Starting phenix.real_space_refine on Tue Mar 3 23:46:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n58_24182/03_2026/7n58_24182.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n58_24182/03_2026/7n58_24182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n58_24182/03_2026/7n58_24182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n58_24182/03_2026/7n58_24182.map" model { file = "/net/cci-nas-00/data/ceres_data/7n58_24182/03_2026/7n58_24182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n58_24182/03_2026/7n58_24182.cif" } resolution = 3.4 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= 0.020 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 5952 2.51 5 N 1598 2.21 5 O 1742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9326 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4663 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 13, 'TRANS': 586} Chain: "B" Number of atoms: 4663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4663 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 13, 'TRANS': 586} Time building chain proxies: 1.97, per 1000 atoms: 0.21 Number of scatterers: 9326 At special positions: 0 Unit cell: (112.005, 98.325, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1742 8.00 N 1598 7.00 C 5952 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: 0.64 Conformation dependent library (CDL) restraints added in 256.5 milliseconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 66.9% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 117 through 132 removed outlier: 3.646A pdb=" N MET A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 169 removed outlier: 4.281A pdb=" N ARG A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Proline residue: A 161 - end of helix removed outlier: 3.518A pdb=" N VAL A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 removed outlier: 3.762A pdb=" N THR A 182 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR A 183 " --> pdb=" O SER A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 179 through 183' Processing helix chain 'A' and resid 197 through 245 removed outlier: 3.889A pdb=" N VAL A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.667A pdb=" N HIS A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 279 removed outlier: 3.584A pdb=" N LEU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 292 Processing helix chain 'A' and resid 293 through 296 Processing helix chain 'A' and resid 299 through 348 removed outlier: 3.715A pdb=" N TRP A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 327 " --> pdb=" O TRP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 355 removed outlier: 3.744A pdb=" N VAL A 352 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 411 removed outlier: 3.602A pdb=" N LYS A 364 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 431 removed outlier: 4.014A pdb=" N VAL A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 removed outlier: 4.310A pdb=" N LEU A 436 " --> pdb=" O PRO A 432 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER A 438 " --> pdb=" O ASN A 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 438' Processing helix chain 'A' and resid 438 through 457 removed outlier: 4.732A pdb=" N GLU A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.956A pdb=" N ARG A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 555 Processing helix chain 'A' and resid 569 through 575 Processing helix chain 'A' and resid 581 through 593 Processing helix chain 'A' and resid 594 through 599 removed outlier: 3.507A pdb=" N SER A 599 " --> pdb=" O HIS A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 633 removed outlier: 4.596A pdb=" N LEU A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 632 " --> pdb=" O ARG A 628 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER A 633 " --> pdb=" O THR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 662 removed outlier: 3.596A pdb=" N GLU A 653 " --> pdb=" O THR A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 702 removed outlier: 3.545A pdb=" N LEU A 700 " --> pdb=" O PRO A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 716 Processing helix chain 'B' and resid 118 through 132 Processing helix chain 'B' and resid 136 through 169 removed outlier: 4.281A pdb=" N ARG B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA B 153 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Proline