: 0.8204 (pp20) cc_final: 0.7986 (pp20) REVERT: B 315 PHE cc_start: 0.9007 (t80) cc_final: 0.8785 (t80) REVERT: B 338 ILE cc_start: 0.8598 (mm) cc_final: 0.8357 (mt) REVERT: B 407 TRP cc_start: 0.8526 (m100) cc_final: 0.7967 (m100) REVERT: B 673 GLU cc_start: 0.8270 (tp30) cc_final: 0.8024 (tp30) REVERT: B 691 GLU cc_start: 0.7840 (pp20) cc_final: 0.7515 (pm20) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1152 time to fit residues: 28.9462 Evaluate side-chains 124 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 HIS A 79 GLN A 374 GLN A 479 HIS A 531 ASN B 58 HIS B 79 GLN B 374 GLN B 378 ASN B 479 HIS B 531 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.119753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.088429 restraints weight = 20775.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.091073 restraints weight = 10578.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.092740 restraints weight = 7293.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.093490 restraints weight = 5999.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.094044 restraints weight = 5473.783| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11154 Z= 0.159 Angle : 0.606 7.323 15126 Z= 0.322 Chirality : 0.040 0.164 1660 Planarity : 0.005 0.038 1920 Dihedral : 4.845 18.659 1446 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.64 % Allowed : 13.30 % Favored : 85.06 % 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: -2.98 (0.19), residues: 1322 helix: -1.78 (0.14), residues: 910 sheet: -1.84 (0.66), residues: 48 loop : -1.97 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 424 TYR 0.016 0.002 TYR A 360 PHE 0.019 0.001 PHE B 205 TRP 0.011 0.001 TRP A 561 HIS 0.002 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (11154) covalent geometry : angle 0.60596 / 0.32 (15126) hydrogen bonds : bond 0.05106 / 3.38 ( 634) hydrogen bonds : angle 4.56626 / 3.25 ( 1884) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.8367 (pp20) cc_final: 0.8110 (pp20) REVERT: A 338 ILE cc_start: 0.8777 (mm) cc_final: 0.8543 (mt) REVERT: A 691 GLU cc_start: 0.7787 (pp20) cc_final: 0.7551 (pm20) REVERT: B 313 GLU cc_start: 0.8311 (pp20) cc_final: 0.8067 (pp20) REVERT: B 315 PHE cc_start: 0.9049 (t80) cc_final: 0.8782 (t80) REVERT: B 338 ILE cc_start: 0.8767 (mm) cc_final: 0.8540 (mt) REVERT: B 406 PHE cc_start: 0.8180 (t80) cc_final: 0.7639 (t80) outliers start: 19 outliers final: 16 residues processed: 146 average time/residue: 0.0996 time to fit residues: 21.1516 Evaluate side-chains 130 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 310 ASN A 378 ASN B 310 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.118414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.085832 restraints weight = 21017.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.088398 restraints weight = 11023.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.089989 restraints weight = 7799.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.090885 restraints weight = 6518.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091170 restraints weight = 5945.971| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11154 Z= 0.217 Angle : 0.603 7.064 15126 Z= 0.317 Chirality : 0.041 0.150 1660 Planarity : 0.004 0.044 1920 Dihedral : 4.532 16.142 1446 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.45 % Allowed : 14.08 % Favored : 82.47 % 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: -1.40 (0.22), residues: 1322 helix: -0.38 (0.16), residues: 920 sheet: -1.61 (0.70), residues: 48 loop : -1.97 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 424 TYR 0.017 0.002 TYR A 26 PHE 0.032 0.002 PHE A 205 TRP 0.013 0.001 TRP A 235 HIS 0.003 0.001 HIS B 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 (11154) covalent geometry : angle 0.60320 / 0.32 (15126) hydrogen bonds : bond 0.04211 / 2.79 ( 634) hydrogen bonds : angle 4.12831 / 2.93 ( 1884) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.8796 (mm) cc_final: 0.8543 (mt) REVERT: A 406 PHE cc_start: 0.7676 (t80) cc_final: 0.7346 (t80) REVERT: B 313 GLU cc_start: 0.8370 (pp20) cc_final: 0.8116 (pp20) REVERT: B 315 PHE cc_start: 0.9071 (t80) cc_final: 0.8582 (t80) REVERT: B 338 ILE cc_start: 0.8814 (mm) cc_final: 0.8547 (mt) REVERT: B 406 PHE cc_start: 0.8112 (t80) cc_final: 0.7625 (t80) outliers start: 40 outliers final: 31 residues processed: 141 average time/residue: 0.0876 time to fit residues: 18.9283 Evaluate side-chains 141 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 68 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 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 = 0.3592 r_free = 0.3592 target = 0.119279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.087600 restraints weight = 20803.