Starting phenix.real_space_refine on Sun Jan 19 10:01:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rz7_19605/01_2025/8rz7_19605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rz7_19605/01_2025/8rz7_19605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rz7_19605/01_2025/8rz7_19605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rz7_19605/01_2025/8rz7_19605.map" model { file = "/net/cci-nas-00/data/ceres_data/8rz7_19605/01_2025/8rz7_19605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rz7_19605/01_2025/8rz7_19605.cif" } resolution = 3.37 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= 0.001 sd= 0.024 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: 6 Type Number sf(0) Gaussians P 42 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 8495 2.51 5 N 2312 2.21 5 O 2633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13544 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6120 Classifications: {'peptide': 773} Link IDs: {'PTRANS': 21, 'TRANS': 751} Chain breaks: 12 Chain: "B" Number of atoms: 6588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6588 Classifications: {'peptide': 820} Link IDs: {'PTRANS': 25, 'TRANS': 794} Chain breaks: 7 Chain: "C" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 373 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain breaks: 1 Chain: "D" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 407 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N GLU A 48 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU A 48 " occ=0.00 residue: pdb=" N LYS A 65 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 65 " occ=0.00 residue: pdb=" N GLN A 76 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN A 76 " occ=0.00 residue: pdb=" N SER A 77 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER A 77 " occ=0.00 residue: pdb=" N LYS A 82 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 82 " occ=0.00 residue: pdb=" N GLU A 101 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU A 101 " occ=0.00 residue: pdb=" N PRO A 259 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 259 " occ=0.00 residue: pdb=" N ILE B 756 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE B 756 " occ=0.00 Time building chain proxies: 8.03, per 1000 atoms: 0.59 Number of scatterers: 13544 At special positions: 0 Unit cell: (92.3342, 127.988, 150.843, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 42 15.00 Mg 2 11.99 O 2633 8.00 N 2312 7.00 C 8495 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: 3.12 Conformation dependent library (CDL) restraints added in 1.5 seconds 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3034 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 14 sheets defined 55.8% alpha, 10.3% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.886A pdb=" N LEU A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.893A pdb=" N LYS A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.690A pdb=" N PHE A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 245 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 352 through 369 removed outlier: 3.646A pdb=" N ASP A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.828A pdb=" N ARG A 396 " --> pdb=" O LYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 425 removed outlier: 3.553A pdb=" N CYS A 404 " --> pdb=" O ASN A 400 " (cutoff:3.500A) Proline residue: A 415 - end of helix removed outlier: 4.458A pdb=" N GLU A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 447 Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 471 through 474 Processing helix chain 'A' and resid 475 through 504 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 553 through 572 Processing helix chain 'A' and resid 574 through 586 Processing helix chain 'A' and resid 589 through 614 Processing helix chain 'A' and resid 674 through 690 Processing helix chain 'A' and resid 723 through 738 Processing helix chain 'A' and resid 755 through 773 Processing helix chain 'A' and resid 784 through 793 Processing helix chain 'A' and resid 827 through 832 Processing helix chain 'A' and resid 837 through 852 removed outlier: 3.546A pdb=" N GLU A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 909 through 916 Processing helix chain 'B' and resid 230 through 243 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 411 through 422 Processing helix chain 'B' and resid 433 through 446 Processing helix chain 'B' and resid 448 through 452 Processing helix chain 'B' and resid 459 through 463 removed outlier: 3.508A pdb=" N TYR B 462 " --> pdb=" O ASP B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 476 removed outlier: 3.711A pdb=" N GLN B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 495 removed outlier: 3.557A pdb=" N ASN B 494 " --> pdb=" O GLY B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 513 removed outlier: 3.772A pdb=" N PHE B 513 " --> pdb=" O TYR B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 520 Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 538 through 545 Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 569 through 582 Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 606 through 615 Processing helix chain 'B' and resid 620 through 630 Processing helix chain 'B' and resid 634 through 660 Proline residue: B 657 - end of helix Processing helix chain 'B' and resid 665 through 680 Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 681 through 689 removed outlier: 4.090A pdb=" N TYR B 685 " --> pdb=" O PRO B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 697 Processing helix chain 'B' and resid 709 through 738 Processing helix chain 'B' and resid 782 through 817 removed outlier: 4.029A pdb=" N HIS B 817 " --> pdb=" O LYS B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 843 removed outlier: 3.778A pdb=" N LEU B 821 " --> pdb=" O HIS B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 871 Processing helix chain 'B' and resid 901 through 919 Processing helix chain 'B' and resid 951 through 966 removed outlier: 3.699A pdb=" N GLU B 955 " --> pdb=" O THR B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1000 Processing helix chain 'B' and resid 1011 through 1016 Processing helix chain 'B' and resid 1017 through 1019 No H-bonds generated for 'chain 