Starting phenix.real_space_refine on Sat Jun 14 23:12:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yum_34108/06_2025/7yum_34108.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yum_34108/06_2025/7yum_34108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yum_34108/06_2025/7yum_34108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yum_34108/06_2025/7yum_34108.map" model { file = "/net/cci-nas-00/data/ceres_data/7yum_34108/06_2025/7yum_34108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yum_34108/06_2025/7yum_34108.cif" } resolution = 3.8 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= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 10480 2.51 5 N 2904 2.21 5 O 3132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16576 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Chain: "B" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Chain: "C" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Chain: "D" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Time building chain proxies: 10.01, per 1000 atoms: 0.60 Number of scatterers: 16576 At special positions: 0 Unit cell: (118.08, 109.88, 143.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 3132 8.00 N 2904 7.00 C 10480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.72 Conformation dependent library (CDL) restraints added in 2.0 seconds 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3904 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 18 sheets defined 44.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 245 through 255 removed outlier: 4.145A pdb=" N LYS A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 removed outlier: 4.254A pdb=" N ARG A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.770A pdb=" N VAL A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 324 through 336 Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 403 through 411 removed outlier: 3.756A pdb=" N HIS A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 444 removed outlier: 3.529A pdb=" N ALA A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 removed outlier: 3.566A pdb=" N THR A 450 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 447 through 451' Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.672A pdb=" N LYS A 509 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.670A pdb=" N GLU A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.733A pdb=" N TYR A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 647 Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 717 through 728 removed outlier: 3.980A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 761 through 770 removed outlier: 3.792A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 283 through 296 removed outlier: 3.847A pdb=" N VAL B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 325 through 339 removed outlier: 4.034A pdb=" N ILE B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 373 removed outlier: 3.660A pdb=" N ASN B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 403 through 412 removed outlier: 3.678A pdb=" N VAL B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 444 removed outlier: 4.122A pdb=" N ALA B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 451 removed outlier: 3.721A pdb=" N THR B 450 " --> pdb=" O GLN B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 506 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.636A pdb=" N ILE B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 573 through 579 removed outlier: 3.651A pdb=" N TYR B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 647 removed outlier: 3.771A pdb=" N LYS B 634 " --> pdb=" O GLY B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 652 removed outlier: 3.749A pdb=" N GLY B 652 " --> pdb=" O GLN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 717 through 728 removed outlier: 4.100A pdb=" N LYS B 721 " --> pdb=" O GLY B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 740 No H-bonds generated for 'chain 'B' and resid 738 through 740' Processing helix chain 'B' and resid 742 through 746 Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.715A pdb=" N LEU B 751 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 769 removed outlier: 3.714A pdb=" N VAL B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.558A pdb=" N ARG C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 338 " --> pdb=" O ALA C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 372 Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 423 through 427 removed outlier: 4.073A pdb=" N MET C 427 " --> pdb=" O ILE C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 444 removed outlier: 3.958A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.548A pdb=" N LEU C 482 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 515 removed outlier: 3.549A pdb=" N TYR C 505 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TRP C 507 " --> pdb=" O ARG C 503 " (cutoff:3.500A) Proline residue: C 508 - end of helix Processing helix chain 'C' and resid 523 through 534 removed outlier: 3.662A pdb=" N ILE C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 removed outlier: 3.514A pdb=" N GLU C 560 " --> pdb=" O LYS C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 579 removed outlier: 3.662A pdb=" N TYR C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 647 removed outlier: 3.652A pdb=" N LYS C 634 " --> pdb=" O GLY C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 693 Processing helix chain 'C' and resid 717 through 728 Processing helix chain 'C' and resid 747 through 752 Processing helix chain 'C' and resid 761 through 770 removed outlier: 3.526A pdb=" N VAL C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 770 " --> pdb=" O LEU C 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 255 removed outlier: 3.832A pdb=" N LYS D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 273 Processing helix chain 'D' and resid 283 through 296 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 324 