Starting phenix.real_space_refine on Mon Dec 30 06:53:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yuh_34107/12_2024/7yuh_34107.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yuh_34107/12_2024/7yuh_34107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yuh_34107/12_2024/7yuh_34107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yuh_34107/12_2024/7yuh_34107.map" model { file = "/net/cci-nas-00/data/ceres_data/7yuh_34107/12_2024/7yuh_34107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yuh_34107/12_2024/7yuh_34107.cif" } resolution = 3.7 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= 0.056 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 45 5.16 5 C 7860 2.51 5 N 2178 2.21 5 O 2349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12432 Number of models: 1 Model: "" Number of chains: 3 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} Time building chain proxies: 7.92, per 1000 atoms: 0.64 Number of scatterers: 12432 At special positions: 0 Unit cell: (97.58, 109.88, 138.58, 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 45 16.00 O 2349 8.00 N 2178 7.00 C 7860 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: 2.97 Conformation dependent library (CDL) restraints added in 2.0 seconds 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 14 sheets defined 46.7% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 243 through 256 removed outlier: 3.899A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 280 through 294 removed outlier: 4.009A pdb=" N THR A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.736A pdb=" N ARG A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 372 Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 424 through 427 removed outlier: 3.774A pdb=" N MET A 427 " --> pdb=" O ILE A 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 424 through 427' Processing helix chain 'A' and resid 434 through 443 removed outlier: 4.164A pdb=" N ALA A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.569A pdb=" N ASP A 483 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 513 removed outlier: 3.999A pdb=" N LYS A 509 " --> pdb=" O TYR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.549A pdb=" N ILE A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.701A pdb=" N GLU A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 4.089A pdb=" N TYR A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 591 removed outlier: 4.309A pdb=" N GLU A 591 " --> pdb=" O ALA A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 645 Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 717 through 728 removed outlier: 3.901A 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 741 through 746 removed outlier: 3.727A pdb=" N LEU A 746 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 removed outlier: 3.595A pdb=" N LEU A 751 " --> pdb=" O PRO A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 770 removed outlier: 3.603A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 254 Processing helix chain 'B' and resid 259 through 273 Processing helix chain 'B' and resid 281 through 296 removed outlier: 3.759A pdb=" N ALA B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 324 through 339 removed outlier: 3.774A pdb=" N THR B 339 " --> pdb=" O VAL B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 373 Processing helix chain 'B' and resid 386 through 391 removed outlier: 3.857A pdb=" N ILE B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.808A pdb=" N HIS B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 444 Processing helix chain 'B' and resid 447 through 451 removed outlier: 3.673A pdb=" N PHE B 451 " --> pdb=" O ASN B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.677A pdb=" N ASP B 483 " --> pdb=" O ARG B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.664A pdb=" N TYR B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 removed outlier: 3.500A pdb=" N GLU B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 579 removed outlier: 3.998A pdb=" N TYR B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.997A pdb=" N GLU B 589 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 647 removed outlier: 3.861A pdb=" N LYS B 634 " --> pdb=" O GLY B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 652 removed outlier: 3.780A pdb=" N TYR B 651 " --> pdb=" O THR B 648 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 