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.090198 restraints weight = 10604.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.091832 restraints weight = 7355.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.092721 restraints weight = 6096.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.092722 restraints weight = 5549.496| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11154 Z= 0.141 Angle : 0.545 7.122 15126 Z= 0.277 Chirality : 0.039 0.142 1660 Planarity : 0.003 0.034 1920 Dihedral : 4.321 14.304 1446 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.37 % Allowed : 15.72 % Favored : 80.92 % 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: -0.61 (0.23), residues: 1322 helix: 0.24 (0.17), residues: 920 sheet: -1.30 (0.74), residues: 48 loop : -1.79 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 82 TYR 0.018 0.001 TYR A 26 PHE 0.029 0.001 PHE B 205 TRP 0.014 0.001 TRP B 235 HIS 0.002 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (11154) covalent geometry : angle 0.54523 / 0.28 (15126) hydrogen bonds : bond 0.03639 / 2.42 ( 634) hydrogen bonds : angle 3.85655 / 2.74 ( 1884) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.8724 (mm) cc_final: 0.8464 (mt) REVERT: A 406 PHE cc_start: 0.7510 (t80) cc_final: 0.7309 (t80) REVERT: A 460 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8422 (mm-40) REVERT: B 313 GLU cc_start: 0.8329 (pp20) cc_final: 0.8088 (pp20) REVERT: B 338 ILE cc_start: 0.8741 (mm) cc_final: 0.8488 (mt) REVERT: B 460 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8420 (mm-40) outliers start: 39 outliers final: 26 residues processed: 155 average time/residue: 0.0922 time to fit residues: 21.4955 Evaluate side-chains 153 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 104 optimal weight: 4.9990 chunk 108 optimal weight: 0.0980 chunk 76 optimal weight: 0.0570 chunk 69 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 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 = 0.3589 r_free = 0.3589 target = 0.118912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.087218 restraints weight = 20738.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.089815 restraints weight = 10735.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.091384 restraints weight = 7521.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.092273 restraints weight = 6272.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.092569 restraints weight = 5714.921| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11154 Z= 0.158 Angle : 0.554 6.938 15126 Z= 0.281 Chirality : 0.040 0.144 1660 Planarity : 0.003 0.030 1920 Dihedral : 4.219 14.058 1446 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.45 % Allowed : 15.46 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.23), residues: 1322 helix: 0.50 (0.17), residues: 922 sheet: -1.09 (0.76), residues: 48 loop : -1.69 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 82 TYR 0.017 0.001 TYR A 26 PHE 0.026 0.001 PHE B 205 TRP 0.013 0.001 TRP A 235 HIS 0.002 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (11154) covalent geometry : angle 0.55369 / 0.28 (15126) hydrogen bonds : bond 0.03650 / 2.42 ( 634) hydrogen bonds : angle 3.82043 / 2.72 ( 1884) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.402 Fit side-chains REVERT: A 141 TRP cc_start: 0.8173 (OUTLIER) cc_final: 0.7167 (p90) REVERT: A 338 ILE cc_start: 0.8717 (mm) cc_final: 0.8464 (mt) REVERT: A 460 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8382 (mm-40) REVERT: B 141 TRP cc_start: 0.8227 (OUTLIER) cc_final: 0.7242 (p90) REVERT: B 313 GLU cc_start: 0.8324 (pp20) cc_final: 0.8100 (pp20) REVERT: B 315 PHE cc_start: 0.8847 (t80) cc_final: 0.8641 (t80) REVERT: B 338 ILE cc_start: 0.8734 (mm) cc_final: 0.8468 (mt) REVERT: B 406 PHE cc_start: 0.7835 (t80) cc_final: 0.7570 (t80) REVERT: B 460 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8382 (mm-40) outliers start: 40 outliers final: 30 residues processed: 150 average time/residue: 0.0945 time to fit residues: 21.3402 Evaluate side-chains 153 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 66 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 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 = 0.3577 r_free = 0.3577 target = 0.118096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.086014 restraints weight = 20762.