'B' and resid 1017 through 1019' Processing helix chain 'B' and resid 1067 through 1076 Processing helix chain 'B' and resid 1079 through 1112 Processing helix chain 'B' and resid 1119 through 1125 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.959A pdb=" N HIS A 46 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ARG A 35 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR A 103 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 149 removed outlier: 7.131A pdb=" N VAL A 148 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N CYS A 199 " --> pdb=" O THR A 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 175 removed outlier: 5.915A pdb=" N LEU A 173 " --> pdb=" O THR A 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 removed outlier: 6.939A pdb=" N LYS A 301 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ALA A 710 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N CYS A 707 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE A 746 " --> pdb=" O CYS A 707 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 709 " --> pdb=" O ILE A 746 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ASP A 748 " --> pdb=" O LEU A 709 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG A 711 " --> pdb=" O ASP A 748 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 745 " --> pdb=" O MET A 779 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ALA A 781 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE A 747 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N HIS A 665 " --> pdb=" O PHE A 780 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 514 through 516 removed outlier: 3.713A pdb=" N GLY A 548 " --> pdb=" O GLN A 545 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 623 through 625 removed outlier: 3.833A pdb=" N SER A 699 " --> pdb=" O LYS A 635 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS A 635 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A 655 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AA9, first strand: chain 'B' and resid 282 through 286 removed outlier: 3.872A pdb=" N VAL B 250 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE B 259 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU B 248 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL B 247 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL B 307 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS B 249 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLN B 309 " --> pdb=" O CYS B 249 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N GLU B 251 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 332 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LYS B 308 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU B 330 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 371 through 373 Processing sheet with id=AB2, first strand: chain 'B' and resid 425 through 429 Processing sheet with id=AB3, first strand: chain 'B' and resid 769 through 773 removed outlier: 5.746A pdb=" N ARG B 779 " --> pdb=" O VAL B 771 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 880 through 885 removed outlier: 4.927A pdb=" N ASN B 880 " --> pdb=" O ASN B 861 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN B 861 " --> pdb=" O ASN B 880 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU B 926 " --> pdb=" O LYS B 860 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 935 through 937 removed outlier: 6.676A pdb=" N VAL B 972 " --> pdb=" O LEU B1006 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL B1008 " --> pdb=" O VAL B 972 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 974 " --> pdb=" O VAL B1008 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET B 892 " --> pdb=" O PHE B1007 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2185 1.30 - 1.44: 3663 1.44 - 1.58: 7783 1.58 - 1.71: 118 1.71 - 1.85: 95 Bond restraints: 13844 Sorted by residual: bond pdb=" CA VAL A 722 " pdb=" CB VAL A 722 " ideal model delta sigma weight residual 1.540 1.434 0.106 1.36e-02 5.41e+03 6.07e+01 bond pdb=" CD ARG B 296 " pdb=" NE ARG B 296 " ideal model delta sigma weight residual 1.458 1.557 -0.099 1.40e-02 5.10e+03 5.01e+01 bond pdb=" CA SER B 773 " pdb=" CB SER B 773 " ideal model delta sigma weight residual 1.526 1.634 -0.108 1.68e-02 3.54e+03 4.16e+01 bond pdb=" CA SER A 144 " pdb=" CB SER A 144 " ideal model delta sigma weight residual 1.530 1.409 0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" CA ARG B 257 " pdb=" CB ARG B 257 " ideal model delta sigma weight residual 1.524 1.438 0.086 1.46e-02 4.69e+03 3.50e+01 ... (remaining 13839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 17979 2.93 - 5.86: 763 5.86 - 8.78: 72 8.78 - 11.71: 19 11.71 - 14.64: 4 Bond angle restraints: 18837 Sorted by residual: angle pdb=" CB GLU B 533 " pdb=" CG GLU B 533 " pdb=" CD GLU B 533 " ideal model delta sigma weight residual 112.60 127.24 -14.64 1.70e+00 3.46e-01 7.41e+01 angle pdb=" CA ASP B1077 " pdb=" CB ASP B1077 " pdb=" CG ASP B1077 " ideal model delta sigma weight residual 112.60 121.10 -8.50 1.00e+00 1.00e+00 7.22e+01 angle pdb=" CB GLU B 701 " pdb=" CG GLU B 701 " pdb=" CD GLU B 701 " ideal model delta sigma weight residual 112.60 126.10 -13.50 1.70e+00 3.46e-01 6.31e+01 angle pdb=" N PRO A 439 " pdb=" CA PRO A 439 " pdb=" C PRO A 439 " ideal model delta sigma weight residual 113.65 104.46 9.19 1.35e+00 5.49e-01 4.63e+01 angle pdb=" CA THR A 810 " pdb=" CB THR A 810 " pdb=" OG1 THR A 810 " ideal model delta sigma weight residual 109.60 100.11 9.49 1.50e+00 4.44e-01 4.01e+01 ... (remaining 18832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 7881 35.45 - 70.89: 399 70.89 - 106.34: 19 106.34 - 141.78: 4 141.78 - 177.23: 3 Dihedral angle restraints: 8306 sinusoidal: 3649 harmonic: 4657 Sorted by residual: dihedral pdb=" C GLU A 132 " pdb=" N GLU A 132 " pdb=" CA GLU A 132 " pdb=" CB GLU A 132 " ideal model delta harmonic sigma weight residual -122.60 -141.06 18.46 0 2.50e+00 1.60e-01 5.45e+01 dihedral pdb=" C5' ADP B2000 " pdb=" O5' ADP B2000 " pdb=" PA ADP B2000 " pdb=" O2A ADP B2000 " ideal model delta sinusoidal sigma weight residual -60.00 109.17 -169.17 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" CD ARG B 322 " pdb=" NE ARG B 322 " pdb=" CZ ARG