through 337 removed outlier: 4.206A pdb=" N ARG D 328 " --> pdb=" O ASP D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 372 Processing helix chain 'D' and resid 386 through 390 removed outlier: 3.639A pdb=" N ILE D 390 " --> pdb=" O GLU D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 435 through 444 removed outlier: 3.822A pdb=" N MET D 439 " --> pdb=" O PRO D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 477 removed outlier: 3.711A pdb=" N THR D 476 " --> pdb=" O THR D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 505 through 514 removed outlier: 3.740A pdb=" N LYS D 509 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 512 " --> pdb=" O PRO D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.914A pdb=" N ILE D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 560 removed outlier: 3.527A pdb=" N GLU D 560 " --> pdb=" O LYS D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 578 Processing helix chain 'D' and resid 630 through 647 removed outlier: 3.965A pdb=" N LYS D 634 " --> pdb=" O GLY D 630 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 636 " --> pdb=" O VAL D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 652 Processing helix chain 'D' and resid 679 through 691 Processing helix chain 'D' and resid 717 through 729 Processing helix chain 'D' and resid 738 through 745 removed outlier: 4.216A pdb=" N ALA D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 744 " --> pdb=" O ALA D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 754 removed outlier: 3.912A pdb=" N LEU D 751 " --> pdb=" O PRO D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 769 Processing sheet with id=AA1, first strand: chain 'A' and resid 352 through 354 removed outlier: 6.014A pdb=" N VAL A 352 " --> pdb=" O ILE A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 418 through 422 removed outlier: 3.504A pdb=" N ILE A 468 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.405A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 596 through 603 removed outlier: 6.736A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 700 through 702 removed outlier: 6.751A pdb=" N ILE A 733 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL A 759 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 735 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 378 through 380 removed outlier: 6.384A pdb=" N ILE B 379 " --> pdb=" O ASP B 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 596 through 603 removed outlier: 3.703A pdb=" N THR B 603 " --> pdb=" O GLY B 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 732 through 736 removed outlier: 6.744A pdb=" N ILE B 733 " --> pdb=" O LYS B 757 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL B 759 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU B 735 " --> pdb=" O VAL B 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AB1, first strand: chain 'C' and resid 418 through 421 removed outlier: 3.604A pdb=" N ILE C 468 " --> pdb=" O ILE C 419 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 521 through 522 removed outlier: 6.302A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 596 through 601 removed outlier: 6.186A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.986A pdb=" N ALA C 701 " --> pdb=" O VAL C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AB6, first strand: chain 'D' and resid 376 through 380 removed outlier: 6.227A pdb=" N HIS D 377 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASP D 422 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE D 379 " --> pdb=" O ASP D 422 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 596 through 603 removed outlier: 5.537A pdb=" N LYS D 622 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL D 665 " --> pdb=" O LYS D 622 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER D 624 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 700 through 702 removed outlier: 6.426A pdb=" N ALA D 701 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE D 733 " --> pdb=" O LYS D 757 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL D 759 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU D 735 " --> pdb=" O VAL D 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 705 through 707 removed outlier: 3.759A pdb=" N GLU D 705 " --> pdb=" O MET D 713 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1818 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: 4.29 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5284 1.34 - 1.45: 2577 1.45 - 1.57: 8903 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 16884 Sorted by residual: bond pdb=" C ILE B 419 " pdb=" N LEU B 420 " ideal model delta sigma weight residual 1.331 1.295 0.036 1.40e-02 5.10e+03 6.73e+00 bond pdb=" CG LEU B 769 " pdb=" CD1 LEU B 769 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.52e+00 bond pdb=" CG LEU B 723 " pdb=" CD1 LEU B 723 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.43e+00 bond pdb=" CB GLN C 499 " pdb=" CG GLN C 499 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.20e+00 bond pdb=" CG1 ILE B 468 " pdb=" CD1 ILE B 468 " ideal model delta sigma weight residual 1.513 1.420 0.093 3.90e-02 6.57e+02 5.69e+00 ... (remaining 16879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 22365 3.51 - 7.02: 461 7.02 - 10.52: 51 10.52 - 14.03: 5 14.03 - 17.54: 2 Bond angle restraints: 22884 Sorted by residual: angle pdb=" N GLY B 539 " pdb=" CA GLY B 539 " pdb=" C GLY B 539 " ideal model delta sigma weight residual 111.21 118.38 -7.17 1.04e+00 9.25e-01 4.76e+01 angle pdb=" C ALA D 400 " pdb=" N MET D 401 " pdb=" CA MET D 401 " ideal model delta sigma weight residual 120.97 138.51 -17.54 2.84e+00 1.24e-01 3.81e+01 angle pdb=" C GLY B 321 " pdb=" N LEU B 322 " pdb=" CA LEU B 322 " ideal model delta sigma weight residual 121.54 131.70 -10.16 1.91e+00 2.74e-01 2.83e+01 angle pdb=" C MET A 698 " pdb=" N ASP A 699 " pdb=" CA ASP A 699 " ideal model delta sigma weight residual 122.08 129.85 -7.77 1.47e+00 4.63e-01 2.80e+01 angle pdb=" N