residue: B 161 - end of helix removed outlier: 3.519A pdb=" N VAL B 168 " --> pdb=" O PHE B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.761A pdb=" N THR B 182 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR B 183 " --> pdb=" O SER B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 183' Processing helix chain 'B' and resid 197 through 245 removed outlier: 3.888A pdb=" N VAL B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 229 " --> pdb=" O LYS B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.667A pdb=" N HIS B 250 " --> pdb=" O ASP B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 279 removed outlier: 3.584A pdb=" N LEU B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 292 Processing helix chain 'B' and resid 293 through 296 Processing helix chain 'B' and resid 299 through 348 removed outlier: 3.715A pdb=" N TRP B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B 327 " --> pdb=" O TRP B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 355 removed outlier: 3.744A pdb=" N VAL B 352 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 411 removed outlier: 3.601A pdb=" N LYS B 364 " --> pdb=" O TYR B 360 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER B 391 " --> pdb=" O ASN B 387 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE B 394 " --> pdb=" O GLN B 390 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 431 removed outlier: 4.014A pdb=" N VAL B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 removed outlier: 4.311A pdb=" N LEU B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 432 through 438' Processing helix chain 'B' and resid 438 through 457 removed outlier: 4.732A pdb=" N GLU B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.955A pdb=" N ARG B 523 " --> pdb=" O SER B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 555 Processing helix chain 'B' and resid 569 through 575 Processing helix chain 'B' and resid 581 through 593 Processing helix chain 'B' and resid 594 through 599 removed outlier: 3.507A pdb=" N SER B 599 " --> pdb=" O HIS B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 633 removed outlier: 4.597A pdb=" N LEU B 631 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 632 " --> pdb=" O ARG B 628 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER B 633 " --> pdb=" O THR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 662 removed outlier: 3.595A pdb=" N GLU B 653 " --> pdb=" O THR B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 702 removed outlier: 3.544A pdb=" N LEU B 700 " --> pdb=" O PRO B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 716 Processing sheet with id=AA1, first strand: chain 'A' and resid 501 through 502 removed outlier: 3.737A pdb=" N ILE A 479 " --> pdb=" O VAL A 502 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A 482 " --> pdb=" O ASN A 535 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN A 535 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 484 through 486 removed outlier: 4.819A pdb=" N VAL A 484 " --> pdb=" O GLY A 497 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 486 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 495 " --> pdb=" O PHE A 486 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 556 through 557 removed outlier: 6.907A pdb=" N GLY A 556 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 670 " --> pdb=" O CYS A 639 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY A 512 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER A 507 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL A 684 " --> pdb=" O SER A 507 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA A 509 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU A 686 " --> pdb=" O ALA A 509 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL A 511 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE A 683 " --> pdb=" O GLN A 694 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN A 694 " --> pdb=" O ILE A 683 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 685 " --> pdb=" O VAL A 692 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 568 Processing sheet with id=AA5, first strand: chain 'B' and resid 501 through 502 removed outlier: 3.737A pdb=" N ILE B 479 " --> pdb=" O VAL B 502 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU B 482 " --> pdb=" O ASN B 535 