Starting phenix.real_space_refine on Tue Jul 29 11:49:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p46_20244/07_2025/6p46_20244.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p46_20244/07_2025/6p46_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/cci-nas-00/data/ceres_data/6p46_20244/07_2025/6p46_20244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p46_20244/07_2025/6p46_20244.map" model { file = "/net/cci-nas-00/data/ceres_data/6p46_20244/07_2025/6p46_20244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p46_20244/07_2025/6p46_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 12.94, per 1000 atoms: 1.14 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=6, 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 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=1.56 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=1.89 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 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: 3.02 Conformation dependent library (CDL) restraints added in 1.4 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: 0.99 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: 2.86 Time building geometry restraints manager: 3.56 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: 5906 17.09 - 34.17: 744 34.17 - 51.26: 168 51.26 - 68.35: 42 68.35 - 85.43: 16 Dihedral angle restraints: 6876 sinusoidal: 2800 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 B 596 " pdb=" SG CYS B 596 " pdb=" SG CYS B 601 " pdb=" CB CYS B 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 ... (remaining 6873 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: 1.80 - 2.42: 80 2.42 - 3.04: 6753 3.04 - 3.66: 17729 3.66 - 4.28: 25929 4.28 - 4.90: 41569 Nonbonded interactions: 92060 Sorted by model distance: 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=" OE1 GLU A 624 " pdb="CA CA A1001 " model vdw 2.034 2.510 nonbonded pdb=" OE1 GLU B 624 " pdb="CA CA B1001 " model vdw 2.035 2.510 nonbonded pdb=" N GLU B 595 " pdb=" OE1 GLU B 595 " model vdw 2.079 3.120 ... (remaining 92055 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: 0.05 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: 2.010 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.750 Find NCS groups from input model: 0.210 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.440 ------------------------------------------------------------------------------- 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 : 0.015 0.714 11692 Z= 0.719 Angle : 1.551 37.722 15844 Z= 0.930 Chirality : 0.084 0.501 1738 Planarity : 0.010 0.101 1944 Dihedral : 16.158 85.434 4234 Min Nonbonded Distance : 1.800 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 Details of bonding type rmsd hydrogen bonds : bond 0.31387 ( 494) hydrogen bonds : angle 12.03939 ( 1464) SS BOND : bond 0.50192 ( 6) SS BOND : angle 21.57957 ( 12) covalent geometry : bond 0.00941 (11686) covalent geometry : angle 1.43371 (15832) *********************** 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 to be fit. rotamer outliers: 46 poor density : 280 time to evaluate : 1.197 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: 0.2390 time to fit residues: 109.4402 Evaluate side-chains 230 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.237625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.197507 restraints weight = 15276.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.199575 restraints weight = 10818.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.201258 restraints weight = 8196.708| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 11692 Z= 0.171 Angle : 0.777 11.093 15844 Z= 0.412 Chirality : 0.045 0.171 1738 Planarity : 0.007 0.075 1944 Dihedral : 8.508 57.921 1560 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.35 % Allowed : 16.69 % Favored : 78.95 % 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: -4.37 (0.18), residues: 1344 helix: -2.30 (0.15), residues: 770 sheet: -5.11 (0.94), residues: 20 loop : -3.64 (0.20), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 397 HIS 0.003 0.001 HIS A 249 PHE 0.015 0.002 PHE A 851 TYR 0.025 0.002 TYR A 406 ARG 0.006 0.001 ARG A 810 Details of bonding type rmsd hydrogen bonds : bond 0.06534 ( 494) hydrogen bonds : angle 6.53663 ( 1464) SS BOND : bond 0.01770 ( 6) SS BOND : angle 0.94024 ( 12) covalent geometry : bond 0.00368 (11686) covalent geometry : angle 0.77715 (15832) *********************** 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 295 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 241 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ARG cc_start: 0.5525 (ttt180) cc_final: 0.5250 (ttp-170) REVERT: A 305 TYR cc_start: 0.7700 (t80) cc_final: 0.7490 (t80) REVERT: A 347 LEU cc_start: 0.6187 (tt) cc_final: 0.5290 (mp) REVERT: A 392 LEU cc_start: 0.8113 (mt) cc_final: 0.7788 (mt) REVERT: A 523 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8920 (mp) REVERT: A 618 ILE cc_start: 0.9055 (mm) cc_final: 0.8725 (mt) REVERT: A 659 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6539 (ptp) REVERT: A 705 TRP cc_start: 0.7932 (t60) cc_final: 