Starting phenix.real_space_refine on Wed Sep 25 21:48:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p46_20244/09_2024/6p46_20244.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p46_20244/09_2024/6p46_20244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p46_20244/09_2024/6p46_20244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p46_20244/09_2024/6p46_20244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p46_20244/09_2024/6p46_20244.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p46_20244/09_2024/6p46_20244.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 2 9.91 5 S 78 5.16 5 C 7508 2.51 5 N 1824 2.21 5 O 1966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11378 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5688 Classifications: {'peptide': 690} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 659} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 11.20, per 1000 atoms: 0.98 Number of scatterers: 11378 At special positions: 0 Unit cell: (81.543, 128.139, 111.195, 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 2 19.99 S 78 16.00 O 1966 8.00 N 1824 7.00 C 7508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=1.56 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=1.89 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=1.32 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.5 seconds 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2624 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 58.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 131 through 140 removed outlier: 3.911A pdb=" N THR A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.718A pdb=" N VAL A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A 219 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 removed outlier: 4.608A pdb=" N ARG A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 237' Processing helix chain 'A' and resid 266 through 273 removed outlier: 3.534A pdb=" N ARG A 271 " --> pdb=" O TYR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.687A pdb=" N ARG A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 312 removed outlier: 3.906A pdb=" N TYR A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 306 " --> pdb=" O TRP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 327 removed outlier: 4.101A pdb=" N PHE A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 369 removed outlier: 3.852A pdb=" N CYS A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU A 366 " --> pdb=" O ASN A 362 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N SER A 367 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 408 removed outlier: 4.134A pdb=" N VAL A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 489 removed outlier: 3.683A pdb=" N PHE A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TRP A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 486 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 539 removed outlier: 3.914A pdb=" N SER A 510 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE A 533 " --> pdb=" O GLU A 529 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 538 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 572 removed outlier: 3.917A pdb=" N MET A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE A 572 " --> pdb=" O PHE A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.618A pdb=" N LEU A 588 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 614 removed outlier: 3.661A pdb=" N GLN A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 638 removed outlier: 3.843A pdb=" N ASN A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A 625 " --> pdb=" O ASN A 621 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) Proline residue: A 628 - end of helix removed outlier: 3.659A pdb=" N GLY A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 656 removed outlier: 3.508A pdb=" N GLN A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 679 removed outlier: 4.205A pdb=" N MET A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.972A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 707 " --> pdb=" O ASP A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 748 removed outlier: 3.767A pdb=" N ILE A 734 " --> pdb=" O GLN A 730 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 760 removed outlier: 3.759A pdb=" N TYR A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 856 removed outlier: 3.788A pdb=" N SER A 854 " --> pdb=" O LYS A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 866 Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'B' and resid 90 through 97 Processing helix chain 'B' and resid 