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN B 535 " --> pdb=" O GLU B 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 484 through 486 removed outlier: 4.819A pdb=" N VAL B 484 " --> pdb=" O GLY B 497 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 486 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 495 " --> pdb=" O PHE B 486 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 556 through 557 removed outlier: 6.908A pdb=" N GLY B 556 " --> pdb=" O LEU B 638 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 670 " --> pdb=" O CYS B 639 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY B 512 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER B 507 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL B 684 " --> pdb=" O SER B 507 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA B 509 " --> pdb=" O VAL B 684 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU B 686 " --> pdb=" O ALA B 509 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B 511 " --> pdb=" O LEU B 686 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 683 " --> pdb=" O GLN B 694 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN B 694 " --> pdb=" O ILE B 683 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 685 " --> pdb=" O VAL B 692 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 567 through 568 548 hydrogen bonds defined for protein. 1626 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: 1.42 Time building geometry restraints manager: 0.84 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: 3028 1.34 - 1.46: 1371 1.46 - 1.57: 5029 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 9490 Sorted by residual: bond pdb=" CB GLU B 651 " pdb=" CG GLU B 651 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.70e+00 bond pdb=" CB GLU A 651 " pdb=" CG GLU A 651 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.67e+00 bond pdb=" CB LYS A 632 " pdb=" CG LYS A 632 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.39e+00 bond pdb=" CB LYS B 632 " pdb=" CG LYS B 632 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CD LYS A 632 " pdb=" CE LYS A 632 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.28e+00 ... (remaining 9485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 12431 2.07 - 4.13: 331 4.13 - 6.20: 64 6.20 - 8.26: 14 8.26 - 10.33: 2 Bond angle restraints: 12842 Sorted by residual: angle pdb=" N VAL A 158 " pdb=" CA VAL A 158 " pdb=" C VAL A 158 " ideal model delta sigma weight residual 113.39 107.51 5.88 1.47e+00 4.63e-01 1.60e+01 angle pdb=" N VAL B 158 " pdb=" CA VAL B 158 " pdb=" C VAL B 158 " ideal model delta sigma weight residual 113.39 107.54 5.85 1.47e+00 4.63e-01 1.58e+01 angle pdb=" CA ARG A 232 " pdb=" CB ARG A 232 " pdb=" CG ARG A 232 " ideal model delta sigma weight residual 114.10 107.07 7.03 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA ARG B 232 " pdb=" CB ARG B 232 " pdb=" CG ARG B 232 " ideal model delta sigma weight residual 114.10 107.10 7.00 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CB LYS B 632 " pdb=" CG LYS B 632 " pdb=" CD LYS B 632 " ideal model delta sigma weight residual 111.30 103.96 7.34 2.30e+00 1.89e-01 1.02e+01 ... (remaining 12837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.39: 5006 14.39 - 28.78: 491 28.78 - 43.17: 141 43.17 - 57.56: 26 57.56 - 71.95: 12 Dihedral angle restraints: 5676 sinusoidal: 2206 harmonic: 3470 Sorted by residual: dihedral pdb=" CA PRO B 696 " pdb=" C PRO B 696 " pdb=" N HIS B 697 " pdb=" CA HIS B 697 " ideal model delta harmonic sigma weight residual 180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA PRO A 696 " pdb=" C PRO A 696 " pdb=" N HIS A 697 " pdb=" CA HIS A 697 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA GLU B 373 " pdb=" CB GLU B 373 " pdb=" CG GLU B 373 " pdb=" CD GLU B 373 " ideal model delta sinusoidal sigma weight residual -60.00 -104.54 44.54 3 1.50e+01 4.44e-03 8.01e+00 ... (remaining 5673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 986 0.036 - 0.073: 366 0.073 - 0.109: 101 0.109 - 0.145: 41 0.145 - 0.182: 12 Chirality restraints: 1506 Sorted by residual: chirality pdb=" CA GLU B 458 " pdb=" N GLU B 458 " pdb=" C GLU B 458 " pdb=" CB GLU B 458 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CA GLU A 458 " pdb=" N GLU A 458 " pdb=" C GLU A 458 " pdb=" CB GLU A 458 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA ILE A 293 " pdb=" N ILE A 293 " pdb=" C ILE A 293 " pdb=" CB ILE A 293 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.70e-01 ... (remaining 1503 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 188 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.71e+01 pdb=" N PRO A 189 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 188 " -0.067 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 189 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 189 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 189 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 213 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C SER B 213 " 0.062 2.00e-02 2.50e+03 pdb=" O SER B 213 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA B 214 " -0.021 2.00e-02 2.50e+03 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 212 2.70 - 3.25: 10201 3.25 - 3.80: 13940 3.80 - 4.35: 18003 4.35 - 4.90: 28592 Nonbonded interactions: 70948 Sorted by model distance: nonbonded pdb=" O ASP A 449 " pdb=" OG SER A 452 " model vdw 2.146 3.040 nonbonded pdb=" O ASP B 449 " pdb=" OG SER B 452 " model vdw 2.147 3.040 nonbonded pdb=" O GLY B 176 " pdb=" OG1 THR B 177 " model vdw 2.223 3.040 nonbonded pdb=" O GLY A 176 " pdb=" OG1 THR A 177 " model vdw 2.224 3.040 nonbonded pdb=" NE2 GLN A 445 " pdb=" OD2 ASP A 449 " model vdw 2.259 3.120 ... (remaining 70943 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.810 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 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 : 0.004 0.049 9490 Z= 0.182 Angle : 0.841 10.328 12842 Z= 0.468 Chirality : 0.045 0.182 1506 Planarity : 0.007 0.104 1630 Dihedral : 13.091 71.950 3436 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.23), residues: 1196 helix: 0.34 (0.19), residues: 734 sheet: -0.40 (0.52), residues: 70 loop : -2.25 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 232 TYR 0.035 0.002 TYR A 354 PHE 0.026 0.002 PHE A 271 TRP 0.013 0.002 TRP A 304 HIS 0.004 0.001 HIS B 595 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9490) covalent geometry : angle 0.84139 (12842) hydrogen bonds : bond 0.14627 ( 548) hydrogen bonds : angle 6.28838 ( 1626) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 ILE cc_start: 0.7990 (tt) cc_final: 0.7686 (tt) REVERT: B 573 ILE cc_start: 0.8013 (tt) cc_final: 0.7699 (tt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0930 time to fit residues: 16.2259 Evaluate side-chains 98 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.1980 chunk 117 optimal weight: 0.0370 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 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 = 0.4479 r_free = 0.4479 target = 0.209137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.177914 restraints weight = 14131.069| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.67 r_work: 0.4099 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9490 Z= 0.145 Angle : 0.646 10.069 12842 Z= 0.339 Chirality : 0.040 0.151 1506 Planarity : 0.005 0.062 1630 Dihedral : 4.021 15.285 1298 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.89 % Allowed : 8.53 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.24), residues: 1196 helix: 1.34 (0.19), residues: 730 sheet: 0.22 (0.56), residues: 70 loop : -1.88 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 232 TYR 0.026 0.002 TYR B 354 PHE 0.014 0.001 PHE B 271 TRP 0.009 0.001 TRP A 170 HIS 0.004 0.001 HIS B 485 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9490) covalent geometry : angle 0.64639 (12842) hydrogen bonds : bond 0.06044 ( 548) hydrogen bonds : angle 4.77267 ( 1626) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 410 MET cc_start: 0.5331 (tmm) cc_final: 0.5065 (tmm) REVERT: A 573 ILE cc_start: 0.8270 (tt) cc_final: 0.7974 (tt) REVERT: B 276 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8252 (ttm) REVERT: B 573 ILE cc_start: 0.8332 (tt) cc_final: 0.8009 (tt) outliers start: 9 outliers final: 6 residues processed: 113 average time/residue: 0.0920 time to fit residues: 14.6630 Evaluate side-chains 110 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN A 679 GLN B 250 HIS ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.204171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.172579 restraints weight = 14095.532| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.52 r_work: 0.4053 