652 " --> pdb=" O GLN B 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 648 through 652' Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 717 through 728 removed outlier: 3.750A pdb=" N LYS B 721 " --> pdb=" O GLY B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 738 No H-bonds generated for 'chain 'B' and resid 736 through 738' Processing helix chain 'B' and resid 739 through 744 removed outlier: 3.764A pdb=" N GLU B 744 " --> pdb=" O GLU B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 769 removed outlier: 3.759A 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 271 Processing helix chain 'C' and resid 282 through 294 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.631A pdb=" N THR C 311 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 339 Processing helix chain 'C' and resid 360 through 372 Processing helix chain 'C' and resid 386 through 391 removed outlier: 3.647A pdb=" N ILE C 390 " --> pdb=" O ASP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 411 Processing helix chain 'C' and resid 434 through 444 removed outlier: 4.158A pdb=" N ALA C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET C 439 " --> pdb=" O PRO C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 451 removed outlier: 3.500A pdb=" N THR C 450 " --> pdb=" O GLN C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.784A pdb=" N ASP C 483 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 505 through 513 removed outlier: 3.651A pdb=" N LYS C 509 " --> pdb=" O TYR C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 533 removed outlier: 3.798A pdb=" N ILE C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 removed outlier: 3.795A pdb=" N GLU C 560 " --> pdb=" O LYS C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 579 Processing helix chain 'C' and resid 630 through 647 removed outlier: 4.096A pdb=" N LYS C 634 " --> pdb=" O GLY C 630 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 652 removed outlier: 4.199A pdb=" N TYR C 651 " --> pdb=" O THR C 648 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY C 652 " --> pdb=" O GLN C 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 648 through 652' Processing helix chain 'C' and resid 679 through 693 Processing helix chain 'C' and resid 717 through 728 removed outlier: 3.642A pdb=" N LYS C 721 " --> pdb=" O GLY C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 745 removed outlier: 4.349A pdb=" N ALA C 741 " --> pdb=" O ASP C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 removed outlier: 4.275A pdb=" N LEU C 751 " --> pdb=" O PRO C 747 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU C 752 " --> pdb=" O LYS C 748 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY C 753 " --> pdb=" O GLU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 769 Processing sheet with id=AA1, first strand: chain 'A' and resid 375 through 380 removed outlier: 6.824A pdb=" N LYS A 375 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A 420 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N HIS A 377 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ASP A 422 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 379 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 468 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ILE A 419 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N THR A 470 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU A 421 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU A 353 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 488 " --> pdb=" O VAL A 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 7.208A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 597 through 603 removed outlier: 6.668A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.008A pdb=" N ILE A 733 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL A 759 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU A 735 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 352 through 354 removed outlier: 6.132A pdb=" N VAL B 352 " --> pdb=" O ILE B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 376 through 380 Processing sheet with id=AA7, first strand: chain 'B' and resid 596 through 603 removed outlier: 3.541A pdb=" N THR B 603 " --> pdb=" O GLY B 606 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 700 through 702 Processing sheet with id=AA9, first