131 through 140 removed outlier: 3.911A pdb=" N THR B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 220 removed outlier: 3.717A pdb=" N VAL B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 237 removed outlier: 4.608A pdb=" N ARG B 235 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 231 through 237' Processing helix chain 'B' and resid 266 through 273 removed outlier: 3.533A pdb=" N ARG B 271 " --> pdb=" O TYR B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 290 removed outlier: 3.687A pdb=" N ARG B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 312 removed outlier: 3.905A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 306 " --> pdb=" O TRP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 327 removed outlier: 4.101A pdb=" N PHE B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 369 removed outlier: 3.852A pdb=" N CYS B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N SER B 367 " --> pdb=" O ILE B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 408 removed outlier: 4.133A pdb=" N VAL B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 489 removed outlier: 3.682A pdb=" N PHE B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 464 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 486 " --> pdb=" O PHE B 482 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B 487 " --> pdb=" O ILE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 539 removed outlier: 3.914A pdb=" N SER B 510 " --> pdb=" O GLN B 506 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B 533 " --> pdb=" O GLU B 529 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 538 " --> pdb=" O MET B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 572 removed outlier: 3.916A pdb=" N MET B 553 " --> pdb=" O ASN B 549 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE B 572 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.619A pdb=" N LEU B 588 " --> pdb=" O VAL B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 614 removed outlier: 3.662A pdb=" N GLN B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 624 removed outlier: 3.844A pdb=" N ASN B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 638 removed outlier: 3.658A pdb=" N GLY B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 656 removed outlier: 3.508A pdb=" N GLN B 652 " --> pdb=" O PRO B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 679 removed outlier: 4.206A pdb=" N MET B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.972A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 707 " --> pdb=" O ASP B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 748 removed outlier: 3.766A pdb=" N ILE B 734 " --> pdb=" O GLN B 730 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 760 removed outlier: 3.759A pdb=" N TYR B 756 " --> pdb=" O PRO B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 856 removed outlier: 3.788A pdb=" N SER B 854 " --> pdb=" O LYS B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 866 Processing helix chain 'B' and resid 867 through 871 494 hydrogen bonds defined for protein. 1464 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: 3.06 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3090 1.33 - 1.45: 2506 1.45 - 1.57: 5970 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 11686 Sorted by residual: bond pdb=" CA ASP A 375 " pdb=" C ASP A 375 " ideal model delta sigma weight residual 1.527 1.567 -0.041 1.21e-02 6.83e+03 1.14e+01 bond pdb=" CA ASP B 375 " pdb=" C ASP B 375 " ideal model delta sigma weight residual 1.527 1.567 -0.041 1.21e-02 6.83e+03 1.13e+01 bond pdb=" CA ALA B 571 " pdb=" C ALA B 571 " ideal model delta sigma weight residual 1.523 1.566 -0.043 1.34e-02 5.57e+03 1.01e+01 bond pdb=" CA ALA A 571 " pdb=" C ALA A 571 " ideal model delta sigma weight residual 1.523 1.565 -0.042 1.34e-02 5.57e+03 9.92e+00 bond pdb=" N SER A 376 " pdb=" CA SER A 376 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.31e+00 ... (remaining 11681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 15203 3.25 - 6.49: 510 6.49 - 9.74: 93 9.74 - 12.99: 24 12.99 - 16.23: 2 Bond angle restraints: 15832 Sorted by residual: angle pdb=" N ALA B 683 " pdb=" CA ALA B 683 " pdb=" C ALA B 683 " ideal model delta sigma weight residual 112.93 96.70 16.23 1.33e+00 5.65e-01 1.49e+02 angle pdb=" N ALA A 683 " pdb=" CA ALA A 683 " pdb=" C ALA A 683 " ideal model delta sigma weight residual 112.93 96.73 16.20 1.33e+00 5.65e-01 1.48e+02 angle pdb=" N LYS B 335 " pdb=" CA LYS B 335 " pdb=" C LYS B 335 " ideal model delta sigma weight residual 112.68 100.25 12.43 1.33e+00 5.65e-01 8.73e+01 angle pdb=" N