ILE B 468 " pdb=" CA ILE B 468 " pdb=" C ILE B 468 " ideal model delta sigma weight residual 109.34 99.73 9.61 2.08e+00 2.31e-01 2.13e+01 ... (remaining 22879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.15: 9612 15.15 - 30.31: 627 30.31 - 45.46: 120 45.46 - 60.62: 9 60.62 - 75.77: 20 Dihedral angle restraints: 10388 sinusoidal: 4300 harmonic: 6088 Sorted by residual: dihedral pdb=" CA GLU D 591 " pdb=" C GLU D 591 " pdb=" N PRO D 592 " pdb=" CA PRO D 592 " ideal model delta harmonic sigma weight residual 180.00 -132.24 -47.76 0 5.00e+00 4.00e-02 9.12e+01 dihedral pdb=" CA PRO B 673 " pdb=" C PRO B 673 " pdb=" N LYS B 674 " pdb=" CA LYS B 674 " ideal model delta harmonic sigma weight residual -180.00 -138.02 -41.98 0 5.00e+00 4.00e-02 7.05e+01 dihedral pdb=" CA LYS B 347 " pdb=" C LYS B 347 " pdb=" N ALA B 348 " pdb=" CA ALA B 348 " ideal model delta harmonic sigma weight residual 180.00 140.73 39.27 0 5.00e+00 4.00e-02 6.17e+01 ... (remaining 10385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2058 0.080 - 0.160: 485 0.160 - 0.240: 52 0.240 - 0.320: 6 0.320 - 0.400: 3 Chirality restraints: 2604 Sorted by residual: chirality pdb=" CB ILE C 379 " pdb=" CA ILE C 379 " pdb=" CG1 ILE C 379 " pdb=" CG2 ILE C 379 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CG LEU C 462 " pdb=" CB LEU C 462 " pdb=" CD1 LEU C 462 " pdb=" CD2 LEU C 462 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 2601 not shown) Planarity restraints: 2972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 434 " -0.051 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PRO D 435 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO D 435 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 435 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 773 " 0.049 5.00e-02 4.00e+02 7.38e-02 8.70e+00 pdb=" N PRO A 774 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 774 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 774 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 356 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO C 357 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 357 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 357 " -0.037 5.00e-02 4.00e+02 ... (remaining 2969 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2181 2.75 - 3.29: 16004 3.29 - 3.82: 27292 3.82 - 4.36: 31640 4.36 - 4.90: 53127 Nonbonded interactions: 130244 Sorted by model distance: nonbonded pdb=" O LYS C 587 " pdb=" OG1 THR C 590 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR D 603 " pdb=" O GLY D 606 " model vdw 2.257 3.040 nonbonded pdb=" OG1 THR A 603 " pdb=" O GLY A 606 " model vdw 2.257 3.040 nonbonded pdb=" OD2 ASP A 425 " pdb=" OG1 THR A 473 " model vdw 2.259 3.040 nonbonded pdb=" O ARG C 336 " pdb=" OG1 THR C 339 " model vdw 2.260 3.040 ... (remaining 130239 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 35.820 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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 : 0.010 0.110 16884 Z= 0.436 Angle : 1.257 17.540 22884 Z= 0.676 Chirality : 0.067 0.400 2604 Planarity : 0.009 0.077 2972 Dihedral : 11.165 75.772 6484 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.31 % Favored : 87.59 % Rotamer: Outliers : 0.34 % Allowed : 3.61 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.34 % Twisted General : 0.45 % 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: -4.61 (0.15), residues: 2120 helix: -2.79 (0.13), residues: 855 sheet: -2.52 (0.30), residues: 229 loop : -3.45 (0.16), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP D 563 HIS 0.020 0.003 HIS B 319 PHE 0.025 0.004 PHE A 467 TYR 0.039 0.004 TYR D 289 ARG 0.020 0.001 ARG D 374 Details of bonding type rmsd hydrogen bonds : bond 0.15022 ( 630) hydrogen bonds : angle 7.67376 ( 1818) covalent geometry : bond 0.01007 (16884) covalent geometry : angle 1.25710 (22884) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 405 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6708 (mtt) cc_final: 0.6261 (mtt) REVERT: A 353 LEU cc_start: 0.7996 (mt) cc_final: 0.7777 (mt) REVERT: A 366 ARG cc_start: 0.8425 (mpt-90) cc_final: 0.8173 (mtt90) REVERT: A 425 ASP cc_start: 0.8147 (p0) cc_final: 0.7810 (p0) REVERT: A 745 GLU cc_start: 0.8168 (mt-10) cc_final: 0.6994 (tm-30) REVERT: B 378 ARG cc_start: 0.7734 (mtp180) cc_final: 0.7462 (mtm180) REVERT: B 380 SER cc_start: 0.8767 (t) cc_final: 0.8554 (t) REVERT: B 387 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7275 (pp20) REVERT: B 422 ASP cc_start: 0.8193 (m-30) cc_final: 0.7571 (m-30) REVERT: B 484 ARG cc_start: 0.6506 (mmt180) cc_final: 0.6301 (mtp85) REVERT: B 698 MET cc_start: 0.7082 (mmt) cc_final: 0.6754 (tpp) REVERT: B 733 ILE cc_start: 0.8943 (mp) cc_final: 0.8731 (mm) REVERT: B 748 LYS cc_start: 0.8055 (ptmm) cc_final: 0.7712 (ptmm) REVERT: C 258 MET cc_start: 0.3766 (mmt) cc_final: 0.2426 (mmt) REVERT: C 405 LEU cc_start: 0.8972 (mt) cc_final: 0.8746 (mm) REVERT: D 276 MET cc_start: 0.5103 (mmt) cc_final: 0.4815 (ptt) REVERT: D 328 ARG cc_start: 0.8262 (mpt180) cc_final: 0.7930 (mmt-90) REVERT: D 331 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7720 (mt-10) REVERT: D 385 ARG cc_start: 0.7032 (ppt-90) cc_final: 0.6224 (mmt-90) REVERT: D 439 MET cc_start: 0.8007 (tpt) cc_final: 0.7726 (tmm) REVERT: D 584 ARG cc_start: 0.7936 (mtp-110) cc_final: 0.7536 (mtm110) REVERT: D 659 ASN cc_start: 0.8421 (m-40) cc_final: 0.7805 (p0) REVERT: D 698 MET cc_start: 0.5322 (mmm) cc_final: 0.4716 (mmm) REVERT: D 705 GLU cc_start: 0.6497 (mt-10) cc_final: 0.6220 (mt-10) REVERT: D 719 LYS cc_start: 0.6900 (tttt) cc_final: 0.6482 (ttpt) outliers start: 6 outliers final: 3 residues processed: 410 average time/residue: 0.3877 time to fit residues: 218.8361 Evaluate side-chains 239 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 236 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 ASN A 472 ASN A 475 GLN A 495 ASN A 598 GLN A 664 HIS B 377 HIS B 449 ASN B 475 GLN B 510 GLN B 726 HIS C 277 GLN C 472 ASN C 726 HIS D 346 ASN ** D 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 GLN D 628 GLN D 726 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.133589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.106671 restraints weight = 51810.