strand: chain 'B' and resid 705 through 707 removed outlier: 4.121A pdb=" N GLU B 705 " --> pdb=" O MET B 713 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS B 711 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 376 through 380 removed outlier: 3.804A pdb=" N LEU C 420 " --> pdb=" O HIS C 377 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU C 353 " --> pdb=" O ALA C 471 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL C 352 " --> pdb=" O ILE C 488 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 520 through 522 removed outlier: 5.967A 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 603 removed outlier: 5.988A 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: 6.758A pdb=" N ALA C 701 " --> pdb=" O VAL C 734 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE C 733 " --> pdb=" O LYS C 757 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL C 759 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU C 735 " --> pdb=" O VAL C 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 705 through 707 removed outlier: 4.050A pdb=" N GLU C 705 " --> pdb=" O MET C 713 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS C 711 " --> pdb=" O SER C 707 " (cutoff:3.500A) 481 hydrogen bonds defined for protein. 1380 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3592 1.33 - 1.45: 1928 1.45 - 1.57: 7053 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 12663 Sorted by residual: bond pdb=" C ARG C 479 " pdb=" N PRO C 480 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.20e-02 6.94e+03 1.27e+01 bond pdb=" C LEU C 771 " pdb=" N PRO C 772 " ideal model delta sigma weight residual 1.333 1.370 -0.037 1.20e-02 6.94e+03 9.42e+00 bond pdb=" C LEU C 381 " pdb=" N GLY C 382 " ideal model delta sigma weight residual 1.331 1.312 0.019 6.60e-03 2.30e+04 8.38e+00 bond pdb=" C LEU B 351 " pdb=" N VAL B 352 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.24e-02 6.50e+03 6.06e+00 bond pdb=" C GLY C 321 " pdb=" N LEU C 322 " ideal model delta sigma weight residual 1.333 1.300 0.032 1.38e-02 5.25e+03 5.54e+00 ... (remaining 12658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 16370 2.50 - 5.00: 677 5.00 - 7.50: 86 7.50 - 10.00: 26 10.00 - 12.50: 4 Bond angle restraints: 17163 Sorted by residual: angle pdb=" N GLY B 341 " pdb=" CA GLY B 341 " pdb=" C GLY B 341 " ideal model delta sigma weight residual 115.00 107.27 7.73 1.44e+00 4.82e-01 2.88e+01 angle pdb=" C GLY B 321 " pdb=" N LEU B 322 " pdb=" CA LEU B 322 " ideal model delta sigma weight residual 121.54 131.18 -9.64 1.91e+00 2.74e-01 2.55e+01 angle pdb=" N PRO A 592 " pdb=" CA PRO A 592 " pdb=" C PRO A 592 " ideal model delta sigma weight residual 112.47 122.78 -10.31 2.06e+00 2.36e-01 2.50e+01 angle pdb=" N PRO B 281 " pdb=" CA PRO B 281 " pdb=" C PRO B 281 " ideal model delta sigma weight residual 112.47 121.60 -9.13 2.06e+00 2.36e-01 1.97e+01 angle pdb=" C GLU A 591 " pdb=" N PRO A 592 " pdb=" CA PRO A 592 " ideal model delta sigma weight residual 119.84 125.07 -5.23 1.25e+00 6.40e-01 1.75e+01 ... (remaining 17158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 7280 15.45 - 30.90: 407 30.90 - 46.36: 83 46.36 - 61.81: 7 61.81 - 77.26: 14 Dihedral angle restraints: 7791 sinusoidal: 3225 harmonic: 4566 Sorted by residual: dihedral pdb=" CA SER B 280 " pdb=" C SER B 280 " pdb=" N PRO B 281 " pdb=" CA PRO B 281 " ideal model delta harmonic sigma weight residual 180.00 -140.53 -39.47 0 5.00e+00 4.00e-02 6.23e+01 dihedral pdb=" CA LEU C 306 " pdb=" C LEU C 306 " pdb=" N ASP C 307 " pdb=" CA ASP C 307 " ideal model delta harmonic sigma weight residual -180.00 -140.66 -39.34 0 5.00e+00 4.00e-02 6.19e+01 dihedral pdb=" CA GLY B 279 " pdb=" C GLY B 279 " pdb=" N SER B 280 " pdb=" CA SER B 280 " ideal model delta harmonic sigma weight residual 180.00 145.73 34.27 0 5.00e+00 4.00e-02 4.70e+01 ... (remaining 7788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1306 0.062 - 0.124: 547 0.124 - 0.185: 81 0.185 - 0.247: 12 0.247 - 0.309: 7 Chirality restraints: 1953 Sorted by residual: chirality pdb=" CB ILE B 468 " pdb=" CA ILE B 468 " pdb=" CG1 ILE B 468 " pdb=" CG2 ILE B 468 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.39e+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 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB ILE B 398 " pdb=" CA ILE B 398 " pdb=" CG1 ILE B 398 " pdb=" CG2 