LYS A 335 " pdb=" CA LYS A 335 " pdb=" C LYS A 335 " ideal model delta sigma weight residual 112.68 100.28 12.40 1.33e+00 5.65e-01 8.69e+01 angle pdb=" N ILE B 622 " pdb=" CA ILE B 622 " pdb=" C ILE B 622 " ideal model delta sigma weight residual 111.90 104.77 7.13 8.10e-01 1.52e+00 7.75e+01 ... (remaining 15827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 5904 17.09 - 34.17: 740 34.17 - 51.26: 167 51.26 - 68.35: 41 68.35 - 85.43: 15 Dihedral angle restraints: 6867 sinusoidal: 2791 harmonic: 4076 Sorted by residual: dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual -86.00 -159.23 73.23 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CB CYS A 338 " pdb=" SG CYS A 338 " pdb=" SG CYS A 365 " pdb=" CB CYS A 365 " ideal model delta sinusoidal sigma weight residual 93.00 37.09 55.91 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CA ARG B 48 " pdb=" C ARG B 48 " pdb=" N THR B 49 " pdb=" CA THR B 49 " ideal model delta harmonic sigma weight residual 180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 6864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1489 0.100 - 0.200: 189 0.200 - 0.301: 32 0.301 - 0.401: 24 0.401 - 0.501: 4 Chirality restraints: 1738 Sorted by residual: chirality pdb=" CA PHE A 577 " pdb=" N PHE A 577 " pdb=" C PHE A 577 " pdb=" CB PHE A 577 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA PHE B 577 " pdb=" N PHE B 577 " pdb=" C PHE B 577 " pdb=" CB PHE B 577 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.21e+00 chirality pdb=" CA ASN A 330 " pdb=" N ASN A 330 " pdb=" C ASN A 330 " pdb=" CB ASN A 330 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.83e+00 ... (remaining 1735 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 599 " 0.022 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C GLY A 599 " -0.079 2.00e-02 2.50e+03 pdb=" O GLY A 599 " 0.030 2.00e-02 2.50e+03 pdb=" N GLY A 600 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 599 " -0.022 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C GLY B 599 " 0.079 2.00e-02 2.50e+03 pdb=" O GLY B 599 " -0.030 2.00e-02 2.50e+03 pdb=" N GLY B 600 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 570 " -0.022 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" C ILE A 570 " 0.076 2.00e-02 2.50e+03 pdb=" O ILE A 570 " -0.029 2.00e-02 2.50e+03 pdb=" N ALA A 571 " -0.025 2.00e-02 2.50e+03 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.03: 5 2.03 - 2.75: 1939 2.75 - 3.47: 16170 3.47 - 4.18: 27215 4.18 - 4.90: 46740 Nonbonded interactions: 92069 Sorted by model distance: nonbonded pdb=" SG CYS B 596 " pdb=" SG CYS B 601 " model vdw 1.317 3.760 nonbonded pdb=" SG CYS B 338 " pdb=" SG CYS B 365 " model vdw 1.557 3.760 nonbonded pdb=" C GLU B 594 " pdb=" OE1 GLU B 595 " model vdw 1.800 3.270 nonbonded pdb=" C GLU A 594 " pdb=" OE1 GLU A 595 " model vdw 1.800 3.270 nonbonded pdb=" SG CYS B 349 " pdb=" SG CYS B 807 " model vdw 1.885 3.760 ... (remaining 92064 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.910 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.750 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 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 : 0.009 0.085 11686 Z= 0.586 Angle : 1.434 16.232 15832 Z= 0.886 Chirality : 0.084 0.501 1738 Planarity : 0.010 0.101 1944 Dihedral : 16.158 85.434 4234 Min Nonbonded Distance : 1.317 Molprobity Statistics. All-atom Clashscore : 25.94 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.99 % Favored : 92.71 % Rotamer: Outliers : 3.71 % Allowed : 11.85 % Favored : 84.44 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.45 (0.16), residues: 1344 helix: -3.36 (0.14), residues: 724 sheet: None (None), residues: 0 loop : -3.94 (0.18), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 397 HIS 0.005 0.002 HIS A 830 PHE 0.025 0.003 PHE B 760 TYR 0.034 0.003 TYR A 809 ARG 0.008 0.001 ARG B 266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 280 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8792 (mp) REVERT: A 534 MET cc_start: 0.7302 (mmt) cc_final: 0.7087 (mmt) REVERT: A 546 ASP cc_start: 0.7978 (t0) cc_final: 0.7654 (t70) REVERT: A 618 ILE cc_start: 0.9052 (mm) cc_final: 0.8779 (mt) REVERT: B 224 VAL cc_start: 0.1020 (OUTLIER) cc_final: 0.0750 (t) REVERT: B 305 TYR cc_start: 0.7810 (t80) cc_final: 0.7366 (t80) REVERT: B 348 MET cc_start: 0.7175 (mpp) cc_final: 0.6651 (mmm) REVERT: B 523 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8735 (mp) REVERT: B 546 ASP cc_start: 0.7936 (t0) cc_final: 0.7646 (t0) REVERT: B 555 MET cc_start: 0.7960 (tpp) cc_final: 0.7733 (tpt) REVERT: B 855 TYR cc_start: 0.7063 (t80) cc_final: 0.6777 (t80) outliers start: 46 outliers final: 25 residues processed: 323 average time/residue: 0.2275 time to fit residues: 103.4407 Evaluate side-chains 230 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 202 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 866 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 80 optimal weight: 0.0470 chunk 125 optimal weight: 0.5980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN A 283 GLN A 328 GLN A 544 GLN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN A 740 ASN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 275 HIS B 283 GLN B 328 GLN B 544 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN B 696 ASN B 710 GLN B 740 ASN ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11686 Z= 0.234 Angle : 0.781 10.866 15832 Z= 0.416 Chirality : 0.046 0.170 1738 Planarity : 0.007 0.075 1944 Dihedral : 8.446 58.033 1560 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.19 % Allowed : 16.94 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.18), residues: 1344 helix: -2.32 (0.15), residues: 772 sheet: -5.17 (0.93), residues: 20 loop : -3.63 (0.20), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 397 HIS 0.003 0.001 HIS A 275 PHE 0.014 0.002 PHE A 851 TYR 0.025 0.002 TYR A 242 ARG 0.006 0.001 ARG A 810 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 239 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 TYR cc_start: 0.7704 (t80) cc_final: 0.7495 (t80) REVERT: A 347 LEU cc_start: 0.6205 (tt) cc_final: 0.5271 (mp) REVERT: A 392 LEU cc_start: 0.8084 (mt) cc_final: 0.7757 (mt) REVERT: A 523 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8925 (mp) REVERT: A 618 ILE cc_start: 0.9056 (mm) cc_final: 0.8728 (mt) REVERT: A 659 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6376 (ptp) REVERT: A 705 TRP cc_start: 0.7954 (t60) cc_final: 0.7654 (t60) REVERT: A 773 MET cc_start: 0.7247 (mmm) cc_final: 0.6554 (tpp) REVERT: B 305 TYR cc_start: 0.7749 (t80) cc_final: 0.7356 (t80) REVERT: B 700 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7894 (tt) REVERT: B 773 MET cc_start: 0.5145 (OUTLIER) cc_final: 0.4599 (mtp) outliers start: 52 outliers final: 19 residues processed: 276 average time/residue: 0.2194 time to fit residues: 87.8830 Evaluate side-chains 228 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 866 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 100 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 HIS ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11686 Z= 0.224 Angle : 0.701 7.996 15832 Z= 0.370 Chirality : 0.044 0.147 1738 Planarity : 0.006 0.069 1944 Dihedral : 7.122 57.391 1531 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.52 % Allowed : 18.47 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.20), residues: 1344 helix: -1.68 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -3.52 (0.21), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 397 HIS 0.003 0.001 HIS A 275 PHE 0.025 0.002 PHE A 321 TYR 0.031 0.002 TYR A 242 ARG 0.007 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 224 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LEU cc_start: 0.8178 (mt) cc_final: 0.7831 (mt) REVERT: A 534 MET cc_start: 0.7367 (mmt) cc_final: 0.7023 (mmt) REVERT: A 618 ILE cc_start: 0.8966 (mm) cc_final: 0.8661 (mt) REVERT: A 700 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7561 (tt) REVERT: A 705 TRP cc_start: 0.7888 (t60) cc_final: 0.7534 (t60) REVERT: A 742 MET cc_start: 0.7029 (mtt) cc_final: 0.6799 (mtp) REVERT: B 70 ARG cc_start: 0.7332 (ptm-80) cc_final: 0.6889 (ptt90) REVERT: B 291 TYR cc_start: 0.6332 (t80) cc_final: 0.6124 (t80) REVERT: B 305 TYR cc_start: 0.7743 (t80) cc_final: 0.7413 (t80) REVERT: B 555 MET cc_start: 0.7529 (tpt) cc_final: 0.7234 (tpt) REVERT: B 700 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7943 (tt) outliers start: 56 outliers final: 31 residues processed: 261 average time/residue: 0.2062 time to fit residues: 78.6595 Evaluate side-chains 241 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 208 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 768 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 133 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN A 506 GLN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN B 362 ASN ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11686 Z= 0.211 Angle : 0.684 7.994 15832 Z= 0.359 Chirality : 0.044 0.138 1738 Planarity : 0.006 0.064 1944 Dihedral : 6.649 56.934 1521 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 4.52 % Allowed : 19.60 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.20), residues: 