0.7641 (t60) REVERT: A 773 MET cc_start: 0.7259 (mmm) cc_final: 0.6564 (tpp) REVERT: B 305 TYR cc_start: 0.7749 (t80) cc_final: 0.7334 (t80) REVERT: B 700 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7965 (tt) REVERT: B 773 MET cc_start: 0.5095 (OUTLIER) cc_final: 0.4553 (mtp) REVERT: B 855 TYR cc_start: 0.6741 (t80) cc_final: 0.6534 (t80) outliers start: 54 outliers final: 23 residues processed: 280 average time/residue: 0.2446 time to fit residues: 99.6914 Evaluate side-chains 238 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LYS 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 524 LEU 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 596 CYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 714 MET 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 128 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** 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** A 844 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.232884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.192076 restraints weight = 15563.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.193755 restraints weight = 10988.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.195371 restraints weight = 8716.768| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11692 Z= 0.217 Angle : 0.746 8.064 15844 Z= 0.394 Chirality : 0.046 0.166 1738 Planarity : 0.007 0.069 1944 Dihedral : 7.401 59.684 1532 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 4.84 % Allowed : 19.19 % Favored : 75.97 % 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: -3.72 (0.19), residues: 1344 helix: -1.74 (0.17), residues: 766 sheet: None (None), residues: 0 loop : -3.50 (0.20), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 397 HIS 0.006 0.001 HIS B 830 PHE 0.029 0.002 PHE A 321 TYR 0.029 0.002 TYR A 242 ARG 0.005 0.000 ARG A 592 Details of bonding type rmsd hydrogen bonds : bond 0.06072 ( 494) hydrogen bonds : angle 5.88302 ( 1464) SS BOND : bond 0.00565 ( 6) SS BOND : angle 0.95302 ( 12) covalent geometry : bond 0.00492 (11686) covalent geometry : angle 0.74550 (15832) *********************** 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 284 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 224 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.7067 (pm20) REVERT: A 266 ARG cc_start: 0.5749 (ttt180) cc_final: 0.5495 (ttp-170) REVERT: A 523 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8930 (mp) REVERT: A 534 MET cc_start: 0.7431 (mmt) cc_final: 0.7008 (mmt) REVERT: A 618 ILE cc_start: 0.9022 (mm) cc_final: 0.8703 (mt) REVERT: A 700 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7697 (tt) REVERT: A 705 TRP cc_start: 0.8049 (t60) cc_final: 0.7671 (t60) REVERT: B 70 ARG cc_start: 0.7469 (ptm-80) cc_final: 0.6960 (ptt90) REVERT: B 305 TYR cc_start: 0.7920 (t80) cc_final: 0.7494 (t80) REVERT: B 700 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7976 (tt) outliers start: 60 outliers final: 34 residues processed: 270 average time/residue: 0.2563 time to fit residues: 100.8985 Evaluate side-chains 242 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU 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 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 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 700 ILE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 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 509 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 596 CYS 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 27 optimal weight: 0.5980 chunk 55 optimal weight: 0.1980 chunk 14 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 69 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 506 GLN ** A 608 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 506 GLN ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.236958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.197342 restraints weight = 15480.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.198829 restraints weight = 10790.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.200662 restraints weight = 8255.849| |-----------------------------------------------------------------------------| r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11692 Z= 0.148 Angle : 0.685 8.085 15844 Z= 0.360 Chirality : 0.044 0.164 1738 Planarity : 0.006 0.065 1944 Dihedral : 6.891 59.488 1524 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.27 % Allowed : 20.97 % Favored : 74.76 % 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: -3.42 (0.20), residues: 1344 helix: -1.43 (0.17), residues: 774 sheet: None (None), residues: 0 loop : -3.49 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 397 HIS 0.003 0.001 HIS A 275 PHE 0.022 0.001 PHE A 321 TYR 0.035 0.002 TYR A 242 ARG 0.008 0.000 ARG B 542 Details of bonding type rmsd hydrogen bonds : bond 0.05416 ( 494) hydrogen bonds : angle 5.59079 ( 1464) SS BOND : bond 0.00344 ( 6) SS BOND : angle 0.92075 ( 12) covalent geometry : bond 0.00320 (11686) covalent geometry : angle 0.68483 (15832) *********************** 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 278 