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.088581 restraints weight = 10878.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.090151 restraints weight = 7691.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.090995 restraints weight = 6431.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.091134 restraints weight = 5889.605| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11154 Z= 0.192 Angle : 0.582 8.589 15126 Z= 0.294 Chirality : 0.041 0.149 1660 Planarity : 0.004 0.034 1920 Dihedral : 4.218 14.142 1446 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.80 % Allowed : 17.18 % Favored : 79.02 % 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: -0.09 (0.23), residues: 1322 helix: 0.65 (0.17), residues: 922 sheet: -1.00 (0.79), residues: 48 loop : -1.68 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 82 TYR 0.018 0.001 TYR A 26 PHE 0.037 0.001 PHE A 205 TRP 0.028 0.002 TRP A 407 HIS 0.003 0.001 HIS B 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (11154) covalent geometry : angle 0.58168 / 0.29 (15126) hydrogen bonds : bond 0.03711 / 2.45 ( 634) hydrogen bonds : angle 3.85621 / 2.73 ( 1884) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 114 time to evaluate : 0.443 Fit side-chains REVERT: A 141 TRP cc_start: 0.8370 (OUTLIER) cc_final: 0.6957 (p90) REVERT: A 338 ILE cc_start: 0.8729 (mm) cc_final: 0.8482 (mt) REVERT: A 460 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8365 (mm-40) REVERT: B 141 TRP cc_start: 0.8436 (OUTLIER) cc_final: 0.6971 (p90) REVERT: B 338 ILE cc_start: 0.8737 (mm) cc_final: 0.8494 (mt) REVERT: B 406 PHE cc_start: 0.7877 (t80) cc_final: 0.7618 (t80) REVERT: B 460 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8356 (mm-40) outliers start: 44 outliers final: 35 residues processed: 138 average time/residue: 0.0895 time to fit residues: 18.7559 Evaluate side-chains 150 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 123 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 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 = 0.3577 r_free = 0.3577 target = 0.118113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.086239 restraints weight = 20667.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.088799 restraints weight = 10740.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.090417 restraints weight = 7547.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.091276 restraints weight = 6281.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.091419 restraints weight = 5742.447| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11154 Z= 0.166 Angle : 0.573 8.055 15126 Z= 0.287 Chirality : 0.040 0.217 1660 Planarity : 0.004 0.030 1920 Dihedral : 4.219 14.243 1446 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.45 % Allowed : 18.31 % Favored : 78.24 % 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: 0.00 (0.23), residues: 1322 helix: 0.72 (0.17), residues: 920 sheet: -0.89 (0.81), residues: 48 loop : -1.65 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 82 TYR 0.018 0.001 TYR B 26 PHE 0.034 0.001 PHE A 205 TRP 0.060 0.002 TRP A 407 HIS 0.002 0.001 HIS B 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (11154) covalent geometry : angle 0.57253 / 0.29 (15126) hydrogen bonds : bond 0.03599 / 2.39 ( 634) hydrogen bonds : angle 3.81243 / 2.70 ( 1884) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 0.424 Fit side-chains REVERT: A 141 TRP cc_start: 0.8480 (OUTLIER) cc_final: 0.7057 (p90) REVERT: A 338 ILE cc_start: 0.8650 (mm) cc_final: 0.8393 (mt) REVERT: A 460 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8356 (mm-40) REVERT: B 141 TRP cc_start: 0.8491 (OUTLIER) cc_final: 0.6980 (p90) REVERT: B 338 ILE cc_start: 0.8678 (mm) cc_final: 0.8427 (mt) REVERT: B 406 PHE cc_start: 0.7629 (t80) cc_final: 0.7408 (t80) REVERT: B 407 TRP cc_start: 0.8584 (m100) cc_final: 0.8312 (m100) REVERT: B 460 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8346 (mm-40) outliers start: 40 outliers final: 32 residues processed: 142 average time/residue: 0.0942 time to fit residues: 20.4525 Evaluate side-chains 155 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 58 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.118327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.086353 restraints weight = 20687.