B 322 " pdb=" NH1 ARG B 322 " ideal model delta sinusoidal sigma weight residual 0.00 58.78 -58.78 1 1.00e+01 1.00e-02 4.62e+01 ... (remaining 8303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1702 0.114 - 0.228: 400 0.228 - 0.342: 53 0.342 - 0.456: 14 0.456 - 0.570: 3 Chirality restraints: 2172 Sorted by residual: chirality pdb=" CA GLU A 132 " pdb=" N GLU A 132 " pdb=" C GLU A 132 " pdb=" CB GLU A 132 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.13e+00 chirality pdb=" CA ASP A 575 " pdb=" N ASP A 575 " pdb=" C ASP A 575 " pdb=" CB ASP A 575 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.93e+00 chirality pdb=" CA GLN A 879 " pdb=" N GLN A 879 " pdb=" C GLN A 879 " pdb=" CB GLN A 879 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.50e+00 ... (remaining 2169 not shown) Planarity restraints: 2249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 322 " -0.924 9.50e-02 1.11e+02 4.14e-01 1.04e+02 pdb=" NE ARG B 322 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG B 322 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 322 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 322 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 793 " 0.029 2.00e-02 2.50e+03 5.43e-02 2.95e+01 pdb=" CD GLN A 793 " -0.094 2.00e-02 2.50e+03 pdb=" OE1 GLN A 793 " 0.037 2.00e-02 2.50e+03 pdb=" NE2 GLN A 793 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 296 " 0.475 9.50e-02 1.11e+02 2.13e-01 2.81e+01 pdb=" NE ARG B 296 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG B 296 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 296 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 296 " 0.017 2.00e-02 2.50e+03 ... (remaining 2246 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 19 2.32 - 2.96: 6353 2.96 - 3.61: 21875 3.61 - 4.25: 31632 4.25 - 4.90: 51994 Nonbonded interactions: 111873 Sorted by model distance: nonbonded pdb=" NH1 ARG A 406 " pdb=" OE1 GLN A 409 " model vdw 1.674 3.120 nonbonded pdb=" O1B ADP A2000 " pdb="MG MG A2001 " model vdw 1.838 2.170 nonbonded pdb=" O1B ADP B2000 " pdb="MG MG B2001 " model vdw 1.931 2.170 nonbonded pdb=" O VAL A 435 " pdb=" CD PRO A 439 " model vdw 2.112 3.440 nonbonded pdb=" OE2 GLU B 725 " pdb=" ND2 ASN B 788 " model vdw 2.165 3.120 ... (remaining 111868 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.88 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.430 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: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.012 0.152 13844 Z= 0.760 Angle : 1.447 14.638 18837 Z= 0.936 Chirality : 0.101 0.570 2172 Planarity : 0.012 0.414 2249 Dihedral : 19.237 177.230 5272 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.61 % Allowed : 20.72 % Favored : 75.67 % Cbeta Deviations : 0.73 % 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: -1.14 (0.21), residues: 1551 helix: 0.07 (0.18), residues: 789 sheet: -1.66 (0.36), residues: 198 loop : -1.45 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.006 TRP B1111 HIS 0.014 0.002 HIS B 781 PHE 0.034 0.004 PHE B1052 TYR 0.032 0.005 TYR A 299 ARG 0.042 0.002 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 386 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 GLN cc_start: 0.8790 (mt0) cc_final: 0.8255 (mm110) REVERT: A 691 ILE cc_start: 0.8168 (tt) cc_final: 0.7931 (tp) REVERT: A 738 SER cc_start: 0.8638 (m) cc_final: 0.8216 (t) REVERT: B 636 GLN cc_start: 0.8718 (tt0) cc_final: 0.8371 (tm-30) REVERT: B 867 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8137 (mt) REVERT: B 876 GLN cc_start: 0.7925 (mt0) cc_final: 0.7540 (mp10) REVERT: B 1053 VAL cc_start: 0.7849 (t) cc_final: 0.7595 (p) outliers start: 51 outliers final: 22 residues processed: 419 average time/residue: 0.3144 time to fit residues: 181.1762 Evaluate side-chains 385 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 362 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 835 ASN Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 830 THR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1032 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 0.0050 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 0.0370 chunk 126 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 overall best weight: 0.4472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN A 535 ASN A 613 ASN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 662 HIS B 852 GLN B 908 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.164538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.127896 restraints weight = 20956.798| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.47 r_work: 0.3526 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13844 Z= 0.218 Angle : 0.661 9.006 18837 Z= 0.340 Chirality : 0.042 0.210 2172 Planarity : 0.004 0.045 2249 Dihedral : 17.885 172.296 2159 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.09 % Allowed : 22.07 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.18 (0.22), residues: 1551 helix: 0.91 (0.18), residues: 808 sheet: -1.15 (0.37), residues: 201 loop : -1.19 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 768 HIS 0.007 0.001 HIS A 424 PHE 0.021 0.002 PHE B 784 TYR 0.016 0.002 TYR B 236 ARG 0.004 0.001 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 366 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7173 (tm-30) REVERT: A 301 LYS cc_start: 0.8132 (mttt) cc_final: 0.7663 (mmtt) REVERT: A 334 LYS cc_start: 0.7672 (mmtm) cc_final: 0.7383 (mmtm) REVERT: A 409 GLN cc_start: 0.8191 (mt0) cc_final: 0.7511 (mp10) REVERT: A 613 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8110 (t0) REVERT: A 691 ILE cc_start: 0.8186 (tt) cc_final: 0.7860 (tp) REVERT: A 707 CYS cc_start: 0.8342 (p) cc_final: 0.8090 (p) REVERT: A 730 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8137 (mm) REVERT: A 738 SER cc_start: 0.8655 (m) cc_final: 0.8176 (t) REVERT: A 743 SER cc_start: 0.7861 (m) cc_final: 0.7617 (t) REVERT: A 757 TYR cc_start: 0.8095 (m-10) cc_final: 0.7717 (m-10) REVERT: A 799 ASN cc_start: 0.7820 (m-40) cc_final: 0.7615 (p0) REVERT: B 275 HIS cc_start: 0.6786 (OUTLIER) cc_final: 0.5358 (p90) REVERT: B 280 PHE cc_start: 0.4941 (OUTLIER) cc_final: 0.4226 (t80) REVERT: B 427 LEU cc_start: 0.7821 (tp) cc_final: 0.7475 (tt) REVERT: B 534 PHE cc_start: 0.8126 (m-10) cc_final: 0.7777 (m-10) REVERT: B 593 ARG cc_start: 0.8508 (mtt180) cc_final: 0.7889 (ttm-80) REVERT: B 636 GLN cc_start: 0.8289 (tt0) cc_final: 0.7824 (tm-30) REVERT: B 703 PHE cc_start: 0.6734 (m-10) cc_final: 0.6120 (m-10) REVERT: B 718 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7527 (tt0) REVERT: B 725 GLU cc_start: 0.8149 (pp20) cc_final: 0.7879 (pp20) REVERT: B 796 ARG cc_start: 0.8216 (mmm-85) cc_final: 0.7873 (mmm-85) REVERT: B 848 ARG cc_start: 0.8943 (ttt-90) cc_final: 0.8475 (ttt180) REVERT: B 899 MET cc_start: 0.7320 (mpp) cc_final: 0.7120 (mpp) REVERT: B 1032 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7729 (m-80) outliers start: 72 outliers final: 30 residues processed: 403 average time/residue: 0.3176 time to fit residues: 174.9630 Evaluate side-chains 386 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 351 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 693 CYS Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 835 ASN Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 830 THR Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1016 GLU Chi-restraints excluded: chain B residue 1032 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 35 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 145 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN B 309 GLN B 394 GLN ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.161986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.125488 restraints weight = 21004.657| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.45 r_work: 0.3488 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13844 Z= 0.310 Angle : 0.661 10.719 18837 Z= 0.341 Chirality : 0.043 0.261 2172 Planarity : 0.005 0.076 2249 Dihedral : 17.711 173.970 2131 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 5.52 % Allowed : 23.48 % Favored : 71.00 % 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: -0.12 (0.22), residues: 1551 helix: 0.94 (0.18), residues: 809 sheet: -1.15 (0.37), residues: 203 loop : -1.12 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 768 HIS 0.005 0.001 HIS A 424 PHE 0.019 0.002 PHE A 551 TYR 0.031 0.002 TYR A 563 ARG 0.007 0.000 ARG B 938 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 370 time to evaluate : 1.410 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: A 347 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8031 (mtpp) REVERT: A 451 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7986 (mm-40) REVERT: A 607 SER cc_start: 0.8587 (OUTLIER) cc_final: 0.8323 (t) REVERT: A 691 ILE cc_start: 0.8313 (tt) cc_final: 0.7989 (tp) REVERT: A 730 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7990 (mm) REVERT: A 738 SER cc_start: 0.8797 (m) cc_final: 0.8320 (t) REVERT: A 757 TYR cc_start: 0.8103 (m-10) cc_final: 0.7733 (m-10) REVERT: A 799 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7611 (p0) REVERT: B 275 HIS cc_start: 0.6661 (OUTLIER) cc_final: 0.5315 (p90) REVERT: B 280 PHE cc_start: 0.4972 (OUTLIER) cc_final: 0.4283 (t80) REVERT: B 336 LYS cc_start: 0.8145 (tptp) cc_final: 0.7901 (tptp) REVERT: B 427 LEU cc_start: 0.7881 (tp) cc_final: 0.7486 (tt) REVERT: B 534 PHE cc_start: 0.8196 (m-80) cc_final: 0.7833 (m-10) REVERT: B 549 GLN cc_start: 0.8361 (pt0) cc_final: 0.8093 (pt0) REVERT: B 565 ASP cc_start: 0.7684 (t0) cc_final: 0.7450 (t0) REVERT: B 584 LEU cc_start: 0.8228 (mt) cc_final: 0.8004 (mm) REVERT: B 613 ASN cc_start: 0.7676 (m-40) cc_final: 0.7301 (m-40) REVERT: B 616 ARG cc_start: 0.7783 (mtm110) cc_final: 0.7502 (mtm110) REVERT: B 687 LYS cc_start: 0.8379 (mmtt) cc_final: 0.8048 (mmtp) REVERT: B 703 PHE cc_start: 0.6961 (m-10) cc_final: 0.6285 (m-10) REVERT: B 725 GLU cc_start: 0.8266 (pp20) cc_final: 0.8023 (pp20) REVERT: B 726 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8879 (mp) REVERT: B 796 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.7920 (mmm-85) REVERT: B 899 MET cc_start: 0.7503 (tpp) cc_final: 0.7251 (mpp) REVERT: B 1028 TYR cc_start: 0.8356 (m-80) cc_final: 0.8144 (m-80) REVERT: B 1053 VAL cc_start: 0.7957 (t) cc_final: 0.7608 (p) REVERT: B 1063 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7949 (pt) outliers start: 78 outliers final: 41 residues processed: 413 average time/residue: 0.3098 time to fit residues: 176.7729 Evaluate side-chains 409 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 359 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 835 ASN Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 713 LYS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 830 THR Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 965 LYS Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1063 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 87 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 154 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN A 681 GLN ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN B 880 ASN B1024 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.166885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.131478 restraints weight = 20868.172| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.45 r_work: 0.3522 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13844 Z= 0.233 Angle : 0.640 11.235 18837 Z= 0.323 Chirality : 0.042 0.207 2172 Planarity : 0.004 0.069 2249 Dihedral : 17.577 168.742 2131 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.37 % Allowed : 24.96 % Favored : 69.66 % 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: 0.06 (0.22), residues: 1551 helix: 1.12 (0.18), residues: 810 sheet: -1.14 (0.37), residues: 211 loop : -1.04 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 768 HIS 0.005 0.001 HIS A 424 PHE 0.027 0.002 PHE B 258 TYR 0.023 0.002 TYR B 744 ARG 0.006 0.000 ARG B 848 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 359 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 LYS cc_start: 0.8056 (mttt) cc_final: 0.7625 (mmmt) REVERT: A 337 GLN cc_start: 0.6943 (OUTLIER) cc_final: 0.6708 (pm20) REVERT: A 451 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8149 (mm-40) REVERT: A 599 LEU cc_start: 0.8554 (tp) cc_final: 0.7992 (tt) REVERT: A 658 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7028 (mm-30) REVERT: A 