ILE B 398 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1950 not shown) Planarity restraints: 2229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 771 " 0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO C 772 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 772 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 772 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 507 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO B 508 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 508 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 508 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 507 " -0.045 5.00e-02 4.00e+02 6.66e-02 7.10e+00 pdb=" N PRO A 508 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 508 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 508 " -0.038 5.00e-02 4.00e+02 ... (remaining 2226 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2707 2.78 - 3.31: 11149 3.31 - 3.84: 19725 3.84 - 4.37: 22730 4.37 - 4.90: 38493 Nonbonded interactions: 94804 Sorted by model distance: nonbonded pdb=" O PRO A 297 " pdb=" OH TYR A 460 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR A 672 " pdb=" O LYS A 674 " model vdw 2.282 3.040 nonbonded pdb=" OD1 ASP A 422 " pdb=" OG1 THR A 470 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR B 603 " pdb=" O GLY B 606 " model vdw 2.286 3.040 nonbonded pdb=" O PRO B 297 " pdb=" OH TYR B 460 " model vdw 2.286 3.040 ... (remaining 94799 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.540 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 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 0.089 12663 Z= 0.634 Angle : 1.176 12.505 17163 Z= 0.628 Chirality : 0.065 0.309 1953 Planarity : 0.009 0.081 2229 Dihedral : 10.784 77.262 4863 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.94 % Favored : 88.93 % Rotamer: Outliers : 0.15 % Allowed : 3.84 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.20 % 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: -4.68 (0.16), residues: 1590 helix: -2.80 (0.15), residues: 638 sheet: -2.89 (0.31), residues: 195 loop : -3.43 (0.18), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP B 558 HIS 0.020 0.003 HIS C 319 PHE 0.029 0.004 PHE C 466 TYR 0.032 0.003 TYR A 289 ARG 0.019 0.002 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 321 time to evaluate : 1.413 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: A 276 MET cc_start: 0.6217 (mtt) cc_final: 0.5102 (tpp) REVERT: A 439 MET cc_start: 0.8421 (mmm) cc_final: 0.8210 (mmm) REVERT: A 453 ASP cc_start: 0.6704 (m-30) cc_final: 0.6322 (m-30) REVERT: A 454 HIS cc_start: 0.7609 (m90) cc_final: 0.7404 (m-70) REVERT: A 469 THR cc_start: 0.9165 (m) cc_final: 0.8840 (p) REVERT: A 516 MET cc_start: 0.8151 (mmm) cc_final: 0.7565 (mtm) REVERT: A 520 ILE cc_start: 0.8595 (mt) cc_final: 0.8349 (mm) REVERT: A 553 LYS cc_start: 0.8785 (mmmm) cc_final: 0.8465 (mmmt) REVERT: A 608 THR cc_start: 0.8551 (t) cc_final: 0.8130 (p) REVERT: A 641 LEU cc_start: 0.8396 (mt) cc_final: 0.8132 (mm) REVERT: B 292 TRP cc_start: 0.7638 (m100) cc_final: 0.7362 (m100) REVERT: B 385 ARG cc_start: 0.7692 (pmt170) cc_final: 0.7191 (mtm-85) REVERT: B 439 MET cc_start: 0.7732 (mmp) cc_final: 0.7484 (mmp) REVERT: C 244 SER cc_start: 0.8386 (p) cc_final: 0.8088 (t) REVERT: C 290 LEU cc_start: 0.8822 (mt) cc_final: 0.8312 (pp) REVERT: C 721 LYS cc_start: 0.8397 (mttm) cc_final: 0.8156 (mtpp) outliers start: 2 outliers final: 1 residues processed: 323 average time/residue: 0.3492 time to fit residues: 147.5467 Evaluate side-chains 164 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 590 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.9990 chunk 120 optimal weight: 0.0470 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 144 optimal weight: 0.0670 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 310 HIS A 319 HIS ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 GLN A 739 ASN B 346 ASN B 447 GLN B 449 ASN B 664 HIS C 277 GLN C 346 ASN C 393 HIS C 407 HIS C 449 ASN C 454 HIS C 472 ASN C 598 GLN C 647 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12663 Z= 0.198 Angle : 0.730 8.795 17163 Z= 0.369 Chirality : 0.046 0.205 1953 Planarity : 0.007 0.065 2229 Dihedral : 6.513 34.857 1744 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.96 % Allowed : 11.51 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.19 (0.19), residues: 1590 helix: -1.11 (0.19), residues: 667 sheet: -2.34 (0.34), residues: 194 loop : -3.05 (0.20), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 558 HIS 0.008 0.001 HIS A 310 PHE 0.009 0.001 PHE A 451 TYR 0.022 0.002 TYR A 289 ARG 0.006 0.001 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 1.423 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: A 276 MET cc_start: 0.6211 (mtt) cc_final: 0.5142 (tpp) REVERT: A 469 THR cc_start: 0.8929 (m) cc_final: 0.8559 (p) REVERT: A 516 MET cc_start: 0.7984 (mmm) cc_final: 0.7505 (mtm) REVERT: A 520 ILE cc_start: 0.8525 (mt) cc_final: 0.8165 (mm) REVERT: A 553 LYS cc_start: 0.8572 (mmmm) cc_final: 0.8296 (mmmt) REVERT: A 608 THR cc_start: 0.8428 (t) cc_final: 0.7902 (p) REVERT: A 620 SER cc_start: 0.9040 (p) cc_final: 0.8792 (t) REVERT: A 631 GLU cc_start: 0.7724 (tp30) cc_final: 0.6461 (tp30) REVERT: A 674 LYS cc_start: 0.3982 (pttp) cc_final: 0.3175 (ttmt) REVERT: A 698 MET cc_start: 0.8009 (mmm) cc_final: 0.7218 (mmm) REVERT: B 287 ARG cc_start: 0.6026 (ttp-110) cc_final: 0.5813 (mtm-85) REVERT: B 385 ARG cc_start: 0.7671 (pmt170) cc_final: 0.7187 (mtm-85) REVERT: B 552 ARG cc_start: 0.7896 (mtt-85) cc_final: 0.7569 (mtt-85) REVERT: B 681 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.7934 (mm) REVERT: C 268 LYS cc_start: 0.8389 (ttpp) cc_final: 0.8028 (tppt) REVERT: C 715 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7947 (pp) outliers start: 26 outliers final: 8 residues processed: 244 average time/residue: 0.3052 time to fit residues: 100.9596 Evaluate side-chains 173 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 723 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS B 454 HIS C 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12663 Z= 0.193 Angle : 0.677 7.540 17163 Z= 0.338 Chirality : 0.045 0.191 1953 Planarity : 0.006 0.063 2229 Dihedral : 5.751 31.190 1743 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.78 % Allowed : 13.32 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.44 (0.20), residues: 1590 helix: -0.36 (0.20), residues: 670 sheet: -1.97 (0.35), residues: 200 loop : -2.78 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 292 HIS 0.008 0.001 HIS A 310 PHE 0.008 0.001 PHE A 467 TYR 0.018 0.002 TYR A 289 ARG 0.009 0.001 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6299 (mtt) cc_final: 0.5145 (tpp) REVERT: A 401 MET cc_start: 0.5390 (tmm) cc_final: 0.5151 (tmm) REVERT: A 423 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7561 (tt0) REVERT: A 469 THR cc_start: 0.9023 (m) cc_final: 0.8674 (p) REVERT: A 516 MET cc_start: 0.7976 (mmm) cc_final: 0.7463 (mtm) REVERT: A 520 ILE cc_start: 0.8554 (mt) cc_final: 0.8194 (mm) REVERT: A 553 LYS cc_start: 0.8571 (mmmm) cc_final: 0.8325 (mmmt) REVERT: A 608 THR cc_start: 0.8364 (t) cc_final: 0.7896 (p) REVERT: A 620 SER cc_start: 0.8984 (p) cc_final: 0.8741 (t) REVERT: A 635 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8040 (mm-30) REVERT: A 638 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8308 (mm-40) REVERT: A 674 LYS cc_start: 0.3998 (pttp) cc_final: 0.2933 (ttpt) REVERT: A 758 LEU cc_start: 0.7661 (mt) cc_final: 0.7459 (mt) REVERT: B 276 MET cc_start: 0.1786 (pmm) cc_final: 0.1205 (pmm) REVERT: B 385 ARG cc_start: 0.7738 (pmt170) cc_final: 0.7228 (mtm-85) REVERT: B 546 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7435 (mp0) outliers start: 37 outliers final: 19 residues processed: 211 average time/residue: 0.2853 time to fit residues: 83.8872 Evaluate side-chains 175 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 746 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.3980 chunk 108 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS A 346 ASN A 407 HIS A 664 HIS C 472 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12663 Z= 0.255 Angle : 0.684 9.131 17163 Z= 0.341 Chirality : 0.046 0.184 1953 Planarity : 0.006 0.064 2229 Dihedral : 5.567 28.479 1743 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.93 % Allowed : 13.77 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.21), residues: 1590 helix: -0.15 (0.20), residues: 682 sheet: -1.87 (0.36), residues: 195 loop : -2.72 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 292 HIS 0.020 0.001 HIS A 407 PHE 0.021 0.002 PHE B 657 TYR 0.022 0.002 TYR A 289 ARG 0.008 0.001 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6412 (mtt) cc_final: 0.5173 (tpp) REVERT: A 401 MET cc_start: 0.5615 (tmm) cc_final: 0.5409 (tmm) REVERT: A 423 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7601 (tt0) REVERT: A 469 THR cc_start: 0.9054 (m) cc_final: 0.8742 (p) REVERT: A 516 MET cc_start: 0.8000 (mmm) cc_final: 0.7498 (mtm) REVERT: A 520 ILE cc_start: 0.8570 (mt) cc_final: 0.8161 (mm) REVERT: A 553 LYS cc_start: 0.8705 (mmmm) cc_final: 0.8428 (mmmt) REVERT: A 608 THR cc_start: 0.8439 (t) cc_final: 0.7972 (p) REVERT: A 620 SER cc_start: 0.8994 (p) cc_final: 0.8745 (t) REVERT: A 635 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8142 (mm-30) REVERT: A 638 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8289 (mm-40) REVERT: B 276 MET cc_start: 0.1653 (pmm) cc_final: 0.1149 (pmm) REVERT: B 385 ARG cc_start: 0.7850 (pmt170) cc_final: 0.7144 (mtm-85) REVERT: B 546 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: C 430 ASP cc_start: 0.8273 (m-30) cc_final: 0.8044 (p0) outliers start: 39 outliers final: 26 residues processed: 199 average time/residue: 0.2927 time to fit residues: 80.6106 Evaluate side-chains 180 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 768 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 114 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 0.2980 chunk 106 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS A 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12663 Z= 0.261 Angle : 0.676 7.696 17163 Z= 0.336 Chirality : 0.045 0.177 1953 Planarity : 0.006 0.063 2229 Dihedral : 5.445 25.630 1743 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.99 % Allowed : 14.75 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.99 (0.21), residues: 1590 helix: 0.05 (0.21), residues: 672 sheet: -1.69 (0.36), residues: 199 loop : -2.60 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 431 HIS 0.007 0.001 HIS C 319 PHE 0.017 0.002 PHE B 657 TYR 0.018 0.002 TYR C 643 ARG 0.008 0.001 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 168 time to evaluate : 1.532 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: A 276 MET cc_start: 0.6373 (mtt) cc_final: 0.5158 (tpp) REVERT: A 423 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7648 (tt0) REVERT: A 516 MET cc_start: 0.7970 (mmm) cc_final: 0.7476 (mtm) REVERT: A 520 ILE cc_start: 0.8615 (mt) cc_final: 0.8187 (mm) REVERT: A 553 LYS cc_start: 0.8747 (mmmm) cc_final: 0.8445 (mmmt) REVERT: A 608 THR cc_start: 0.8428 (t) cc_final: 0.7953 (p) REVERT: A 620 SER cc_start: 0.8968 (p) cc_final: 0.8713 (t) REVERT: B 546 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: B 681 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8154 (mm) REVERT: C 430 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8114 (p0) REVERT: C 479 ARG cc_start: 0.7897 (tpm170) cc_final: 0.7600 (tpm170) REVERT: C 516 MET cc_start: 0.5593 (OUTLIER) cc_final: 0.4513 (mmm) outliers start: 53 outliers final: 37 residues processed: 198 average time/residue: 0.2827 time to fit residues: 77.8918 Evaluate side-chains 192 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 768 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.0970 chunk 37 optimal weight: 0.4980 chunk 153 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 HIS C 666 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 12663 Z= 0.386 Angle : 0.754 10.291 17163 Z= 0.375 Chirality : 0.048 0.203 1953 Planarity : 0.006 0.063 2229 Dihedral : 5.654 27.967 1743 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.46 % Allowed : 16.10 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.21), residues: 1590 helix: -0.04 (0.21), residues: 659 sheet: -1.93 (0.35), residues: 196 loop : -2.43 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 563 HIS 0.009 0.001 HIS A 407 PHE 0.017 0.002 PHE C 466 TYR 0.021 0.002 TYR C 643 ARG 0.010 0.001 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6359 (mtt) cc_final: 0.5113 (tpp) REVERT: A 401 MET cc_start: 0.5546 (tmm) cc_final: 0.5238 (tmm) REVERT: A 423 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7700 (tt0) REVERT: A 516 MET cc_start: 0.7988 (mmm) cc_final: 0.7499 (mtm) REVERT: A 520 ILE cc_start: 0.8665 (mt) cc_final: 0.8221 (mm) REVERT: A 553 LYS cc_start: 0.8884 (mmmm) cc_final: 0.8509 (mmmt) REVERT: A 608 THR cc_start: 0.8428 (t) cc_final: 0.7917 (p) REVERT: A 620 SER cc_start: 0.8988 (p) cc_final: 0.8724 (t) REVERT: B 681 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8163 (mm) REVERT: C 258 MET cc_start: 0.6723 (mtp) cc_final: 0.6517 (mtp) REVERT: C 430 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8145 (p0) REVERT: C 516 MET cc_start: 0.5757 (OUTLIER) cc_final: 0.4706 (mmm) outliers start: 46 outliers final: 37 residues processed: 181 average time/residue: 0.2808 time to fit residues: 71.0590 Evaluate side-chains 188 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 768 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 129 optimal weight: 0.0050 chunk 85 optimal weight: 0.3980 chunk 153 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS A 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12663 Z= 0.181 Angle : 0.653 9.258 17163 Z= 0.321 Chirality : 0.044 0.156 1953 Planarity : 0.005 0.063 2229 Dihedral : 5.171 24.319 1743 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.01 % Allowed : 16.33 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.21), residues: 1590 helix: 0.31 (0.21), residues: 680 sheet: -1.41 (0.39), residues: 177 loop : -2.45 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 431 HIS 0.005 0.001 HIS A 407 PHE 0.013 0.001 PHE B 657 TYR 0.017 0.001 TYR C 643 ARG 0.008 0.001 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6385 (mtt) cc_final: 0.5096 (tpp) REVERT: A 401 MET cc_start: 0.5565 (tmm) cc_final: 0.5329 (tmm) REVERT: A 423 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7632 (tt0) REVERT: A 516 MET cc_start: 0.7933 (mmm) cc_final: 0.7384 (mtm) REVERT: A 520 ILE cc_start: 0.8624 (mt) cc_final: 0.8191 (mm) REVERT: A 553 LYS cc_start: 0.8674 (mmmm) cc_final: 0.8376 (mmmt) REVERT: A 608 THR cc_start: 0.8304 (t) cc_final: 0.7832 (p) REVERT: A 620 SER cc_start: 0.8985 (p) cc_final: 0.8705 (t) REVERT: B 258 MET cc_start: 0.6365 (mmp) cc_final: 0.6062 (mmp) REVERT: B 546 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: B 681 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8053 (mm) REVERT: C 516 MET cc_start: 0.5528 (OUTLIER) cc_final: 0.4445 (mmm) outliers start: 40 outliers final: 27 residues processed: 193 average time/residue: 0.2914 time to fit residues: 77.7570 Evaluate side-chains 179 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 768 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 0.1980 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12663 Z= 0.215 Angle : 0.668 9.584 17163 Z= 0.326 Chirality : 0.045 0.188 1953 Planarity : 0.005 0.062 2229 Dihedral : 5.094 23.070 1743 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.78 % Allowed : 17.46 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.22), residues: 1590 helix: 0.45 (0.21), residues: 672 sheet: -1.34 (0.38), residues: 188 loop : -2.29 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 431 HIS 0.024 0.001 HIS A 407 PHE 0.012 0.001 PHE B 657 TYR 0.018 0.001 TYR C 643 ARG 0.009 0.001 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6390 (mtt) cc_final: 0.5051 (tpp) REVERT: A 401 MET cc_start: 0.5646 (tmm) cc_final: 0.5397 (tmm) REVERT: A 423 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7678 (tt0) REVERT: A 516 MET cc_start: 0.7960 (mmm) cc_final: 0.7681 (mmp) REVERT: A 553 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8382 (mmmt) REVERT: A 608 THR cc_start: 0.8320 (t) cc_final: 0.7848 (p) REVERT: A 620 SER cc_start: 0.8981 (p) cc_final: 0.8707 (t) REVERT: A 631 GLU cc_start: 0.7129 (tp30) cc_final: 0.6446 (tp30) REVERT: B 258 MET cc_start: 0.6445 (mmp) cc_final: 0.6184 (mmp) REVERT: B 546 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: B 681 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8105 (mm) REVERT: C 516 MET cc_start: 0.5567 (OUTLIER) cc_final: 0.4472 (mmm) outliers start: 37 outliers final: 29 residues processed: 176 average time/residue: 0.2922 time to fit residues: 71.7563 Evaluate side-chains 176 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 664 HIS Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 768 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.6980 chunk 142 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12663 Z= 0.204 Angle : 0.666 8.924 17163 Z= 0.324 Chirality : 0.044 0.158 1953 Planarity : 0.005 0.062 2229 Dihedral : 5.014 23.455 1743 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.16 % Allowed : 17.31 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.22), residues: 