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 225 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LEU cc_start: 0.6362 (tt) cc_final: 0.5290 (mp) REVERT: A 534 MET cc_start: 0.7300 (mmt) cc_final: 0.6910 (mmt) REVERT: A 618 ILE cc_start: 0.8973 (mm) cc_final: 0.8663 (mt) REVERT: A 700 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7672 (tt) REVERT: A 705 TRP cc_start: 0.7938 (t60) cc_final: 0.7513 (t60) REVERT: B 305 TYR cc_start: 0.7753 (t80) cc_final: 0.7411 (t80) REVERT: B 591 TYR cc_start: 0.5788 (p90) cc_final: 0.5367 (t80) REVERT: B 700 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7886 (tt) outliers start: 53 outliers final: 32 residues processed: 257 average time/residue: 0.2746 time to fit residues: 102.5105 Evaluate side-chains 244 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU 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 363 ILE 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 128 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 LEU 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 573 PHE Chi-restraints excluded: chain B residue 596 CYS 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 777 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 103 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 81 optimal weight: 0.0270 chunk 127 optimal weight: 0.5980 chunk 15 optimal weight: 0.0370 chunk 78 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 overall best weight: 0.4516 ------------------------------------------------------------------------------- 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 674 GLN A 696 ASN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.239008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.201567 restraints weight = 15455.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.202683 restraints weight = 10648.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.203982 restraints weight = 9480.849| |-----------------------------------------------------------------------------| r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11692 Z= 0.142 Angle : 0.657 8.059 15844 Z= 0.346 Chirality : 0.044 0.165 1738 Planarity : 0.006 0.063 1944 Dihedral : 6.618 58.282 1522 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 4.52 % Allowed : 21.05 % Favored : 74.44 % 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: -3.13 (0.20), residues: 1344 helix: -1.17 (0.17), residues: 792 sheet: None (None), residues: 0 loop : -3.47 (0.21), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 397 HIS 0.003 0.001 HIS A 275 PHE 0.028 0.001 PHE B 321 TYR 0.042 0.002 TYR A 242 ARG 0.009 0.000 ARG B 542 Details of bonding type rmsd hydrogen bonds : bond 0.05058 ( 494) hydrogen bonds : angle 5.39635 ( 1464) SS BOND : bond 0.00951 ( 6) SS BOND : angle 0.59887 ( 12) covalent geometry : bond 0.00308 (11686) covalent geometry : angle 0.65691 (15832) *********************** 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 270 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 214 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.7224 (mmt) cc_final: 0.6929 (mmt) REVERT: A 618 ILE cc_start: 0.8974 (mm) cc_final: 0.8651 (mt) REVERT: A 700 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7676 (tt) REVERT: A 705 TRP cc_start: 0.7841 (t60) cc_final: 0.7566 (t60) REVERT: A 742 MET cc_start: 0.7086 (mtt) cc_final: 0.6761 (mtp) REVERT: A 750 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.7148 (ptp) REVERT: B 305 TYR cc_start: 0.7792 (t80) cc_final: 0.7477 (t80) REVERT: B 591 TYR cc_start: 0.5624 (p90) cc_final: 0.5358 (t80) REVERT: B 700 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7876 (tt) REVERT: B 742 MET cc_start: 0.7057 (mtp) cc_final: 0.6835 (mtt) REVERT: B 863 ILE cc_start: 0.5952 (OUTLIER) cc_final: 0.5458 (mp) outliers start: 56 outliers final: 39 residues processed: 250 average time/residue: 0.2103 time to fit residues: 77.3933 Evaluate side-chains 245 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU 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 395 GLU Chi-restraints excluded: chain A residue 460 VAL 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 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 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 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 236 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 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 596 CYS 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 842 MET Chi-restraints excluded: chain B residue 863 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 7 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 80 optimal weight: 0.0980 chunk 69 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.233771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.194371 restraints weight = 15598.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.195260 restraints weight = 11007.