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9490 Z= 0.142 Angle : 0.590 8.204 12842 Z= 0.313 Chirality : 0.040 0.157 1506 Planarity : 0.004 0.052 1630 Dihedral : 4.013 17.142 1298 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.88 % Allowed : 11.81 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.63 (0.24), residues: 1196 helix: 1.66 (0.19), residues: 724 sheet: 0.61 (0.66), residues: 44 loop : -1.87 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 441 TYR 0.019 0.002 TYR A 354 PHE 0.015 0.001 PHE A 302 TRP 0.008 0.001 TRP B 170 HIS 0.006 0.001 HIS A 574 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9490) covalent geometry : angle 0.59019 (12842) hydrogen bonds : bond 0.05604 ( 548) hydrogen bonds : angle 4.35749 ( 1626) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.361 Fit side-chains REVERT: A 159 GLN cc_start: 0.7222 (tp40) cc_final: 0.6589 (tt0) REVERT: A 573 ILE cc_start: 0.8168 (tt) cc_final: 0.7861 (tt) REVERT: B 442 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7813 (mm-30) REVERT: B 567 ASP cc_start: 0.8038 (t0) cc_final: 0.7825 (t0) REVERT: B 573 ILE cc_start: 0.8228 (tt) cc_final: 0.7904 (tt) outliers start: 19 outliers final: 10 residues processed: 122 average time/residue: 0.0911 time to fit residues: 15.7050 Evaluate side-chains 113 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 18 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 73 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN B 566 ASN ** B 714 GLN ** 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 = 0.4427 r_free = 0.4427 target = 0.203510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.171788 restraints weight = 14179.797| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.54 r_work: 0.4046 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9490 Z= 0.124 Angle : 0.536 6.801 12842 Z= 0.285 Chirality : 0.039 0.145 1506 Planarity : 0.004 0.056 1630 Dihedral : 3.874 14.710 1298 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.98 % Allowed : 13.59 % Favored : 84.42 % 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: 0.82 (0.24), residues: 1196 helix: 1.88 (0.19), residues: 726 sheet: 0.72 (0.56), residues: 68 loop : -2.13 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 232 TYR 0.014 0.002 TYR B 360 PHE 0.010 0.001 PHE A 302 TRP 0.004 0.001 TRP B 304 HIS 0.006 0.001 HIS A 485 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9490) covalent geometry : angle 0.53646 (12842) hydrogen bonds : bond 0.05186 ( 548) hydrogen bonds : angle 4.09438 ( 1626) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.244 Fit side-chains REVERT: A 159 GLN cc_start: 0.7211 (tp40) cc_final: 0.6646 (tt0) REVERT: A 407 GLN cc_start: 0.6185 (mt0) cc_final: 0.5099 (tm-30) REVERT: A 573 ILE cc_start: 0.8231 (tt) cc_final: 0.7943 (tt) REVERT: B 159 GLN cc_start: 0.7361 (tp40) cc_final: 0.6467 (tt0) REVERT: B 364 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6242 (mptt) REVERT: B 407 GLN cc_start: 0.5951 (mt0) cc_final: 0.5125 (tm-30) REVERT: B 441 ARG cc_start: 0.7990 (ptp90) cc_final: 0.7630 (ptp90) REVERT: B 442 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7831 (mm-30) REVERT: B 573 ILE cc_start: 0.8257 (tt) cc_final: 0.7928 (tt) outliers start: 20 outliers final: 14 residues processed: 124 average time/residue: 0.0906 time to fit residues: 15.7918 Evaluate side-chains 115 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 82 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.197654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.165853 restraints weight = 14312.721| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.54 r_work: 0.3981 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9490 Z= 0.161 Angle : 0.579 7.018 12842 Z= 0.312 Chirality : 0.041 0.152 1506 Planarity : 0.005 0.054 1630 Dihedral : 4.027 15.053 1298 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.18 % Allowed : 14.98 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.24), residues: 1196 helix: 1.82 (0.19), residues: 728 sheet: 0.54 (0.55), residues: 70 loop : -2.31 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 590 TYR 0.015 0.002 TYR A 205 PHE 0.017 0.002 PHE B 601 TRP 0.007 0.001 TRP B 304 HIS 0.006 0.001 HIS A 574 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9490) covalent geometry : angle 0.57864 (12842) hydrogen bonds : bond 0.05626 ( 