1344 helix: -1.43 (0.17), residues: 786 sheet: None (None), residues: 0 loop : -3.56 (0.21), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 397 HIS 0.004 0.001 HIS A 844 PHE 0.021 0.001 PHE A 321 TYR 0.041 0.002 TYR A 242 ARG 0.009 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 221 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 TYR cc_start: 0.6131 (t80) cc_final: 0.5885 (t80) REVERT: A 380 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6636 (mp) REVERT: A 523 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8946 (mp) REVERT: A 534 MET cc_start: 0.7378 (mmt) cc_final: 0.7126 (mmt) REVERT: A 618 ILE cc_start: 0.8981 (mm) cc_final: 0.8670 (mt) REVERT: A 700 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7616 (tt) REVERT: A 705 TRP cc_start: 0.7876 (t60) cc_final: 0.7476 (t60) REVERT: A 742 MET cc_start: 0.7077 (mtt) cc_final: 0.6797 (mtp) REVERT: B 70 ARG cc_start: 0.7244 (ptm-80) cc_final: 0.6791 (ptt90) REVERT: B 242 TYR cc_start: 0.7737 (m-10) cc_final: 0.7482 (m-10) REVERT: B 305 TYR cc_start: 0.7746 (t80) cc_final: 0.7415 (t80) REVERT: B 700 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7910 (tt) REVERT: B 839 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.7466 (mm) outliers start: 56 outliers final: 32 residues processed: 253 average time/residue: 0.2183 time to fit residues: 80.5480 Evaluate side-chains 245 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 208 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 0.0170 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 119 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11686 Z= 0.313 Angle : 0.737 7.992 15832 Z= 0.388 Chirality : 0.047 0.173 1738 Planarity : 0.006 0.063 1944 Dihedral : 6.647 58.206 1521 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 4.76 % Allowed : 21.45 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.20), residues: 1344 helix: -1.36 (0.17), residues: 786 sheet: None (None), residues: 0 loop : -3.35 (0.22), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 397 HIS 0.005 0.001 HIS A 830 PHE 0.034 0.002 PHE B 685 TYR 0.038 0.002 TYR A 242 ARG 0.009 0.001 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 212 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 TYR cc_start: 0.8038 (t80) cc_final: 0.7680 (t80) REVERT: A 347 LEU cc_start: 0.6151 (tt) cc_final: 0.5257 (mp) REVERT: A 523 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8996 (mp) REVERT: A 534 MET cc_start: 0.7370 (mmt) cc_final: 0.6984 (mmt) REVERT: A 618 ILE cc_start: 0.8999 (mm) cc_final: 0.8718 (mt) REVERT: A 632 ASN cc_start: 0.7991 (m-40) cc_final: 0.7789 (m-40) REVERT: A 700 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7756 (tt) REVERT: A 705 TRP cc_start: 0.8101 (t60) cc_final: 0.7689 (t60) REVERT: B 305 TYR cc_start: 0.7937 (t80) cc_final: 0.7567 (t80) REVERT: B 321 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.6531 (p90) REVERT: B 659 MET cc_start: 0.6256 (ptt) cc_final: 0.6012 (ptt) REVERT: B 700 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7904 (tt) outliers start: 59 outliers final: 38 residues processed: 251 average time/residue: 0.2180 time to fit residues: 79.0642 Evaluate side-chains 237 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 195 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 128 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11686 Z= 0.212 Angle : 0.685 8.176 15832 Z= 0.360 Chirality : 0.045 0.200 1738 Planarity : 0.006 0.061 1944 Dihedral : 6.421 57.115 1521 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 4.27 % Allowed : 22.10 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.20), residues: 1344 helix: -1.15 (0.17), residues: 796 sheet: None (None), residues: 0 loop : -3.35 (0.22), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 397 HIS 0.004 0.001 HIS A 844 PHE 0.035 0.001 PHE B 685 TYR 0.030 0.001 TYR A 242 ARG 0.009 0.001 ARG B 592 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 204 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7806 (mm-30) REVERT: A 523 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8926 (mp) REVERT: A 534 MET cc_start: 0.7247 (mmt) cc_final: 0.6973 (mmt) REVERT: A 618 ILE cc_start: 0.8972 (mm) cc_final: 0.8682 (mt) REVERT: A 700 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7705 (tt) REVERT: A 705 TRP cc_start: 0.7986 (t60) cc_final: 0.7535 (t60) REVERT: A 750 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6702 (ptp) REVERT: A 863 ILE cc_start: 0.6246 (OUTLIER) cc_final: 0.5840 (mp) REVERT: B 305 TYR cc_start: 0.7708 (t80) cc_final: 0.7439 (t80) REVERT: B 321 PHE cc_start: 0.6607 (OUTLIER) cc_final: 0.6332 (p90) REVERT: B 591 TYR cc_start: 0.5970 (p90) cc_final: 0.5449 (t80) REVERT: B 631 MET cc_start: 0.7221 (mmm) cc_final: 0.7008 (mmm) REVERT: B 700 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7839 (tt) outliers start: 53 outliers final: 37 residues processed: 238 average time/residue: 0.2142 time to fit residues: 75.1406 Evaluate side-chains 237 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 194 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 777 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 97 optimal weight: 0.0040 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 133 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN A 696 ASN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11686 Z= 0.208 Angle : 0.677 9.567 15832 Z= 0.355 Chirality : 0.045 0.194 1738 Planarity : 0.006 0.061 1944 Dihedral : 6.261 57.031 1521 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 4.84 % Allowed : 22.58 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.21), residues: 1344 helix: -0.94 (0.17), residues: 798 sheet: None (None), residues: 0 loop : -3.22 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 397 HIS 0.003 0.001 HIS A 275 PHE 0.030 0.002 PHE B 685 TYR 0.030 0.002 TYR A 305 ARG 0.005 0.000 ARG B 592 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 207 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.5489 (t80) cc_final: 0.4749 (t80) REVERT: A 523 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8874 (mp) REVERT: A 534 MET cc_start: 0.7367 (mmt) cc_final: 0.7150 (mmt) REVERT: A 705 TRP cc_start: 0.7883 (t60) cc_final: 0.7529 (t60) REVERT: A 750 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6713 (ptp) REVERT: A 863 ILE cc_start: 0.6159 (OUTLIER) cc_final: 0.5775 (mp) REVERT: B 305 TYR cc_start: 0.7776 (t80) cc_final: 0.7499 (t80) REVERT: B 321 PHE cc_start: 0.6535 (OUTLIER) cc_final: 0.6261 (p90) REVERT: B 591 TYR cc_start: 0.5883 (p90) cc_final: 0.5353 (t80) REVERT: B 700 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7853 (tt) outliers start: 60 outliers final: 41 residues processed: 244 average time/residue: 0.2044 time to fit residues: 72.8334 Evaluate side-chains 242 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 196 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 542 ARG Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11686 Z= 0.219 Angle : 0.697 9.905 15832 Z= 0.362 Chirality : 0.045 0.169 1738 Planarity : 0.006 0.060 1944 Dihedral : 6.191 56.507 1521 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 4.44 % Allowed : 23.63 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.21), residues: 1344 helix: -0.88 (0.17), residues: 798 sheet: None (None), residues: 0 loop : -3.16 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 705 HIS 0.004 0.001 HIS A 275 PHE 0.028 0.001 PHE B 685 TYR 0.028 0.001 TYR A 242 ARG 0.008 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 200 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.6688 (tptp) cc_final: 0.6280 (mtmm) REVERT: A 523 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8859 (mp) REVERT: A 555 MET cc_start: 0.7645 (tpt) cc_final: 0.7291 (tpt) REVERT: A 618 ILE cc_start: 0.8921 (mm) cc_final: 0.8603 (mt) REVERT: A 705 TRP cc_start: 0.7810 (t60) cc_final: 0.7514 (t60) REVERT: A 750 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6690 (ptp) REVERT: A 863 ILE cc_start: 0.6148 (OUTLIER) cc_final: 0.5757 (mp) REVERT: B 305 TYR cc_start: 0.7766 (t80) cc_final: 0.7485 (t80) REVERT: B 321 PHE cc_start: 0.6653 (OUTLIER) cc_final: 0.5985 (p90) REVERT: B 591 TYR cc_start: 0.5923 (p90) cc_final: 0.5332 (t80) REVERT: B 700 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7844 (tt) REVERT: B 750 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7897 (ptm) outliers start: 55 outliers final: 38 residues processed: 232 average time/residue: 0.2131 time to fit residues: 72.4924 Evaluate side-chains 242 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 198 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 768 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 0.0000 chunk 116 optimal weight: 0.1980 chunk 123 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 112 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 131 optimal weight: 0.5980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11686 Z= 0.189 Angle : 0.681 11.334 15832 Z= 0.352 Chirality : 0.044 0.222 1738 Planarity : 0.006 0.060 1944 Dihedral : 5.947 54.511 1521 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.71 % Allowed : 24.27 