691 ILE cc_start: 0.8315 (tt) cc_final: 0.7990 (tp) REVERT: A 730 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8017 (mm) REVERT: A 738 SER cc_start: 0.8808 (m) cc_final: 0.8339 (t) REVERT: A 757 TYR cc_start: 0.8106 (m-10) cc_final: 0.7796 (m-10) REVERT: A 799 ASN cc_start: 0.7884 (m-40) cc_final: 0.7601 (p0) REVERT: A 841 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8099 (mm) REVERT: A 842 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 265 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7997 (mp) REVERT: B 275 HIS cc_start: 0.6694 (OUTLIER) cc_final: 0.5274 (p90) REVERT: B 280 PHE cc_start: 0.4974 (OUTLIER) cc_final: 0.4326 (t80) REVERT: B 336 LYS cc_start: 0.8187 (tptp) cc_final: 0.7803 (tptm) REVERT: B 421 LEU cc_start: 0.7657 (mt) cc_final: 0.7408 (mt) REVERT: B 427 LEU cc_start: 0.7857 (tp) cc_final: 0.7477 (tt) REVERT: B 457 ARG cc_start: 0.7828 (tpp80) cc_final: 0.7583 (tpp80) REVERT: B 534 PHE cc_start: 0.8144 (m-80) cc_final: 0.7835 (m-10) REVERT: B 565 ASP cc_start: 0.7705 (t0) cc_final: 0.7457 (t0) REVERT: B 584 LEU cc_start: 0.8212 (mt) cc_final: 0.7965 (mm) REVERT: B 636 GLN cc_start: 0.8172 (tt0) cc_final: 0.7754 (tm-30) REVERT: B 687 LYS cc_start: 0.8339 (mmtt) cc_final: 0.7961 (mmtm) REVERT: B 703 PHE cc_start: 0.6963 (m-10) cc_final: 0.6277 (m-10) REVERT: B 726 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8962 (mp) REVERT: B 752 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.7071 (p90) REVERT: B 796 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7971 (mmt90) REVERT: B 852 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: B 899 MET cc_start: 0.7436 (tpp) cc_final: 0.7178 (mpp) REVERT: B 915 MET cc_start: 0.8244 (mtm) cc_final: 0.8037 (mtm) REVERT: B 989 ILE cc_start: 0.7965 (mm) cc_final: 0.7728 (mt) REVERT: B 1028 TYR cc_start: 0.8376 (m-80) cc_final: 0.8146 (m-80) outliers start: 76 outliers final: 48 residues processed: 403 average time/residue: 0.3308 time to fit residues: 186.5328 Evaluate side-chains 406 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 349 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 835 ASN Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 713 LYS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 806 GLU Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 830 THR Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 880 ASN Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1016 GLU Chi-restraints excluded: chain B residue 1032 PHE Chi-restraints excluded: chain B residue 1063 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 70 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 76 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 147 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.166689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.131279 restraints weight = 21025.900| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.46 r_work: 0.3512 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13844 Z= 0.242 Angle : 0.639 12.863 18837 Z= 0.322 Chirality : 0.041 0.178 2172 Planarity : 0.005 0.067 2249 Dihedral : 17.371 175.798 2126 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.59 % Allowed : 25.39 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.22), residues: 1551 helix: 1.15 (0.18), residues: 811 sheet: -1.17 (0.37), residues: 211 loop : -1.08 (0.29), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 807 HIS 0.004 0.001 HIS A 424 PHE 0.021 0.001 PHE A 276 TYR 0.034 0.002 TYR B 236 ARG 0.005 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 356 time to evaluate : 1.810 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 337 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.6714 (pm20) REVERT: A 416 ASN cc_start: 0.8402 (t0) cc_final: 0.8196 (t0) REVERT: A 599 LEU cc_start: 0.8555 (tp) cc_final: 0.8239 (tt) REVERT: A 658 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7014 (mm-30) REVERT: A 691 ILE cc_start: 0.8337 (tt) cc_final: 0.8016 (tp) REVERT: A 730 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8038 (mm) REVERT: A 738 SER cc_start: 0.8671 (m) cc_final: 0.8267 (t) REVERT: A 799 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7643 (p0) REVERT: A 842 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7569 (mm-30) REVERT: B 265 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7485 (mp) REVERT: B 275 HIS cc_start: 0.6772 (OUTLIER) cc_final: 0.5305 (p90) REVERT: B 280 PHE cc_start: 0.4904 (OUTLIER) cc_final: 0.4242 (t80) REVERT: B 336 LYS cc_start: 0.8158 (tptp) cc_final: 0.7779 (tptm) REVERT: B 427 LEU cc_start: 0.7856 (tp) cc_final: 0.7491 (tt) REVERT: B 457 ARG cc_start: 0.7840 (tpp80) cc_final: 0.7594 (tpp80) REVERT: B 534 PHE cc_start: 0.8139 (m-80) cc_final: 0.7812 (m-10) REVERT: B 565 ASP cc_start: 0.7770 (t0) cc_final: 0.7288 (t0) REVERT: B 584 LEU cc_start: 0.8182 (mt) cc_final: 0.7939 (mm) REVERT: B 595 ASP cc_start: 0.6862 (p0) cc_final: 0.6564 (p0) REVERT: B 636 GLN cc_start: 0.8160 (tt0) cc_final: 0.7760 (tm-30) REVERT: B 687 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7940 (mmtm) REVERT: B 703 PHE cc_start: 0.6951 (m-10) cc_final: 0.6293 (m-10) REVERT: B 726 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8740 (mp) REVERT: B 752 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.7202 (p90) REVERT: B 796 ARG cc_start: 0.8231 (mmm-85) cc_final: 0.8001 (mmt90) REVERT: B 830 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.7515 (p) REVERT: B 852 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: B 899 MET cc_start: 0.7392 (tpp) cc_final: 0.7137 (mpp) REVERT: B 989 ILE cc_start: 0.8008 (mm) cc_final: 0.7793 (mt) REVERT: B 1074 LYS cc_start: 0.8384 (tptp) cc_final: 0.8052 (tptp) outliers start: 79 outliers final: 52 residues processed: 406 average time/residue: 0.3125 time to fit residues: 175.0548 Evaluate side-chains 410 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 348 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 835 ASN Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 713 LYS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 806 GLU Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 830 THR Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1032 