548) hydrogen bonds : angle 4.15710 ( 1626) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.330 Fit side-chains REVERT: A 323 TRP cc_start: 0.7468 (t-100) cc_final: 0.6555 (t60) REVERT: A 573 ILE cc_start: 0.8263 (tt) cc_final: 0.8004 (tt) REVERT: A 632 LYS cc_start: 0.5030 (mttt) cc_final: 0.4243 (tttp) REVERT: B 159 GLN cc_start: 0.7441 (tp40) cc_final: 0.6573 (tt0) REVERT: B 364 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6582 (mptt) REVERT: B 441 ARG cc_start: 0.8052 (ptp90) cc_final: 0.7712 (ptp90) REVERT: B 442 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7854 (mm-30) REVERT: B 567 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7955 (t0) REVERT: B 573 ILE cc_start: 0.8321 (tt) cc_final: 0.8001 (tt) REVERT: B 638 LEU cc_start: 0.7287 (tp) cc_final: 0.7077 (pp) REVERT: B 668 ILE cc_start: 0.7254 (mp) cc_final: 0.6962 (pt) outliers start: 22 outliers final: 15 residues processed: 126 average time/residue: 0.0836 time to fit residues: 15.0226 Evaluate side-chains 119 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN B 566 ASN ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.198641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.167088 restraints weight = 14282.714| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.53 r_work: 0.3994 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9490 Z= 0.132 Angle : 0.540 6.654 12842 Z= 0.290 Chirality : 0.039 0.147 1506 Planarity : 0.004 0.056 1630 Dihedral : 3.942 14.505 1298 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.08 % Allowed : 16.27 % Favored : 81.65 % 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: 0.78 (0.24), residues: 1196 helix: 1.95 (0.19), residues: 728 sheet: 0.52 (0.55), residues: 70 loop : -2.37 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 341 TYR 0.013 0.001 TYR B 205 PHE 0.011 0.001 PHE B 601 TRP 0.005 0.001 TRP B 304 HIS 0.005 0.001 HIS A 574 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9490) covalent geometry : angle 0.53961 (12842) hydrogen bonds : bond 0.05231 ( 548) hydrogen bonds : angle 4.04315 ( 1626) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.253 Fit side-chains REVERT: A 323 TRP cc_start: 0.7420 (t-100) cc_final: 0.6510 (t60) REVERT: A 407 GLN cc_start: 0.6348 (mt0) cc_final: 0.5059 (tm-30) REVERT: A 573 ILE cc_start: 0.8292 (tt) cc_final: 0.8020 (tt) REVERT: A 632 LYS cc_start: 0.5116 (mttt) cc_final: 0.4272 (tttm) REVERT: B 159 GLN cc_start: 0.7387 (tp40) cc_final: 0.6538 (tt0) REVERT: B 364 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6451 (mptt) REVERT: B 370 LYS cc_start: 0.7002 (tppt) cc_final: 0.6546 (ttmm) REVERT: B 441 ARG cc_start: 0.8076 (ptp90) cc_final: 0.7728 (ptp90) REVERT: B 442 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7884 (mm-30) REVERT: B 573 ILE cc_start: 0.8248 (tt) cc_final: 0.7919 (tt) REVERT: B 638 LEU cc_start: 0.7248 (tp) cc_final: 0.7035 (pp) REVERT: B 668 ILE cc_start: 0.7137 (mp) cc_final: 0.6841 (pt) outliers start: 21 outliers final: 16 residues processed: 116 average time/residue: 0.0916 time to fit residues: 14.9210 Evaluate side-chains 118 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 118 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN B 566 ASN ** B 714 GLN ** 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 = 0.4363 r_free = 0.4363 target = 0.197061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.165472 restraints weight = 14314.736| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.54 r_work: 0.3977 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9490 Z= 0.141 Angle : 0.543 6.735 12842 Z= 0.292 Chirality : 0.040 0.165 1506 Planarity : 0.005 0.057 1630 Dihedral : 3.961 14.588 1298 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.08 % Allowed : 17.66 % Favored : 80.26 % 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: 0.72 (0.24), residues: 1196 helix: 1.91 (0.19), residues: 732 sheet: 0.40 (0.56), residues: 70 loop : -2.43 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 232 TYR 0.014 0.002 TYR B 205 PHE 0.012 0.001 PHE B 601 TRP 0.004 0.001 TRP B 304 HIS 0.005 0.001 HIS A 574 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9490) covalent geometry : angle 0.54345 (12842) hydrogen bonds : bond 0.05312 ( 548) hydrogen bonds : angle 4.02465 ( 1626) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.360 Fit side-chains REVERT: A 