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.108087 restraints weight = 34960.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.108952 restraints weight = 24547.007| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16884 Z= 0.168 Angle : 0.804 13.184 22884 Z= 0.408 Chirality : 0.048 0.374 2604 Planarity : 0.007 0.062 2972 Dihedral : 7.256 46.891 2329 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 2.14 % Allowed : 10.89 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.10 % 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: -3.33 (0.16), residues: 2120 helix: -1.35 (0.16), residues: 862 sheet: -1.97 (0.31), residues: 213 loop : -3.07 (0.17), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 563 HIS 0.006 0.001 HIS B 319 PHE 0.015 0.002 PHE A 466 TYR 0.021 0.002 TYR B 768 ARG 0.009 0.001 ARG B 503 Details of bonding type rmsd hydrogen bonds : bond 0.04486 ( 630) hydrogen bonds : angle 5.75053 ( 1818) covalent geometry : bond 0.00368 (16884) covalent geometry : angle 0.80442 (22884) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 282 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6214 (mtt) cc_final: 0.5984 (mtt) REVERT: A 378 ARG cc_start: 0.8078 (ttp80) cc_final: 0.7677 (mtp180) REVERT: A 407 HIS cc_start: 0.8736 (m-70) cc_final: 0.7973 (m-70) REVERT: A 422 ASP cc_start: 0.7549 (m-30) cc_final: 0.5606 (m-30) REVERT: A 702 MET cc_start: 0.6906 (ptt) cc_final: 0.6069 (ptt) REVERT: A 703 THR cc_start: 0.6141 (t) cc_final: 0.5771 (m) REVERT: B 378 ARG cc_start: 0.7831 (mtp180) cc_final: 0.7496 (mtp180) REVERT: B 422 ASP cc_start: 0.7996 (m-30) cc_final: 0.7259 (m-30) REVERT: B 673 PRO cc_start: 0.7712 (Cg_exo) cc_final: 0.7476 (Cg_endo) REVERT: B 733 ILE cc_start: 0.8985 (mp) cc_final: 0.8548 (mm) REVERT: C 258 MET cc_start: 0.4443 (mmt) cc_final: 0.3196 (mmt) REVERT: C 401 MET cc_start: 0.7782 (tpp) cc_final: 0.6638 (pmm) REVERT: C 409 MET cc_start: 0.5909 (mmm) cc_final: 0.5632 (mmm) REVERT: C 425 ASP cc_start: 0.7719 (p0) cc_final: 0.6928 (p0) REVERT: C 726 HIS cc_start: 0.8023 (OUTLIER) cc_final: 0.7532 (t70) REVERT: D 258 MET cc_start: 0.2140 (mtt) cc_final: 0.1538 (mtt) REVERT: D 328 ARG cc_start: 0.8162 (mpt180) cc_final: 0.7871 (mmt-90) REVERT: D 331 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7591 (mt-10) REVERT: D 385 ARG cc_start: 0.7103 (ppt-90) cc_final: 0.6281 (mmt-90) REVERT: D 553 LYS cc_start: 0.6722 (mttt) cc_final: 0.6444 (mtmt) REVERT: D 557 PHE cc_start: 0.8492 (m-80) cc_final: 0.8071 (m-80) REVERT: D 578 LEU cc_start: 0.7799 (tt) cc_final: 0.7487 (tt) REVERT: D 705 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6072 (pt0) REVERT: D 713 MET cc_start: 0.7910 (mmm) cc_final: 0.7198 (mmm) outliers start: 38 outliers final: 19 residues processed: 305 average time/residue: 0.3273 time to fit residues: 142.0550 Evaluate side-chains 226 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 726 HIS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 82 optimal weight: 0.0010 chunk 195 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 70 optimal weight: 0.0000 chunk 79 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 HIS D 377 HIS ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.134101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.108289 restraints weight = 51590.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.109483 restraints weight = 33598.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.109990 restraints weight = 24219.442| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16884 Z= 0.137 Angle : 0.726 10.788 22884 Z= 0.367 Chirality : 0.046 0.180 2604 Planarity : 0.006 0.065 2972 Dihedral : 6.545 44.860 2327 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 2.37 % Allowed : 13.60 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.05 % 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: -2.64 (0.17), residues: 2120 helix: -0.63 (0.17), residues: 857 sheet: -1.92 (0.29), residues: 252 loop : -2.75 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 298 HIS 0.006 0.001 HIS C 726 PHE 0.017 0.001 PHE D 466 TYR 0.015 0.001 TYR D 534 ARG 0.007 0.001 ARG B 391 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 630) hydrogen bonds : angle 5.27851 ( 1818) covalent geometry : bond 0.00303 (16884) covalent geometry : angle 0.72628 (22884) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 242 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 HIS cc_start: 0.8852 (m-70) cc_final: 0.8341 (m-70) REVERT: A 422 ASP cc_start: 0.7230 (m-30) cc_final: 0.5576 (m-30) REVERT: A 702 MET cc_start: 0.6894 (ptt) cc_final: 0.6245 (ptt) REVERT: A 703 THR cc_start: 0.5910 (t) cc_final: 0.5642 (m) REVERT: B 673 PRO cc_start: 0.7722 (Cg_exo) cc_final: 0.7458 (Cg_endo) REVERT: B 698 MET cc_start: 0.6885 (tpp) cc_final: 0.6654 (mmt) REVERT: B 733 ILE cc_start: 0.8891 (mp) cc_final: 0.8585 (mm) REVERT: C 258 MET cc_start: 0.4183 (mmt) cc_final: 0.2996 (mmt) REVERT: C 401 MET cc_start: 0.6983 (tpp) cc_final: 0.6492 (pmm) REVERT: C 409 MET cc_start: 0.5690 (mmm) cc_final: 0.5349 (mmm) REVERT: C 425 ASP cc_start: 0.7594 (p0) cc_final: 0.6836 (p0) REVERT: D 368 ILE cc_start: 0.9447 (mt) cc_final: 0.9090 (mt) REVERT: D 557 PHE cc_start: 0.8527 (m-80) cc_final: 0.8077 (m-80) REVERT: D 578 LEU cc_start: 0.7793 (tt) cc_final: 0.7581 (tt) REVERT: D 598 GLN cc_start: 0.5775 (tp-100) cc_final: 0.5535 (mm110) REVERT: D 698 MET cc_start: 0.3860 (tpt) cc_final: 0.3491 (tpt) REVERT: D 705 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6096 (pt0) REVERT: D 713 MET cc_start: 0.7939 (mmm) cc_final: 0.7067 (mmm) REVERT: D 719 LYS cc_start: 0.6972 (ttpt) cc_final: 0.6711 (tttt) outliers start: 42 outliers final: 25 residues processed: 264 average time/residue: 0.3132 time to fit residues: 120.8224 Evaluate side-chains 231 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 35 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 167 optimal weight: 0.8980 chunk 194 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 726 HIS D 319 HIS D 727 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.132792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.106549 restraints weight = 51986.