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.197032 restraints weight = 8477.428| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11692 Z= 0.202 Angle : 0.702 8.613 15844 Z= 0.369 Chirality : 0.046 0.163 1738 Planarity : 0.006 0.063 1944 Dihedral : 6.718 59.803 1522 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 5.00 % Allowed : 21.77 % Favored : 73.23 % 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: -3.06 (0.20), residues: 1344 helix: -1.15 (0.17), residues: 798 sheet: None (None), residues: 0 loop : -3.38 (0.21), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 397 HIS 0.004 0.001 HIS A 844 PHE 0.030 0.002 PHE B 321 TYR 0.031 0.002 TYR A 242 ARG 0.008 0.001 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.05493 ( 494) hydrogen bonds : angle 5.38266 ( 1464) SS BOND : bond 0.00396 ( 6) SS BOND : angle 1.12021 ( 12) covalent geometry : bond 0.00457 (11686) covalent geometry : angle 0.70155 (15832) *********************** 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 274 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 212 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7817 (mm-30) REVERT: A 534 MET cc_start: 0.7239 (mmt) cc_final: 0.7020 (mmt) REVERT: A 618 ILE cc_start: 0.8976 (mm) cc_final: 0.8644 (mt) REVERT: A 700 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7741 (tt) REVERT: A 863 ILE cc_start: 0.6107 (OUTLIER) cc_final: 0.5773 (mp) REVERT: B 305 TYR cc_start: 0.7864 (t80) cc_final: 0.7539 (t80) REVERT: B 591 TYR cc_start: 0.5885 (p90) cc_final: 0.5439 (t80) REVERT: B 631 MET cc_start: 0.7281 (mmm) cc_final: 0.7066 (mmm) REVERT: B 700 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7850 (tt) REVERT: B 843 GLU cc_start: 0.8164 (mp0) cc_final: 0.7942 (mp0) outliers start: 62 outliers final: 38 residues processed: 254 average time/residue: 0.2121 time to fit residues: 79.2111 Evaluate side-chains 245 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU 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 460 VAL 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 863 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 236 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 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 596 CYS 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 39 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 85 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.238375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.199161 restraints weight = 15602.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.200252 restraints weight = 10730.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.202034 restraints weight = 8121.937| |-----------------------------------------------------------------------------| r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11692 Z= 0.152 Angle : 0.671 9.506 15844 Z= 0.350 Chirality : 0.044 0.152 1738 Planarity : 0.006 0.060 1944 Dihedral : 6.603 59.650 1522 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.11 % Allowed : 22.66 % Favored : 73.23 % 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: -2.85 (0.20), residues: 1344 helix: -0.99 (0.17), residues: 800 sheet: None (None), residues: 0 loop : -3.31 (0.22), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 397 HIS 0.003 0.001 HIS A 275 PHE 0.030 0.002 PHE B 321 TYR 0.029 0.002 TYR A 242 ARG 0.008 0.000 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.05051 ( 494) hydrogen bonds : angle 5.30454 ( 1464) SS BOND : bond 0.00231 ( 6) SS BOND : angle 0.86612 ( 12) covalent geometry : bond 0.00336 (11686) covalent geometry : angle 0.67067 (15832) *********************** 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 262 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 211 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7356 (ptm-80) cc_final: 0.7128 (ptm-80) REVERT: A 305 TYR cc_start: 0.7857 (t80) cc_final: 0.7606 (t80) REVERT: A 534 MET cc_start: 0.7354 (mmt) cc_final: 0.7142 (mmt) REVERT: A 618 ILE cc_start: 0.8950 (mm) cc_final: 0.8619 (mt) REVERT: A 700 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7722 (tt) REVERT: A 742 MET cc_start: 0.7137 (mtt) cc_final: 0.6841 (mtt) REVERT: A 750 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6900 (ptp) REVERT: B 305 TYR cc_start: 0.7810 (t80) cc_final: 0.7500 (t80) REVERT: B 321 PHE cc_start: 0.6204 (OUTLIER) cc_final: 0.5619 (p90) REVERT: B 591 TYR cc_start: 0.5901 (p90) cc_final: 0.5422 (t80) REVERT: B 700 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7810 (tt) outliers start: 51 outliers final: 37 residues processed: 242 average time/residue: 0.2134 time to fit residues: 76.8183 Evaluate side-chains 245 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU 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 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 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 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 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 596 CYS 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 714 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 112 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.236585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.198048 restraints weight = 15519.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.198654 restraints weight = 10465.