323 TRP cc_start: 0.7475 (t-100) cc_final: 0.6568 (t60) REVERT: A 407 GLN cc_start: 0.6390 (mt0) cc_final: 0.5119 (tm-30) REVERT: A 573 ILE cc_start: 0.8350 (tt) cc_final: 0.8095 (tt) REVERT: A 632 LYS cc_start: 0.5144 (mttt) cc_final: 0.4306 (tttm) REVERT: B 159 GLN cc_start: 0.7419 (tp40) cc_final: 0.6592 (tt0) REVERT: B 364 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6533 (mptt) REVERT: B 370 LYS cc_start: 0.7177 (tppt) cc_final: 0.6694 (ttmm) REVERT: B 441 ARG cc_start: 0.8079 (ptp90) cc_final: 0.7703 (ptp90) REVERT: B 442 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7926 (mm-30) REVERT: B 573 ILE cc_start: 0.8305 (tt) cc_final: 0.7949 (tt) REVERT: B 638 LEU cc_start: 0.7307 (tp) cc_final: 0.7099 (pp) REVERT: B 668 ILE cc_start: 0.7146 (mp) cc_final: 0.6858 (pt) outliers start: 21 outliers final: 15 residues processed: 121 average time/residue: 0.0932 time to fit residues: 15.7587 Evaluate side-chains 119 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 11 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 4 optimal weight: 0.0050 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 HIS ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.198308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.166936 restraints weight = 14203.447| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.52 r_work: 0.3995 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9490 Z= 0.121 Angle : 0.525 6.636 12842 Z= 0.281 Chirality : 0.039 0.168 1506 Planarity : 0.004 0.058 1630 Dihedral : 3.860 14.675 1298 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.88 % Allowed : 18.85 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.25), residues: 1196 helix: 2.03 (0.19), residues: 730 sheet: 0.36 (0.58), residues: 68 loop : -2.47 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.015 0.001 TYR B 349 PHE 0.009 0.001 PHE A 302 TRP 0.004 0.000 TRP B 304 HIS 0.004 0.001 HIS A 574 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9490) covalent geometry : angle 0.52496 (12842) hydrogen bonds : bond 0.04985 ( 548) hydrogen bonds : angle 3.94130 ( 1626) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.320 Fit side-chains REVERT: A 323 TRP cc_start: 0.7463 (t-100) cc_final: 0.6570 (t60) REVERT: A 407 GLN cc_start: 0.6297 (mt0) cc_final: 0.5126 (tm-30) REVERT: A 573 ILE cc_start: 0.8354 (tt) cc_final: 0.8113 (tt) REVERT: A 632 LYS cc_start: 0.5149 (mttt) cc_final: 0.4377 (tttm) REVERT: B 159 GLN cc_start: 0.7360 (tp40) cc_final: 0.6552 (tt0) REVERT: B 364 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6555 (mptt) REVERT: B 370 LYS cc_start: 0.7140 (tppt) cc_final: 0.6727 (ttmm) REVERT: B 441 ARG cc_start: 0.8050 (ptp90) cc_final: 0.7710 (ptp90) REVERT: B 442 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7921 (mm-30) REVERT: B 573 ILE cc_start: 0.8285 (tt) cc_final: 0.7942 (tt) REVERT: B 668 ILE cc_start: 0.7119 (mp) cc_final: 0.6835 (pt) REVERT: B 709 GLN cc_start: 0.2473 (OUTLIER) cc_final: 0.2008 (pt0) outliers start: 19 outliers final: 16 residues processed: 112 average time/residue: 0.1024 time to fit residues: 15.9669 Evaluate side-chains 116 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 364 LYS Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 709 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 9 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 76 optimal weight: 0.5980 chunk 64 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.199138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.167903 restraints weight = 14272.517| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 2.53 r_work: 0.4004 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9490 Z= 0.118 Angle : 0.528 8.158 12842 Z= 0.279 Chirality : 0.039 0.184 1506 Planarity : 0.004 0.057 1630 Dihedral : 3.809 14.496 1298 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.88 % Allowed : 19.05 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.25), residues: 1196 helix: 2.04 (0.19), residues: 732 sheet: 0.34 (0.58), residues: 68 loop : -2.45 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.016 0.001 TYR B 349 PHE 0.008 0.001 PHE A 302 TRP 0.003 0.000 TRP A 323 HIS 0.004 0.001 HIS A 574 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 9490) covalent geometry : angle 0.52752 (12842) hydrogen bonds : bond 0.04780 ( 548) hydrogen bonds : angle 3.88270 ( 