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.166078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.130530 restraints weight = 21104.962| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.47 r_work: 0.3505 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13844 Z= 0.260 Angle : 0.655 14.048 18837 Z= 0.328 Chirality : 0.042 0.174 2172 Planarity : 0.005 0.081 2249 Dihedral : 17.136 164.146 2126 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 5.87 % Allowed : 25.67 % Favored : 68.46 % 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: 0.10 (0.22), residues: 1551 helix: 1.22 (0.18), residues: 811 sheet: -1.24 (0.36), residues: 213 loop : -1.10 (0.29), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 807 HIS 0.005 0.001 HIS A 424 PHE 0.021 0.002 PHE B 784 TYR 0.024 0.002 TYR B 744 ARG 0.006 0.000 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 348 time to evaluate : 1.346 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 337 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6714 (pm20) REVERT: A 377 GLN cc_start: 0.7455 (tp-100) cc_final: 0.7233 (tp40) REVERT: A 416 ASN cc_start: 0.8443 (t0) cc_final: 0.8196 (t0) REVERT: A 451 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7933 (mm-40) REVERT: A 658 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7062 (mm-30) REVERT: A 691 ILE cc_start: 0.8349 (tt) cc_final: 0.8029 (tp) REVERT: A 730 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8029 (mm) REVERT: A 738 SER cc_start: 0.8747 (m) cc_final: 0.8251 (t) REVERT: A 757 TYR cc_start: 0.8121 (m-10) cc_final: 0.7715 (m-10) REVERT: A 799 ASN cc_start: 0.7878 (OUTLIER) cc_final: 0.7651 (p0) REVERT: A 841 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8156 (mm) REVERT: A 842 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7569 (mm-30) REVERT: B 265 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7579 (mp) REVERT: B 275 HIS cc_start: 0.6701 (OUTLIER) cc_final: 0.5148 (p90) REVERT: B 280 PHE cc_start: 0.4977 (OUTLIER) cc_final: 0.4365 (t80) REVERT: B 336 LYS cc_start: 0.8161 (tptp) cc_final: 0.7816 (tptm) REVERT: B 427 LEU cc_start: 0.7842 (tp) cc_final: 0.7481 (tt) REVERT: B 565 ASP cc_start: 0.7844 (t0) cc_final: 0.7163 (t0) REVERT: B 584 LEU cc_start: 0.8172 (mt) cc_final: 0.7951 (mm) REVERT: B 595 ASP cc_start: 0.6853 (p0) cc_final: 0.6578 (p0) REVERT: B 632 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8258 (mtpp) REVERT: B 636 GLN cc_start: 0.8188 (tt0) cc_final: 0.7749 (tm-30) REVERT: B 687 LYS cc_start: 0.8328 (mmtt) cc_final: 0.8006 (mmtm) REVERT: B 703 PHE cc_start: 0.6981 (m-10) cc_final: 0.6356 (m-10) REVERT: B 752 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7286 (p90) REVERT: B 796 ARG cc_start: 0.8206 (mmm-85) cc_final: 0.7979 (mmt90) REVERT: B 830 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.7476 (p) REVERT: B 852 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: B 899 MET cc_start: 0.7402 (tpp) cc_final: 0.7132 (mpp) REVERT: B 989 ILE cc_start: 0.8019 (mm) cc_final: 0.7790 (mt) REVERT: B 1028 TYR cc_start: 0.8469 (m-80) cc_final: 0.8159 (m-80) REVERT: B 1053 VAL cc_start: 0.7874 (t) cc_final: 0.7538 (p) outliers start: 83 outliers final: 56 residues processed: 397 average time/residue: 0.3208 time to fit residues: 175.7963 Evaluate side-chains 414 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 347 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 713 LYS Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 806 GLU Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 823 LYS Chi-restraints excluded: chain B residue 830 THR Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 965 LYS Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1032 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 90 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 111 optimal weight: 0.0010 chunk 2 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 451 GLN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.168412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.133174 restraints weight = 21077.116| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.47 r_work: 0.3551 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13844 Z= 0.205 Angle : 0.644 13.810 18837 Z= 0.321 Chirality : 0.040 0.173 2172 Planarity : 0.005 0.061 2249 Dihedral : 16.903 165.774 2124 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.16 % Allowed : 27.51 % Favored : 67.33 % 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: 0.27 (0.22), residues: 1551 helix: 1.38 (0.18), residues: 805 sheet: -1.08 (0.36), residues: 211 loop : -1.09 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 807 HIS 0.004 0.001 HIS A 424 PHE 0.025 0.001 PHE A 276 TYR 0.033 0.001 TYR B 236 ARG 0.007 0.001 ARG A 621 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 349 time to evaluate : 1.497 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 301 LYS cc_start: 0.8177 (mttt) cc_final: 0.7928 (mmmt) REVERT: A 416 ASN cc_start: 0.8475 (t0) cc_final: 0.8224 (t0) REVERT: A 658 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7019 (mm-30) REVERT: A 691 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8024 (tp) REVERT: A 738 SER cc_start: 0.8656 (m) cc_final: 0.8342 (t) REVERT: A 747 ILE cc_start: 0.8634 (mt) cc_final: 0.8352 (mm) REVERT: A 757 TYR cc_start: 0.8131 (m-10) cc_final: 0.7750 (m-10) REVERT: A 768 GLU cc_start: 0.7987 (tt0) cc_final: 0.7743 (tt0) REVERT: A 772 THR cc_start: 0.7925 (p) cc_final: 0.7716 (t) REVERT: A 799 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.7548 (p0) REVERT: A 841 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8119 (mm) REVERT: A 842 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7573 (mm-30) REVERT: B 265 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7529 (mp) REVERT: B 275 HIS cc_start: 0.6465 (OUTLIER) cc_final: 0.4905 (p90) REVERT: B 280 PHE cc_start: 0.4936 (OUTLIER) cc_final: 0.4306 (t80) REVERT: B 336 LYS cc_start: 0.8145 (tptp) cc_final: 0.7807 (tptm) REVERT: B 427 LEU cc_start: 0.7831 (tp) cc_final: 0.7465 (tt) REVERT: B 432 LEU cc_start: 0.3664 (OUTLIER) cc_final: 0.3403 (pp) REVERT: B 565 ASP cc_start: 0.7850 (t0) cc_final: 0.7162 (t0) REVERT: B 584 LEU cc_start: 0.8117 (mt) cc_final: 0.7909 (mm) REVERT: B 595 ASP cc_start: 0.6744 (p0) cc_final: 