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.200106 restraints weight = 9382.357| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11692 Z= 0.171 Angle : 0.689 11.408 15844 Z= 0.357 Chirality : 0.045 0.143 1738 Planarity : 0.006 0.060 1944 Dihedral : 6.530 59.887 1522 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 4.35 % Allowed : 22.90 % Favored : 72.74 % 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: -2.69 (0.21), residues: 1344 helix: -0.92 (0.17), residues: 796 sheet: None (None), residues: 0 loop : -3.10 (0.23), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 397 HIS 0.004 0.001 HIS A 275 PHE 0.029 0.002 PHE B 321 TYR 0.029 0.002 TYR A 242 ARG 0.011 0.000 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.05088 ( 494) hydrogen bonds : angle 5.28847 ( 1464) SS BOND : bond 0.00326 ( 6) SS BOND : angle 0.92855 ( 12) covalent geometry : bond 0.00387 (11686) covalent geometry : angle 0.68854 (15832) *********************** 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 264 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 210 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 TYR cc_start: 0.7873 (t80) cc_final: 0.7652 (t80) REVERT: A 618 ILE cc_start: 0.8969 (mm) cc_final: 0.8635 (mt) REVERT: A 700 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7738 (tt) REVERT: A 742 MET cc_start: 0.7173 (mtt) cc_final: 0.6887 (mtt) REVERT: A 750 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6778 (ptp) REVERT: A 863 ILE cc_start: 0.6215 (OUTLIER) cc_final: 0.5799 (mp) REVERT: B 305 TYR cc_start: 0.7870 (t80) cc_final: 0.7541 (t80) REVERT: B 321 PHE cc_start: 0.6267 (OUTLIER) cc_final: 0.5760 (p90) REVERT: B 358 PHE cc_start: 0.6287 (m-80) cc_final: 0.5981 (m-10) REVERT: B 404 LEU cc_start: 0.7720 (mt) cc_final: 0.7416 (mt) REVERT: B 591 TYR cc_start: 0.5911 (p90) cc_final: 0.5301 (t80) REVERT: B 700 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7851 (tt) REVERT: B 742 MET cc_start: 0.7276 (mtt) cc_final: 0.6920 (mtt) outliers start: 54 outliers final: 40 residues processed: 242 average time/residue: 0.2248 time to fit residues: 80.3110 Evaluate side-chains 248 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU 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 460 VAL 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 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 863 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 TYR 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 596 CYS 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 714 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 91 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 104 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 111 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 657 GLN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.238340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.203576 restraints weight = 15479.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.204151 restraints weight = 11814.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.205859 restraints weight = 10787.759| |-----------------------------------------------------------------------------| r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 11692 Z= 0.141 Angle : 0.677 11.663 15844 Z= 0.352 Chirality : 0.044 0.209 1738 Planarity : 0.006 0.060 1944 Dihedral : 6.076 57.524 1520 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.71 % Allowed : 23.55 % Favored : 72.74 % 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: -2.47 (0.21), residues: 1344 helix: -0.74 (0.17), residues: 796 sheet: None (None), residues: 0 loop : -3.02 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 397 HIS 0.005 0.001 HIS B 844 PHE 0.028 0.001 PHE A 321 TYR 0.024 0.001 TYR A 242 ARG 0.003 0.000 ARG B 810 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 494) hydrogen bonds : angle 5.23597 ( 1464) SS BOND : bond 0.00501 ( 6) SS BOND : angle 0.85271 ( 12) covalent geometry : bond 0.00319 (11686) covalent geometry : angle 0.67694 (15832) *********************** 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 269 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.5224 (t80) cc_final: 0.4717 (t80) REVERT: A 321 PHE cc_start: 0.6501 (OUTLIER) cc_final: 0.6195 (p90) REVERT: A 613 MET cc_start: 0.8311 (ptm) cc_final: 0.8066 (ttp) REVERT: A 618 ILE cc_start: 0.8924 (mm) cc_final: 0.8585 (mt) REVERT: A 700 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7722 (tt) REVERT: A 705 TRP cc_start: 0.7659 (t60) cc_final: 0.7429 (t60) REVERT: A 742 MET cc_start: 0.7097 (mtt) cc_final: 0.6816 (mtp) REVERT: A 750 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6542 (ptp) REVERT: B 305 TYR cc_start: 0.7693 (t80) cc_final: 0.7415 (t80) REVERT: B 321 PHE cc_start: 0.5798 (OUTLIER) cc_final: 0.5325 (p90) REVERT: B 358 PHE cc_start: 0.6342 (m-80) cc_final: 0.6076 (m-10) REVERT: B 404 LEU cc_start: 0.7751 (mt) cc_final: 0.7427 (mt) REVERT: B 591 TYR cc_start: 0.5861 (p90) cc_final: 0.5350 (t80) REVERT: B 700 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7831 (tt) outliers start: 46 outliers final: 36 residues processed: 248 average time/residue: 0.2118 time to fit residues: 77.1567 Evaluate side-chains 244 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU 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 321 PHE Chi-restraints excluded: chain A residue 460 VAL 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 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 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 596 CYS 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 714 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 8 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 85 optimal weight: 0.0870 chunk 99 optimal weight: 7.