1626) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.357 Fit side-chains REVERT: A 323 TRP cc_start: 0.7419 (t-100) cc_final: 0.6513 (t60) REVERT: A 407 GLN cc_start: 0.6210 (mt0) cc_final: 0.5067 (tm-30) REVERT: A 573 ILE cc_start: 0.8354 (tt) cc_final: 0.8102 (tt) REVERT: A 632 LYS cc_start: 0.5151 (mttt) cc_final: 0.4413 (tttm) REVERT: B 159 GLN cc_start: 0.7342 (tp40) cc_final: 0.6510 (tt0) REVERT: B 370 LYS cc_start: 0.7071 (tppt) cc_final: 0.6749 (ttmm) REVERT: B 442 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7940 (mm-30) REVERT: B 552 ARG cc_start: 0.5909 (mtt180) cc_final: 0.5600 (mpt-90) REVERT: B 573 ILE cc_start: 0.8335 (tt) cc_final: 0.7967 (tt) REVERT: B 668 ILE cc_start: 0.6929 (mp) cc_final: 0.6702 (pt) REVERT: B 709 GLN cc_start: 0.2441 (OUTLIER) cc_final: 0.1991 (pt0) outliers start: 19 outliers final: 17 residues processed: 116 average time/residue: 0.0998 time to fit residues: 16.1825 Evaluate side-chains 118 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 709 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 63 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 38 optimal weight: 0.0030 chunk 94 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.201618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.170551 restraints weight = 14214.822| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 2.53 r_work: 0.4033 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9490 Z= 0.114 Angle : 0.529 8.935 12842 Z= 0.277 Chirality : 0.038 0.172 1506 Planarity : 0.004 0.059 1630 Dihedral : 3.661 14.349 1298 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.79 % Allowed : 19.44 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.25), residues: 1196 helix: 2.13 (0.19), residues: 732 sheet: 0.50 (0.57), residues: 68 loop : -2.40 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.017 0.001 TYR B 349 PHE 0.008 0.001 PHE A 271 TRP 0.004 0.001 TRP A 323 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 9490) covalent geometry : angle 0.52899 (12842) hydrogen bonds : bond 0.04343 ( 548) hydrogen bonds : angle 3.75513 ( 1626) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 159 GLN cc_start: 0.7557 (tp40) cc_final: 0.6755 (tt0) REVERT: A 323 TRP cc_start: 0.7348 (t-100) cc_final: 0.6412 (t60) REVERT: A 407 GLN cc_start: 0.6083 (mt0) cc_final: 0.4973 (tm-30) REVERT: A 410 MET cc_start: 0.5627 (tmm) cc_final: 0.5419 (tmm) REVERT: A 573 ILE cc_start: 0.8385 (tt) cc_final: 0.8117 (tt) REVERT: A 632 LYS cc_start: 0.5082 (mttt) cc_final: 0.4457 (tttm) REVERT: B 159 GLN cc_start: 0.7207 (tp40) cc_final: 0.6439 (tt0) REVERT: B 407 GLN cc_start: 0.5868 (mt0) cc_final: 0.5163 (tm-30) REVERT: B 410 MET cc_start: 0.6085 (mmm) cc_final: 0.5380 (tmm) REVERT: B 442 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7941 (mm-30) REVERT: B 573 ILE cc_start: 0.8339 (tt) cc_final: 0.7976 (tt) REVERT: B 668 ILE cc_start: 0.6879 (mp) cc_final: 0.6647 (pt) REVERT: B 709 GLN cc_start: 0.2270 (OUTLIER) cc_final: 0.1927 (pt0) outliers start: 18 outliers final: 16 residues processed: 119 average time/residue: 0.0895 time to fit residues: 15.0735 Evaluate side-chains 122 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 709 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 0.0970 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.197066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.165737 restraints weight = 14217.119| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.52 r_work: 0.3983 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9490 Z= 0.137 Angle : 0.564 7.696 12842 Z= 0.298 Chirality : 0.039 0.181 1506 Planarity : 0.004 0.056 1630 Dihedral : 3.803 15.646 1298 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.79 % Allowed : 19.94 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.25), residues: 1196 helix: 2.00 (0.19), residues: 734 sheet: 0.38 (0.58), residues: 68 loop : -2.51 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 264 TYR 0.016 0.002 TYR B 349 PHE 0.012 0.001 PHE B 601 TRP 0.004 0.001 TRP B 304 HIS 0.004 0.001 HIS A 574 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9490) covalent geometry : angle 0.56417 (12842) hydrogen bonds : bond 0.04944 ( 548) hydrogen bonds : angle 3.86707 ( 1626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1901.54 seconds wall clock time: 33 minutes 17.20 seconds (1997.20 seconds total)