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.106627 restraints weight = 31858.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.107969 restraints weight = 26551.043| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16884 Z= 0.168 Angle : 0.728 9.516 22884 Z= 0.368 Chirality : 0.046 0.197 2604 Planarity : 0.005 0.061 2972 Dihedral : 6.356 45.541 2327 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 3.10 % Allowed : 14.45 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.18), residues: 2120 helix: -0.42 (0.17), residues: 869 sheet: -1.46 (0.31), residues: 237 loop : -2.65 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 563 HIS 0.007 0.001 HIS B 319 PHE 0.022 0.002 PHE D 466 TYR 0.017 0.002 TYR D 643 ARG 0.012 0.000 ARG D 479 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 630) hydrogen bonds : angle 5.19103 ( 1818) covalent geometry : bond 0.00378 (16884) covalent geometry : angle 0.72812 (22884) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 222 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6362 (mtt) cc_final: 0.6131 (mtt) REVERT: A 366 ARG cc_start: 0.8372 (mtt90) cc_final: 0.8109 (mtt90) REVERT: A 378 ARG cc_start: 0.8097 (mtp180) cc_final: 0.7602 (mmm-85) REVERT: A 401 MET cc_start: 0.7640 (tmm) cc_final: 0.7353 (tmm) REVERT: A 407 HIS cc_start: 0.8872 (m-70) cc_final: 0.8441 (m-70) REVERT: A 420 LEU cc_start: 0.8525 (tp) cc_final: 0.8286 (tp) REVERT: A 702 MET cc_start: 0.6962 (ptt) cc_final: 0.6265 (ptt) REVERT: A 703 THR cc_start: 0.6056 (t) cc_final: 0.5756 (m) REVERT: B 401 MET cc_start: 0.6002 (mmp) cc_final: 0.5255 (mmm) REVERT: B 504 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7180 (mp10) REVERT: B 673 PRO cc_start: 0.7645 (Cg_exo) cc_final: 0.7414 (Cg_endo) REVERT: B 691 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8704 (tt) REVERT: C 258 MET cc_start: 0.4274 (mmt) cc_final: 0.3012 (mmt) REVERT: C 401 MET cc_start: 0.6888 (tpp) cc_final: 0.6504 (pmm) REVERT: C 409 MET cc_start: 0.5784 (mmm) cc_final: 0.5462 (mmm) REVERT: C 425 ASP cc_start: 0.7432 (p0) cc_final: 0.6761 (p0) REVERT: D 557 PHE cc_start: 0.8491 (m-80) cc_final: 0.8187 (m-80) REVERT: D 705 GLU cc_start: 0.6665 (mt-10) cc_final: 0.6046 (pt0) REVERT: D 713 MET cc_start: 0.7877 (mmm) cc_final: 0.7046 (mmm) REVERT: D 719 LYS cc_start: 0.6885 (ttpt) cc_final: 0.6662 (tppp) outliers start: 55 outliers final: 36 residues processed: 258 average time/residue: 0.3012 time to fit residues: 114.2482 Evaluate side-chains 244 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 726 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 80 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 0.0060 chunk 98 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 189 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 726 HIS D 664 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.134752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.108134 restraints weight = 51885.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.108810 restraints weight = 32281.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.110481 restraints weight = 24349.580| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16884 Z= 0.121 Angle : 0.678 8.903 22884 Z= 0.339 Chirality : 0.045 0.207 2604 Planarity : 0.005 0.059 2972 Dihedral : 5.920 47.064 2327 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.99 % Allowed : 15.41 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.18), residues: 2120 helix: 0.05 (0.18), residues: 860 sheet: -1.38 (0.32), residues: 245 loop : -2.48 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 298 HIS 0.024 0.001 HIS C 726 PHE 0.010 0.001 PHE D 466 TYR 0.025 0.001 TYR C 768 ARG 0.011 0.000 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 630) hydrogen bonds : angle 4.82050 ( 1818) covalent geometry : bond 0.00267 (16884) covalent geometry : angle 0.67835 (22884) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 230 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6399 (mtt) cc_final: 0.6131 (mtt) REVERT: A 353 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7404 (mm) REVERT: A 366 ARG cc_start: 0.8297 (mtt90) cc_final: 0.8091 (mtt90) REVERT: A 378 ARG cc_start: 0.8239 (mtp180) cc_final: 0.7765 (mmm-85) REVERT: A 401 MET cc_start: 0.7663 (tmm) cc_final: 0.7203 (tmm) REVERT: A 407 HIS cc_start: 0.8904 (m-70) cc_final: 0.8701 (m-70) REVERT: A 420 LEU cc_start: 0.8531 (tp) cc_final: 0.8161 (tp) REVERT: A 422 ASP cc_start: 0.7346 (m-30) cc_final: 0.6352 (m-30) REVERT: A 702 MET cc_start: 0.6780 (ptt) cc_final: 0.5933 (ptt) REVERT: A 703 THR cc_start: 0.5848 (t) cc_final: 0.5638 (m) REVERT: B 504 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7165 (mp10) REVERT: B 673 PRO cc_start: 0.7687 (Cg_exo) cc_final: 0.7457 (Cg_endo) REVERT: C 258 MET cc_start: 0.4409 (mmt) cc_final: 0.3119 (mmt) REVERT: C 401 MET cc_start: 0.6737 (tpp) cc_final: 0.6467 (pmm) REVERT: C 409 MET cc_start: 0.5537 (mmm) cc_final: 0.5255 (mmm) REVERT: C 425 ASP cc_start: 0.7533 (p0) cc_final: 0.6862 (p0) REVERT: D 385 ARG cc_start: 0.7393 (ppt-90) cc_final: 0.6545 (mmt90) REVERT: D 557 PHE cc_start: 0.8534 (m-80) cc_final: 0.8213 (m-80) REVERT: D 657 PHE cc_start: 0.7528 (p90) cc_final: 0.7185 (p90) REVERT: D 698 MET cc_start: 0.3876 (tpt) cc_final: 0.3524 (tpp) REVERT: D 705 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6042 (pt0) REVERT: D 713 MET cc_start: 0.7866 (mmm) cc_final: 0.7043 (mmm) outliers start: 53 outliers final: 29 residues processed: 263 average time/residue: 0.2944 time to fit residues: 115.4815 Evaluate side-chains 231 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 545 ARG Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 181 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 156 optimal weight: 0.0040 chunk 62 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 14 optimal weight: 0.0170 chunk 126 optimal weight: 0.2980 chunk 113 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.4632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 HIS C 726 HIS D 340 GLN D 499 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.136224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.109577 restraints weight = 52113.