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.088905 restraints weight = 10845.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.090501 restraints weight = 7618.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.091230 restraints weight = 6361.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.091800 restraints weight = 5846.058| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11154 Z= 0.179 Angle : 0.590 8.158 15126 Z= 0.296 Chirality : 0.041 0.165 1660 Planarity : 0.004 0.030 1920 Dihedral : 4.228 14.054 1446 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.80 % Allowed : 18.31 % Favored : 77.89 % 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: 0.07 (0.23), residues: 1322 helix: 0.75 (0.17), residues: 922 sheet: -0.77 (0.83), residues: 48 loop : -1.58 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 710 TYR 0.018 0.001 TYR B 26 PHE 0.039 0.001 PHE B 205 TRP 0.057 0.002 TRP A 407 HIS 0.002 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (11154) covalent geometry : angle 0.59037 / 0.30 (15126) hydrogen bonds : bond 0.03638 / 2.41 ( 634) hydrogen bonds : angle 3.81013 / 2.69 ( 1884) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 141 TRP cc_start: 0.8547 (OUTLIER) cc_final: 0.6948 (p90) REVERT: A 338 ILE cc_start: 0.8663 (mm) cc_final: 0.8404 (mt) REVERT: A 460 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8340 (mm-40) REVERT: A 521 TRP cc_start: 0.8995 (OUTLIER) cc_final: 0.8702 (t60) REVERT: B 141 TRP cc_start: 0.8543 (OUTLIER) cc_final: 0.6933 (p90) REVERT: B 338 ILE cc_start: 0.8707 (mm) cc_final: 0.8457 (mt) REVERT: B 460 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8338 (mm-40) REVERT: B 521 TRP cc_start: 0.9001 (OUTLIER) cc_final: 0.8707 (t60) outliers start: 44 outliers final: 36 residues processed: 143 average time/residue: 0.0867 time to fit residues: 18.9573 Evaluate side-chains 157 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 68 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 120 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 0.0470 chunk 49 optimal weight: 0.0870 chunk 125 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 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 = 0.3644 r_free = 0.3644 target = 0.122764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.091411 restraints weight = 20382.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094113 restraints weight = 10421.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.095782 restraints weight = 7237.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.096683 restraints weight = 5993.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.097005 restraints weight = 5455.176| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11154 Z= 0.101 Angle : 0.549 8.631 15126 Z= 0.270 Chirality : 0.038 0.143 1660 Planarity : 0.003 0.031 1920 Dihedral : 4.040 13.575 1446 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.85 % Allowed : 19.52 % Favored : 77.63 % 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: 0.33 (0.23), residues: 1322 helix: 0.95 (0.17), residues: 924 sheet: -0.74 (0.82), residues: 48 loop : -1.50 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 710 TYR 0.014 0.001 TYR B 26 PHE 0.042 0.001 PHE B 205 TRP 0.040 0.001 TRP A 407 HIS 0.002 0.000 HIS B 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (11154) covalent geometry : angle 0.54881 / 0.27 (15126) hydrogen bonds : bond 0.03162 / 2.12 ( 634) hydrogen bonds : angle 3.58094 / 2.54 ( 1884) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8006 (tp) REVERT: A 141 TRP cc_start: 0.8265 (OUTLIER) cc_final: 0.7531 (p90) REVERT: A 197 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8136 (mtt90) REVERT: A 338 ILE cc_start: 0.8683 (mm) cc_final: 0.8451 (mt) REVERT: A 357 MET cc_start: 0.7562 (ppp) cc_final: 0.6452 (ppp) REVERT: A 460 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8303 (mm-40) REVERT: A 610 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8373 (tt0) REVERT: A 638 GLU cc_start: 0.8434 (tp30) cc_final: 0.8142 (mt-10) REVERT: A 711 MET cc_start: 0.8379 (tpp) cc_final: 0.8076 (mmt) REVERT: B 43 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8005 (tp) REVERT: B 141 TRP cc_start: 0.8272 (OUTLIER) cc_final: 0.7436 (p90) REVERT: B 338 ILE cc_start: 0.8692 (mm) cc_final: 0.8470 (mt) REVERT: B 357 MET cc_start: 0.7536 (ppp) cc_final: 0.6400 (ppp) REVERT: B 406 PHE cc_start: 0.8203 (t80) cc_final: 0.7613 (t80) REVERT: B 460 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8275 (mm-40) REVERT: B 610 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8370 (tt0) REVERT: B 638 GLU cc_start: 0.8443 (tp30) cc_final: 0.8144 (mt-10) REVERT: B 711 MET cc_start: 0.8386 (tpp) cc_final: 0.8082 (mmt) outliers start: 33 outliers final: 19 residues processed: 161 average time/residue: 0.0912 time to fit residues: 22.1265 Evaluate side-chains 150 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 108 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.120440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.088514 restraints weight = 20629.