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.21), residues: 1344 helix: -0.69 (0.18), residues: 796 sheet: None (None), residues: 0 loop : -3.04 (0.23), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 705 HIS 0.006 0.001 HIS A 844 PHE 0.033 0.001 PHE A 321 TYR 0.023 0.001 TYR A 242 ARG 0.005 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 210 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8793 (mp) REVERT: A 555 MET cc_start: 0.7705 (tpt) cc_final: 0.7333 (tpt) REVERT: A 618 ILE cc_start: 0.8925 (mm) cc_final: 0.8569 (mt) REVERT: A 773 MET cc_start: 0.7097 (tpp) cc_final: 0.6285 (tpp) REVERT: B 321 PHE cc_start: 0.6498 (OUTLIER) cc_final: 0.5599 (p90) REVERT: B 591 TYR cc_start: 0.5878 (p90) cc_final: 0.5280 (t80) REVERT: B 629 TRP cc_start: 0.6877 (t60) cc_final: 0.5987 (t60) REVERT: B 700 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7781 (tt) REVERT: B 742 MET cc_start: 0.7210 (mtt) cc_final: 0.6731 (mtt) REVERT: B 750 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7885 (ptm) outliers start: 46 outliers final: 35 residues processed: 236 average time/residue: 0.2131 time to fit residues: 73.3296 Evaluate side-chains 231 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 768 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 0.0470 chunk 137 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 109 optimal weight: 0.3980 chunk 11 optimal weight: 0.0170 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN A 674 GLN ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11686 Z= 0.212 Angle : 0.703 11.958 15832 Z= 0.365 Chirality : 0.045 0.208 1738 Planarity : 0.006 0.059 1944 Dihedral : 5.868 53.821 1519 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.55 % Allowed : 24.52 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.21), residues: 1344 helix: -0.62 (0.18), residues: 794 sheet: None (None), residues: 0 loop : -2.99 (0.23), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 397 HIS 0.005 0.001 HIS B 844 PHE 0.027 0.001 PHE A 321 TYR 0.047 0.001 TYR B 305 ARG 0.006 0.000 ARG A 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 203 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.6612 (tptp) cc_final: 0.6271 (mtmm) REVERT: A 523 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8771 (mp) REVERT: A 555 MET cc_start: 0.7650 (tpt) cc_final: 0.7342 (tpt) REVERT: A 618 ILE cc_start: 0.8902 (mm) cc_final: 0.8568 (mt) REVERT: A 629 TRP cc_start: 0.6986 (t60) cc_final: 0.6118 (t60) REVERT: A 863 ILE cc_start: 0.6066 (OUTLIER) cc_final: 0.5706 (mp) REVERT: B 48 ARG cc_start: 0.3545 (tmt170) cc_final: 0.2785 (ttp-170) REVERT: B 321 PHE cc_start: 0.6515 (OUTLIER) cc_final: 0.5674 (p90) REVERT: B 591 TYR cc_start: 0.5912 (p90) cc_final: 0.5289 (t80) REVERT: B 629 TRP cc_start: 0.6827 (t60) cc_final: 0.6056 (t60) REVERT: B 700 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7778 (tt) REVERT: B 742 MET cc_start: 0.7078 (mtt) cc_final: 0.6629 (mtt) REVERT: B 750 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7776 (ptm) outliers start: 44 outliers final: 34 residues processed: 229 average time/residue: 0.2123 time to fit residues: 71.3718 Evaluate side-chains 232 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 768 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 777 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 112 optimal weight: 0.0010 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN ** B 825 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 = 0.4779 r_free = 0.4779 target = 0.242413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.202934 restraints weight = 15392.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.204480 restraints weight = 11733.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.206220 restraints weight = 8922.654| |-----------------------------------------------------------------------------| r_work (final): 0.4430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11686 Z= 0.208 Angle : 0.702 12.639 15832 Z= 0.361 Chirality : 0.044 0.211 1738 Planarity : 0.006 0.064 1944 Dihedral : 5.842 55.725 1519 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.39 % Allowed : 25.08 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.22), residues: 1344 helix: -0.56 (0.18), residues: 796 sheet: None (None), residues: 0 loop : -2.98 (0.23), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 397 HIS 0.005 0.001 HIS B 844 PHE 0.027 0.001 PHE A 321 TYR 0.035 0.002 TYR B 477 ARG 0.004 0.000 ARG B 592 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2368.81 seconds wall clock time: 43 minutes 24.75 seconds (2604.75 seconds total)