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.110916 restraints weight = 35810.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.111305 restraints weight = 25279.900| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16884 Z= 0.114 Angle : 0.680 10.050 22884 Z= 0.336 Chirality : 0.044 0.218 2604 Planarity : 0.005 0.057 2972 Dihedral : 5.584 48.729 2327 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.77 % Allowed : 16.37 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.18), residues: 2120 helix: 0.29 (0.18), residues: 868 sheet: -1.45 (0.33), residues: 216 loop : -2.32 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 292 HIS 0.007 0.001 HIS B 454 PHE 0.017 0.001 PHE A 466 TYR 0.012 0.001 TYR C 505 ARG 0.008 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 630) hydrogen bonds : angle 4.63252 ( 1818) covalent geometry : bond 0.00250 (16884) covalent geometry : angle 0.68018 (22884) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 236 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6830 (tp) REVERT: A 353 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7251 (mm) REVERT: A 372 MET cc_start: 0.7005 (tpp) cc_final: 0.6415 (ttm) REVERT: A 378 ARG cc_start: 0.8081 (mtp180) cc_final: 0.7799 (mmm-85) REVERT: A 407 HIS cc_start: 0.8911 (m-70) cc_final: 0.8655 (m-70) REVERT: A 420 LEU cc_start: 0.8595 (tp) cc_final: 0.8324 (tp) REVERT: A 422 ASP cc_start: 0.7304 (m-30) cc_final: 0.6524 (m-30) REVERT: A 485 MET cc_start: 0.7946 (mmm) cc_final: 0.7673 (mmt) REVERT: A 632 VAL cc_start: 0.6098 (OUTLIER) cc_final: 0.5773 (p) REVERT: A 657 PHE cc_start: 0.6927 (p90) cc_final: 0.6713 (p90) REVERT: A 702 MET cc_start: 0.6638 (ptt) cc_final: 0.6373 (ptp) REVERT: A 703 THR cc_start: 0.5949 (t) cc_final: 0.5708 (m) REVERT: B 504 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7123 (mp10) REVERT: B 673 PRO cc_start: 0.7828 (Cg_exo) cc_final: 0.7580 (Cg_endo) REVERT: C 258 MET cc_start: 0.4240 (mmt) cc_final: 0.2910 (mmt) REVERT: C 401 MET cc_start: 0.6660 (tpp) cc_final: 0.6454 (pmm) REVERT: C 405 LEU cc_start: 0.9061 (mm) cc_final: 0.8739 (mm) REVERT: C 425 ASP cc_start: 0.7539 (p0) cc_final: 0.6894 (p0) REVERT: D 385 ARG cc_start: 0.7092 (ppt-90) cc_final: 0.6343 (mmt90) REVERT: D 557 PHE cc_start: 0.8479 (m-80) cc_final: 0.8189 (m-80) REVERT: D 657 PHE cc_start: 0.7335 (p90) cc_final: 0.7009 (p90) REVERT: D 698 MET cc_start: 0.3526 (tpt) cc_final: 0.3100 (tpp) REVERT: D 705 GLU cc_start: 0.6431 (mt-10) cc_final: 0.6012 (pt0) REVERT: D 713 MET cc_start: 0.8027 (mmm) cc_final: 0.7175 (mmm) outliers start: 49 outliers final: 29 residues processed: 270 average time/residue: 0.3467 time to fit residues: 138.1103 Evaluate side-chains 246 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 664 HIS Chi-restraints excluded: chain C residue 726 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 60 optimal weight: 0.1980 chunk 181 optimal weight: 1.9990 chunk 156 optimal weight: 0.0020 chunk 165 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 48 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN C 664 HIS C 726 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.136130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.109523 restraints weight = 51919.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.110317 restraints weight = 35877.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.111446 restraints weight = 25585.915| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16884 Z= 0.118 Angle : 0.691 14.232 22884 Z= 0.339 Chirality : 0.044 0.238 2604 Planarity : 0.005 0.057 2972 Dihedral : 5.442 49.739 2327 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.54 % Allowed : 17.38 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.19), residues: 2120 helix: 0.47 (0.18), residues: 871 sheet: -1.06 (0.33), residues: 240 loop : -2.25 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 298 HIS 0.019 0.001 HIS C 726 PHE 0.013 0.001 PHE D 466 TYR 0.012 0.001 TYR C 505 ARG 0.013 0.000 ARG D 584 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 630) hydrogen bonds : angle 4.57121 ( 1818) covalent geometry : bond 0.00264 (16884) covalent geometry : angle 0.69099 (22884) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 224 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6054 (mtt) cc_final: 0.5681 (mpp) REVERT: A 290 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6802 (tp) REVERT: A 353 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7188 (mm) REVERT: A 372 MET cc_start: 0.6993 (tpp) cc_final: 0.6414 (ttm) REVERT: A 401 MET cc_start: 0.7404 (tpp) cc_final: 0.6093 (pmm) REVERT: A 420 LEU cc_start: 0.8574 (tp) cc_final: 0.8340 (tp) REVERT: A 422 ASP cc_start: 0.7363 (m-30) cc_final: 0.6750 (m-30) REVERT: A 482 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7741 (mm) REVERT: A 485 MET cc_start: 0.7914 (mmm) cc_final: 0.7690 (mmt) REVERT: A 657 PHE cc_start: 0.6935 (p90) cc_final: 0.6719 (p90) REVERT: B 504 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7088 (mp10) REVERT: B 673 PRO cc_start: 0.7870 (Cg_exo) cc_final: 0.7642 (Cg_endo) REVERT: B 756 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7688 (mm) REVERT: C 258 MET cc_start: 0.4224 (mmt) cc_final: 0.2925 (mmt) REVERT: C 401 MET cc_start: 0.6698 (tpp) cc_final: 0.6485 (pmm) REVERT: C 425 ASP cc_start: 0.7576 (p0) cc_final: 0.6945 (p0) REVERT: D 276 MET cc_start: 0.6165 (tmm) cc_final: 0.5947 (tmm) REVERT: D 557 PHE cc_start: 0.8489 (m-80) cc_final: 0.8200 (m-80) REVERT: D 698 MET cc_start: 0.3589 (tpt) cc_final: 0.3155 (tpp) REVERT: D 705 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6028 (pt0) REVERT: D 713 MET cc_start: 0.7973 (mmm) cc_final: 0.7112 (mmm) REVERT: D 727 GLN cc_start: 0.8098 (mm110) cc_final: 0.7885 (mp10) outliers start: 45 outliers final: 34 residues processed: 255 average time/residue: 0.2709 time to fit residues: 104.9498 Evaluate side-chains 247 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 726 HIS Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 42 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 HIS C 726 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.135013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.108578 restraints weight = 52218.