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- 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 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.234815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.194802 restraints weight = 15593.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.194571 restraints weight = 11093.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.196464 restraints weight = 9245.972| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11692 Z= 0.231 Angle : 0.767 11.885 15844 Z= 0.401 Chirality : 0.048 0.224 1738 Planarity : 0.006 0.058 1944 Dihedral : 6.345 59.592 1520 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.87 % Allowed : 23.95 % Favored : 72.18 % 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: -2.67 (0.21), residues: 1344 helix: -0.93 (0.17), residues: 796 sheet: None (None), residues: 0 loop : -3.06 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 273 HIS 0.005 0.001 HIS A 844 PHE 0.030 0.002 PHE A 321 TYR 0.045 0.002 TYR A 305 ARG 0.009 0.001 ARG B 592 Details of bonding type rmsd hydrogen bonds : bond 0.05499 ( 494) hydrogen bonds : angle 5.41024 ( 1464) SS BOND : bond 0.00476 ( 6) SS BOND : angle 1.36539 ( 12) covalent geometry : bond 0.00533 (11686) covalent geometry : angle 0.76672 (15832) ********************** 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 249 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 201 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.6724 (tptp) cc_final: 0.6248 (mtmm) REVERT: A 523 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8878 (mp) REVERT: A 742 MET cc_start: 0.7134 (mtt) cc_final: 0.6884 (mtt) REVERT: A 750 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6659 (ptp) REVERT: A 863 ILE cc_start: 0.6158 (OUTLIER) cc_final: 0.5815 (mp) REVERT: B 58 LYS cc_start: 0.6328 (tptp) cc_final: 0.5823 (ptpp) REVERT: B 305 TYR cc_start: 0.7930 (t80) cc_final: 0.7602 (t80) REVERT: B 321 PHE cc_start: 0.6412 (OUTLIER) cc_final: 0.5902 (p90) REVERT: B 404 LEU cc_start: 0.7748 (mt) cc_final: 0.7454 (mt) REVERT: B 591 TYR cc_start: 0.5968 (p90) cc_final: 0.5299 (t80) REVERT: B 700 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7848 (tt) REVERT: B 742 MET cc_start: 0.7320 (mtt) cc_final: 0.6978 (mtt) outliers start: 48 outliers final: 35 residues processed: 232 average time/residue: 0.2059 time to fit residues: 70.7459 Evaluate side-chains 239 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU 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 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 534 MET 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 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 863 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 315 VAL 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 548 GLU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 697 ILE 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 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 3 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 127 optimal weight: 0.4980 chunk 85 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.236935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.200824 restraints weight = 15501.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.201995 restraints weight = 11552.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.203829 restraints weight = 9440.004| |-----------------------------------------------------------------------------| r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11692 Z= 0.156 Angle : 0.718 12.100 15844 Z= 0.373 Chirality : 0.045 0.223 1738 Planarity : 0.006 0.067 1944 Dihedral : 6.233 58.945 1520 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.63 % Allowed : 24.19 % Favored : 72.18 % 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: -2.49 (0.21), residues: 1344 helix: -0.77 (0.17), residues: 794 sheet: None (None), residues: 0 loop : -3.00 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 359 HIS 0.004 0.001 HIS A 844 PHE 0.042 0.002 PHE B 685 TYR 0.032 0.002 TYR A 305 ARG 0.023 0.001 ARG B 542 Details of bonding type rmsd hydrogen bonds : bond 0.04960 ( 494) hydrogen bonds : angle 5.33938 ( 1464) SS BOND : bond 0.00256 ( 6) SS BOND : angle 0.83091 ( 12) covalent geometry : bond 0.00353 (11686) covalent geometry : angle 0.71820 (15832) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3641.33 seconds wall clock time: 66 minutes 0.54 seconds (3960.54 seconds total)