1590 helix: 0.50 (0.21), residues: 681 sheet: -1.19 (0.38), residues: 188 loop : -2.35 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 292 HIS 0.004 0.001 HIS C 319 PHE 0.011 0.001 PHE B 657 TYR 0.016 0.001 TYR C 643 ARG 0.009 0.001 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6397 (mtt) cc_final: 0.4939 (tpp) REVERT: A 423 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7784 (tt0) REVERT: A 516 MET cc_start: 0.7875 (mmm) cc_final: 0.7668 (mmp) REVERT: A 553 LYS cc_start: 0.8732 (mmmm) cc_final: 0.8393 (mmmt) REVERT: A 608 THR cc_start: 0.8318 (t) cc_final: 0.7824 (p) REVERT: A 620 SER cc_start: 0.8951 (p) cc_final: 0.8684 (t) REVERT: A 631 GLU cc_start: 0.7390 (tp30) cc_final: 0.6878 (tp30) REVERT: B 258 MET cc_start: 0.6465 (mmp) cc_final: 0.6207 (mmp) REVERT: B 479 ARG cc_start: 0.7911 (mmm160) cc_final: 0.7674 (tpm170) REVERT: B 546 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: C 516 MET cc_start: 0.5547 (OUTLIER) cc_final: 0.4450 (mmm) outliers start: 42 outliers final: 30 residues processed: 175 average time/residue: 0.2968 time to fit residues: 71.8944 Evaluate side-chains 175 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 726 HIS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 664 HIS Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 768 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 158 optimal weight: 0.0770 chunk 145 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS A 407 HIS A 411 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12663 Z= 0.177 Angle : 0.661 9.984 17163 Z= 0.319 Chirality : 0.044 0.158 1953 Planarity : 0.005 0.061 2229 Dihedral : 4.838 21.679 1743 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.18 % Allowed : 17.83 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.22), residues: 1590 helix: 0.57 (0.21), residues: 686 sheet: -1.09 (0.38), residues: 186 loop : -2.26 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 292 HIS 0.003 0.001 HIS C 319 PHE 0.011 0.001 PHE B 657 TYR 0.013 0.001 TYR A 289 ARG 0.009 0.001 ARG A 545 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6315 (mtt) cc_final: 0.4843 (tpp) REVERT: A 423 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7803 (tt0) REVERT: A 516 MET cc_start: 0.7828 (mmm) cc_final: 0.7611 (mmp) REVERT: A 553 LYS cc_start: 0.8671 (mmmm) cc_final: 0.8350 (mmmt) REVERT: A 608 THR cc_start: 0.8337 (t) cc_final: 0.7824 (p) REVERT: A 620 SER cc_start: 0.8944 (p) cc_final: 0.8676 (t) REVERT: A 631 GLU cc_start: 0.7391 (tp30) cc_final: 0.7090 (tp30) REVERT: B 345 ARG cc_start: 0.7400 (mpt180) cc_final: 0.7160 (mmt180) REVERT: B 447 GLN cc_start: 0.8462 (tp40) cc_final: 0.8234 (tp40) REVERT: B 546 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: B 648 THR cc_start: 0.7812 (p) cc_final: 0.7562 (t) REVERT: C 516 MET cc_start: 0.5490 (OUTLIER) cc_final: 0.4379 (mmm) outliers start: 29 outliers final: 25 residues processed: 170 average time/residue: 0.2937 time to fit residues: 69.4098 Evaluate side-chains 172 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 726 HIS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 664 HIS Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 768 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.0670 chunk 126 optimal weight: 0.0050 chunk 52 optimal weight: 0.0870 chunk 129 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.139401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.113140 restraints weight = 29216.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.113089 restraints weight = 18960.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.113739 restraints weight = 15240.559| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12663 Z= 0.164 Angle : 0.660 10.417 17163 Z= 0.318 Chirality : 0.043 0.157 1953 Planarity : 0.005 0.063 2229 Dihedral : 4.737 21.075 1743 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.96 % Allowed : 18.36 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.22), residues: 1590 helix: 0.68 (0.21), residues: 686 sheet: -0.75 (0.40), residues: 170 loop : -2.19 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 431 HIS 0.020 0.001 HIS A 407 PHE 0.010 0.001 PHE B 657 TYR 0.016 0.001 TYR C 643 ARG 0.010 0.001 ARG A 545 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2671.42 seconds wall clock time: 50 minutes 9.23 seconds (3009.23 seconds total)