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.108974 restraints weight = 35500.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.109982 restraints weight = 26152.136| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16884 Z= 0.132 Angle : 0.700 14.581 22884 Z= 0.344 Chirality : 0.044 0.246 2604 Planarity : 0.005 0.057 2972 Dihedral : 5.405 50.464 2327 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.82 % Allowed : 17.27 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.19), residues: 2120 helix: 0.58 (0.18), residues: 865 sheet: -1.08 (0.33), residues: 242 loop : -2.20 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 298 HIS 0.022 0.001 HIS C 726 PHE 0.013 0.001 PHE D 466 TYR 0.012 0.001 TYR D 643 ARG 0.009 0.000 ARG D 584 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 630) hydrogen bonds : angle 4.61260 ( 1818) covalent geometry : bond 0.00306 (16884) covalent geometry : angle 0.69979 (22884) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 218 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6130 (mtt) cc_final: 0.5836 (mtt) REVERT: A 290 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6907 (tp) REVERT: A 353 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7239 (mm) REVERT: A 366 ARG cc_start: 0.8269 (mtt90) cc_final: 0.8045 (mpt90) REVERT: A 372 MET cc_start: 0.7133 (tpp) cc_final: 0.6440 (ttm) REVERT: A 378 ARG cc_start: 0.8085 (mmm-85) cc_final: 0.7769 (tpp80) REVERT: A 401 MET cc_start: 0.7624 (tpp) cc_final: 0.6212 (pmm) REVERT: A 422 ASP cc_start: 0.7193 (m-30) cc_final: 0.6287 (m-30) REVERT: A 482 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7720 (mm) REVERT: A 485 MET cc_start: 0.7936 (mmm) cc_final: 0.7688 (mmt) REVERT: A 513 GLU cc_start: 0.7620 (pt0) cc_final: 0.7374 (pt0) REVERT: A 657 PHE cc_start: 0.7062 (p90) cc_final: 0.6840 (p90) REVERT: A 713 MET cc_start: 0.8803 (mmm) cc_final: 0.7965 (mpp) REVERT: B 504 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7059 (mp10) REVERT: B 673 PRO cc_start: 0.7948 (Cg_exo) cc_final: 0.7713 (Cg_endo) REVERT: B 756 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7702 (mm) REVERT: C 258 MET cc_start: 0.4524 (mmt) cc_final: 0.3249 (mmt) REVERT: C 401 MET cc_start: 0.6778 (tpp) cc_final: 0.6550 (pmm) REVERT: C 425 ASP cc_start: 0.7584 (p0) cc_final: 0.6978 (p0) REVERT: C 479 ARG cc_start: 0.8483 (tpm170) cc_final: 0.8181 (tpm170) REVERT: D 557 PHE cc_start: 0.8563 (m-80) cc_final: 0.8254 (m-80) REVERT: D 698 MET cc_start: 0.3577 (tpt) cc_final: 0.3134 (tpp) REVERT: D 705 GLU cc_start: 0.6525 (mt-10) cc_final: 0.6050 (pt0) REVERT: D 709 ARG cc_start: 0.8401 (mmm160) cc_final: 0.7740 (tpt90) REVERT: D 713 MET cc_start: 0.7937 (mmm) cc_final: 0.7151 (mmm) outliers start: 50 outliers final: 37 residues processed: 253 average time/residue: 0.2646 time to fit residues: 102.0792 Evaluate side-chains 250 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 726 HIS Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 183 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 161 optimal weight: 6.9990 chunk 202 optimal weight: 8.9990 chunk 132 optimal weight: 0.1980 chunk 175 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 147 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 727 GLN ** 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 = 0.4316 r_free = 0.4316 target = 0.136513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.110239 restraints weight = 51848.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.111403 restraints weight = 34276.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.112268 restraints weight = 23395.227| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16884 Z= 0.114 Angle : 0.690 13.346 22884 Z= 0.337 Chirality : 0.045 0.388 2604 Planarity : 0.005 0.056 2972 Dihedral : 5.256 51.199 2327 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.37 % Allowed : 18.00 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.19), residues: 2120 helix: 0.75 (0.18), residues: 858 sheet: -0.82 (0.32), residues: 253 loop : -2.12 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 298 HIS 0.023 0.001 HIS C 726 PHE 0.010 0.001 PHE D 466 TYR 0.016 0.001 TYR D 643 ARG 0.009 0.000 ARG B 275 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 630) hydrogen bonds : angle 4.47478 ( 1818) covalent geometry : bond 0.00254 (16884) covalent geometry : angle 0.68996 (22884) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6100 (mtt) cc_final: 0.5809 (mtt) REVERT: A 290 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6877 (tp) REVERT: A 353 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7187 (mm) REVERT: A 372 MET cc_start: 0.7113 (tpp) cc_final: 0.6446 (ttm) REVERT: A 378 ARG cc_start: 0.8071 (mmm-85) cc_final: 0.7717 (tpp80) REVERT: A 401 MET cc_start: 0.7551 (tpp) cc_final: 0.6410 (pmm) REVERT: A 422 ASP cc_start: 0.7319 (m-30) cc_final: 0.6300 (m-30) REVERT: A 482 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7659 (mm) REVERT: A 485 MET cc_start: 0.7961 (mmm) cc_final: 0.7740 (mmt) REVERT: A 657 PHE cc_start: 0.6951 (p90) cc_final: 0.6723 (p90) REVERT: A 698 MET cc_start: 