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.091102 restraints weight = 10842.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.092656 restraints weight = 7668.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.093548 restraints weight = 6425.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.093824 restraints weight = 5861.709| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11154 Z= 0.156 Angle : 0.577 9.076 15126 Z= 0.287 Chirality : 0.040 0.153 1660 Planarity : 0.003 0.030 1920 Dihedral : 4.012 13.406 1446 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.33 % Allowed : 19.86 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.23), residues: 1322 helix: 1.03 (0.17), residues: 924 sheet: -0.71 (0.82), residues: 48 loop : -1.37 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 710 TYR 0.014 0.001 TYR B 26 PHE 0.039 0.001 PHE B 205 TRP 0.040 0.001 TRP A 407 HIS 0.002 0.001 HIS B 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (11154) covalent geometry : angle 0.57734 / 0.29 (15126) hydrogen bonds : bond 0.03359 / 2.24 ( 634) hydrogen bonds : angle 3.62832 / 2.56 ( 1884) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 141 TRP cc_start: 0.8355 (OUTLIER) cc_final: 0.7367 (p90) REVERT: A 338 ILE cc_start: 0.8700 (mm) cc_final: 0.8474 (mt) REVERT: A 357 MET cc_start: 0.7661 (ppp) cc_final: 0.6556 (ppp) REVERT: A 460 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8322 (mm-40) REVERT: A 638 GLU cc_start: 0.8441 (tp30) cc_final: 0.8149 (mt-10) REVERT: B 141 TRP cc_start: 0.8344 (OUTLIER) cc_final: 0.7342 (p90) REVERT: B 338 ILE cc_start: 0.8712 (mm) cc_final: 0.8486 (mt) REVERT: B 357 MET cc_start: 0.7645 (ppp) cc_final: 0.6543 (ppp) REVERT: B 460 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8309 (mm-40) REVERT: B 638 GLU cc_start: 0.8449 (tp30) cc_final: 0.8151 (mt-10) outliers start: 27 outliers final: 20 residues processed: 136 average time/residue: 0.0887 time to fit residues: 18.4515 Evaluate side-chains 141 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 603 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 100 optimal weight: 9.9990 chunk 103 optimal weight: 0.5980 chunk 98 optimal weight: 0.0770 chunk 110 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 79 optimal weight: 0.1980 chunk 102 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 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 = 0.3650 r_free = 0.3650 target = 0.123156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.091231 restraints weight = 20581.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.093995 restraints weight = 10513.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.095686 restraints weight = 7300.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.096619 restraints weight = 6050.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096780 restraints weight = 5505.502| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11154 Z= 0.105 Angle : 0.557 8.875 15126 Z= 0.273 Chirality : 0.039 0.147 1660 Planarity : 0.003 0.031 1920 Dihedral : 3.978 13.918 1446 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.25 % Allowed : 20.03 % Favored : 77.72 % 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: 0.59 (0.23), residues: 1322 helix: 1.12 (0.17), residues: 926 sheet: -0.68 (0.84), residues: 48 loop : -1.35 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 710 TYR 0.012 0.001 TYR B 26 PHE 0.041 0.001 PHE B 205 TRP 0.032 0.001 TRP A 407 HIS 0.002 0.000 HIS B 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (11154) covalent geometry : angle 0.55717 / 0.27 (15126) hydrogen bonds : bond 0.03134 / 2.10 ( 634) hydrogen bonds : angle 3.54705 / 2.51 ( 1884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1719.60 seconds wall clock time: 30 minutes 35.26 seconds (1835.26 seconds total)