0.6606 (mmm) cc_final: 0.5251 (mmm) REVERT: A 713 MET cc_start: 0.8820 (mmm) cc_final: 0.8047 (mpp) REVERT: B 258 MET cc_start: 0.4666 (tpp) cc_final: 0.3464 (tpp) REVERT: B 423 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6648 (tm-30) REVERT: B 504 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7028 (mp10) REVERT: B 673 PRO cc_start: 0.7911 (Cg_exo) cc_final: 0.7693 (Cg_endo) REVERT: B 756 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7667 (mm) REVERT: C 258 MET cc_start: 0.4427 (mmt) cc_final: 0.3149 (mmt) REVERT: C 401 MET cc_start: 0.6688 (tpp) cc_final: 0.6482 (pmm) REVERT: C 425 ASP cc_start: 0.7572 (p0) cc_final: 0.7049 (p0) REVERT: C 479 ARG cc_start: 0.8530 (tpm170) cc_final: 0.8196 (tpm170) REVERT: D 331 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7526 (mt-10) REVERT: D 557 PHE cc_start: 0.8521 (m-80) cc_final: 0.8236 (m-80) REVERT: D 705 GLU cc_start: 0.6480 (mt-10) cc_final: 0.6005 (pt0) REVERT: D 709 ARG cc_start: 0.8288 (mmm160) cc_final: 0.7223 (tpt90) REVERT: D 713 MET cc_start: 0.7985 (mmm) cc_final: 0.7218 (mmm) outliers start: 42 outliers final: 28 residues processed: 247 average time/residue: 0.2951 time to fit residues: 110.0106 Evaluate side-chains 241 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 128 optimal weight: 0.0570 chunk 119 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 chunk 178 optimal weight: 30.0000 chunk 12 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 GLN C 726 HIS ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.133544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.106951 restraints weight = 52277.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.107198 restraints weight = 35102.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.108622 restraints weight = 26624.394| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16884 Z= 0.173 Angle : 0.748 15.178 22884 Z= 0.364 Chirality : 0.046 0.268 2604 Planarity : 0.005 0.058 2972 Dihedral : 5.482 52.140 2327 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.43 % Allowed : 18.06 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.19), residues: 2120 helix: 0.56 (0.18), residues: 863 sheet: -1.06 (0.31), residues: 267 loop : -2.24 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 298 HIS 0.007 0.001 HIS B 319 PHE 0.020 0.002 PHE D 657 TYR 0.023 0.002 TYR D 643 ARG 0.009 0.001 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 630) hydrogen bonds : angle 4.73786 ( 1818) covalent geometry : bond 0.00401 (16884) covalent geometry : angle 0.74815 (22884) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6330 (mtt) cc_final: 0.6012 (mtt) REVERT: A 290 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6903 (tp) REVERT: A 353 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7224 (mm) REVERT: A 372 MET cc_start: 0.7436 (tpp) cc_final: 0.6434 (ttm) REVERT: A 378 ARG cc_start: 0.8056 (mmm-85) cc_final: 0.7827 (tpp80) REVERT: A 401 MET cc_start: 0.7673 (tpp) cc_final: 0.6432 (pmm) REVERT: A 482 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7748 (mm) REVERT: A 485 MET cc_start: 0.7993 (mmm) cc_final: 0.7681 (mmt) REVERT: A 713 MET cc_start: 0.8800 (mmm) cc_final: 0.7954 (mpp) REVERT: B 504 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7096 (mp10) REVERT: B 756 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7678 (mm) REVERT: C 258 MET cc_start: 0.4454 (mmt) cc_final: 0.3135 (mmt) REVERT: C 306 LEU cc_start: 0.7230 (mt) cc_final: 0.7027 (mp) REVERT: C 401 MET cc_start: 0.6723 (tpp) cc_final: 0.6507 (pmm) REVERT: C 425 ASP cc_start: 0.7641 (p0) cc_final: 0.7168 (p0) REVERT: C 479 ARG cc_start: 0.8655 (tpm170) cc_final: 0.8286 (tpm170) REVERT: D 385 ARG cc_start: 0.7202 (ppt-90) cc_final: 0.6449 (mmt90) REVERT: D 427 MET cc_start: 0.7589 (ptm) cc_final: 0.7346 (ptp) REVERT: D 557 PHE cc_start: 0.8597 (m-80) cc_final: 0.8293 (m-80) REVERT: D 705 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6131 (pt0) REVERT: D 709 ARG cc_start: 0.8349 (mmm160) cc_final: 0.7188 (tpt90) REVERT: D 713 MET cc_start: 0.7974 (mmm) cc_final: 0.7255 (mmm) outliers start: 43 outliers final: 36 residues processed: 239 average time/residue: 0.2939 time to fit residues: 108.1956 Evaluate side-chains 246 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 726 HIS Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 12 optimal weight: 5.9990 chunk 117 optimal weight: 0.0980 chunk 121 optimal weight: 9.9990 chunk 193 optimal weight: 0.0020 chunk 46 optimal weight: 0.0770 chunk 180 optimal weight: 0.0870 chunk 19 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 41 optimal weight: 0.0060 chunk 144 optimal weight: 0.2980 chunk 143 optimal weight: 1.9990 overall best weight: 0.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN C 726 HIS D 447 GLN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.137732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.111626 restraints weight = 51778.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.112372 restraints weight = 35081.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.112697 restraints weight = 26650.563| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16884 Z= 0.120 Angle : 0.714 12.402 22884 Z= 0.347 Chirality : 0.045 0.253 2604 Planarity : 0.005 0.065 2972 Dihedral : 5.206 52.782 2327 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.09 % Allowed : 18.57 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.19), residues: 2120 helix: 0.84 (0.18), residues: 853 sheet: -0.81 (0.31), residues: 268 loop : -2.08 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 298 HIS 0.022 0.001 HIS C 726 PHE 0.021 0.002 PHE D 467 TYR 0.013 0.001 TYR D 651 ARG 0.017 0.001 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 630) hydrogen bonds : angle 4.42674 ( 1818) covalent geometry : bond 0.00259 (16884) covalent geometry : angle 0.71393 (22884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6332.80 seconds wall clock time: 112 minutes 23.47 seconds (6743.47 seconds total)