0.6437 (p0) REVERT: B 632 LYS cc_start: 0.8497 (mmmt) cc_final: 0.8256 (mtpp) REVERT: B 636 GLN cc_start: 0.8076 (tt0) cc_final: 0.7636 (tm-30) REVERT: B 687 LYS cc_start: 0.8245 (mmtt) cc_final: 0.8002 (mmtt) REVERT: B 703 PHE cc_start: 0.6976 (m-10) cc_final: 0.6329 (m-10) REVERT: B 796 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.8064 (mmt90) REVERT: B 830 THR cc_start: 0.8176 (m) cc_final: 0.7485 (p) REVERT: B 852 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: B 899 MET cc_start: 0.7345 (tpp) cc_final: 0.7105 (mpp) REVERT: B 989 ILE cc_start: 0.7977 (mm) cc_final: 0.7730 (mt) outliers start: 73 outliers final: 55 residues processed: 391 average time/residue: 0.3333 time to fit residues: 182.1932 Evaluate side-chains 411 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 348 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 713 LYS Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 806 GLU Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1032 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 106 optimal weight: 2.9990 chunk 89 optimal weight: 0.0570 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 71 optimal weight: 0.0670 chunk 152 optimal weight: 0.0870 chunk 148 optimal weight: 0.1980 overall best weight: 0.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 729 HIS B 852 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.170063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.134984 restraints weight = 20967.106| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.48 r_work: 0.3580 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13844 Z= 0.188 Angle : 0.648 12.682 18837 Z= 0.322 Chirality : 0.040 0.229 2172 Planarity : 0.004 0.060 2249 Dihedral : 16.770 165.772 2123 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.16 % Allowed : 27.58 % Favored : 67.26 % 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: 0.33 (0.22), residues: 1551 helix: 1.45 (0.18), residues: 805 sheet: -1.00 (0.37), residues: 211 loop : -1.11 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 768 HIS 0.003 0.001 HIS A 424 PHE 0.025 0.001 PHE B 784 TYR 0.053 0.001 TYR B 236 ARG 0.008 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 357 time to evaluate : 1.360 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 301 LYS cc_start: 0.8137 (mttt) cc_final: 0.7889 (mmmt) REVERT: A 377 GLN cc_start: 0.7413 (tp-100) cc_final: 0.7206 (tp-100) REVERT: A 406 ARG cc_start: 0.8265 (mmm160) cc_final: 0.7918 (mmm-85) REVERT: A 416 ASN cc_start: 0.8463 (t0) cc_final: 0.8171 (t0) REVERT: A 430 LYS cc_start: 0.7780 (mtpp) cc_final: 0.7498 (mmmm) REVERT: A 438 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7780 (p) REVERT: A 451 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8092 (mm-40) REVERT: A 621 ARG cc_start: 0.8533 (ttm-80) cc_final: 0.8314 (ttm-80) REVERT: A 658 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7033 (mm-30) REVERT: A 691 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7958 (tp) REVERT: A 730 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8024 (mm) REVERT: A 738 SER cc_start: 0.8624 (m) cc_final: 0.8355 (t) REVERT: A 799 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7530 (p0) REVERT: A 842 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7556 (mm-30) REVERT: B 265 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7392 (mp) REVERT: B 280 PHE cc_start: 0.4898 (OUTLIER) cc_final: 0.4293 (t80) REVERT: B 336 LYS cc_start: 0.8200 (tptp) cc_final: 0.7832 (tptm) REVERT: B 373 GLU cc_start: 0.8135 (mp0) cc_final: 0.7211 (pt0) REVERT: B 393 VAL cc_start: 0.7952 (p) cc_final: 0.7564 (m) REVERT: B 415 GLU cc_start: 0.7541 (tp30) cc_final: 0.6968 (tp30) REVERT: B 427 LEU cc_start: 0.7871 (tp) cc_final: 0.7516 (tt) REVERT: B 565 ASP cc_start: 0.7805 (t0) cc_final: 0.7335 (t0) REVERT: B 595 ASP cc_start: 0.6705 (p0) cc_final: 0.6416 (p0) REVERT: B 632 LYS cc_start: 0.8404 (mmmt) cc_final: 0.8163 (mtpp) REVERT: B 636 GLN cc_start: 0.8055 (tt0) cc_final: 0.7611 (tm-30) REVERT: B 687 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7798 (mmtm) REVERT: B 703 PHE cc_start: 0.6893 (m-10) cc_final: 0.6181 (m-10) REVERT: B 830 THR cc_start: 0.8125 (m) cc_final: 0.7492 (p) REVERT: B 852 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: B 886 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7374 (mm-30) REVERT: B 899 MET cc_start: 0.7284 (tpp) cc_final: 0.7042 (mpp) REVERT: B 969 GLN cc_start: 0.8275 (mt0) cc_final: 0.7356 (mm110) REVERT: B 989 ILE cc_start: 0.7989 (mm) cc_final: 0.7758 (mt) outliers start: 73 outliers final: 50 residues processed: 398 average time/residue: 0.3213 time to fit residues: 175.2524 Evaluate side-chains 404 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 347 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 713 LYS Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 806 GLU Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1032 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 105 optimal weight: 0.0770 chunk 81 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN B 917 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.165353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.130408 restraints weight = 20719.723| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.37 r_work: 0.3492 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13844 Z= 0.371 Angle : 0.721 13.674 18837 Z= 0.367 Chirality : 0.044 0.239 2172 Planarity : 0.005 0.062 2249 Dihedral : 16.813 159.224 2123 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.81 % Allowed : 28.22 % Favored : 66.97 % 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: 0.09 (0.22), residues: 1551 helix: 1.19 (0.18), residues: 810 sheet: -1.27 (0.38), residues: 201 loop : -1.07 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 579 HIS 0.009 0.001 HIS B 630 PHE 0.027 0.002 PHE B 784 TYR 0.063 0.002 TYR B 236 ARG 0.012 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 361 time to evaluate : 1.456 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 301 LYS cc_start: 0.8268 (mttt) cc_final: 0.7918 (mmmt) REVERT: A 337 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.6737 (pm20) REVERT: A 406 ARG cc_start: 0.8325 (mmm160) cc_final: 0.7991 (mmm-85) REVERT: A 416 ASN cc_start: 0.8543 (t0) cc_final: 0.8264 (t0) REVERT: A 451 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8041 (mm-40) REVERT: A 658 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7087 (mm-30) REVERT: A 691 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8063 (tp) REVERT: A 730 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8070 (mm) REVERT: A 738 SER cc_start: 0.8680 (m) cc_final: 0.8255 (t) REVERT: A 799 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7644 (p0) REVERT: A 842 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7604 (mm-30) REVERT: B 265 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7552 (mp) REVERT: B 280 PHE cc_start: 0.5040 (OUTLIER) cc_final: 0.4362 (t80) REVERT: B 336 LYS cc_start: 0.8249 (tptp) cc_final: 0.7879 (tptm) REVERT: B 373 GLU cc_start: 0.8344 (mp0) cc_final: 0.7495 (pt0) REVERT: B 415 GLU cc_start: 0.7539 (tp30) cc_final: 0.7235 (tp30) REVERT: B 565 ASP cc_start: 0.7897 (t0) cc_final: 0.7281 (t0) REVERT: B 632 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8287 (mtpp) REVERT: B 636 GLN cc_start: 0.8157 (tt0) cc_final: 0.7750 (tm-30) REVERT: B 651 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6904 (mm-30) REVERT: B 687 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7919 (mmtm) REVERT: B 689 LEU cc_start: 0.8724 (mp) cc_final: 0.8502 (mm) REVERT: B 730 LEU cc_start: 0.8480 (tp) cc_final: 0.8274 (tp) REVERT: B 752 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7576 (p90) REVERT: B 781 HIS cc_start: 0.6949 (OUTLIER) cc_final: 0.6557 (m90) REVERT: B 830 THR cc_start: 0.8272 (m) cc_final: 0.7563 (p) REVERT: B 852 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: B 899 MET cc_start: 0.7357 (tpp) cc_final: 0.7151 (mpp) REVERT: B 989 ILE cc_start: 0.8001 (mm) cc_final: 0.7775 (mt) REVERT: B 1053 VAL cc_start: 0.7948 (t) cc_final: 0.7639 (p) outliers start: 68 outliers final: 45 residues processed: 401 average time/residue: 0.3202 time to fit residues: 176.1348 Evaluate side-chains 403 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 349 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 806 GLU Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1032 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 146 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.165935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.130143 restraints weight = 21090.107| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.45 r_work: 0.3500 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13844 Z= 0.320 Angle : 0.743 17.350 18837 Z= 0.374 Chirality : 0.044 0.234 2172 Planarity : 0.005 0.062 2249 Dihedral : 16.835 162.353 2123 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.68 % Allowed : 29.49 % Favored : 66.83 % 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: -0.02 (0.22), residues: 1551 helix: 1.09 (0.18), residues: 809 sheet: -1.23 (0.39), residues: 189 loop : -1.16 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 764 HIS 0.005 0.001 HIS A 424 PHE 0.025 0.002 PHE B 784 TYR 0.055 0.002 TYR B 236 ARG 0.009 0.001 ARG A 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 354 time to evaluate : 1.400 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 301 LYS cc_start: 0.8236 (mttt) cc_final: 0.7852 (mmmt) REVERT: A 377 GLN cc_start: 0.7600 (tp-100) cc_final: 0.7309 (tp-100) REVERT: A 406 ARG cc_start: 0.8320 (mmm160) cc_final: 0.7981 (mmm-85) REVERT: A 416 ASN cc_start: 0.8541 (t0) cc_final: 0.8255 (t0) REVERT: A 430 LYS cc_start: 0.7779 (mmmt) cc_final: 0.7309 (mmmm) REVERT: A 621 ARG cc_start: 0.8635 (ttm-80) cc_final: 0.8424 (ttm-80) REVERT: A 658 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7005 (mm-30) REVERT: A 730 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8082 (mm) REVERT: A 738 SER cc_start: 0.8678 (m) cc_final: 0.8263 (t) REVERT: A 747 ILE cc_start: 0.8461 (mm) cc_final: 0.8089 (mt) REVERT: A 757 TYR cc_start: 0.8143 (m-10) cc_final: 0.7739 (m-10) REVERT: A 799 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7604 (p0) REVERT: A 842 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7607 (mm-30) REVERT: B 264 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7768 (tm-30) REVERT: B 265 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7263 (mp) REVERT: B 280 PHE cc_start: 0.5014 (OUTLIER) cc_final: 0.4352 (t80) REVERT: B 336 LYS cc_start: 0.8248 (tptp) cc_final: 0.7879 (tptm) REVERT: B 454 ARG cc_start: 0.8166 (ttt-90) cc_final: 0.7865 (ttt-90) REVERT: B 565 ASP cc_start: 0.7894 (t0) cc_final: 0.7326 (t0) REVERT: B 632 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8294 (mtpp) REVERT: B 636 GLN cc_start: 0.8174 (tt0) cc_final: 0.7749 (tm-30) REVERT: B 687 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7894 (mmtm) REVERT: B 689 LEU cc_start: 0.8711 (mp) cc_final: 0.8497 (mm) REVERT: B 793 ASN cc_start: 0.8450 (m-40) cc_final: 0.8017 (m-40) REVERT: B 830 THR cc_start: 0.8272 (m) cc_final: 0.7565 (p) REVERT: B 852 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: B 899 MET cc_start: 0.7356 (tpp) cc_final: 0.7121 (mpp) REVERT: B 989 ILE cc_start: 0.8004 (mm) cc_final: 0.7770 (mt) REVERT: B 1028 TYR cc_start: 0.8385 (m-80) cc_final: 0.8088 (m-80) REVERT: B 1053 VAL cc_start: 0.7952 (t) cc_final: 0.7639 (p) outliers start: 52 outliers final: 43 residues processed: 383 average time/residue: 0.3254 time to fit residues: 171.1292 Evaluate side-chains 396 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 348 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 806 GLU Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1032 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 22 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 158 optimal weight: 20.0000 chunk 129 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.167578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.132967 restraints weight = 20923.442| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.40 r_work: 0.3530 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13844 Z= 0.273 Angle : 0.731 14.377 18837 Z= 0.368 Chirality : 0.044 0.437 2172 Planarity : 0.005 0.062 2249 Dihedral : 16.780 161.822 2123 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.54 % Allowed : 29.70 % Favored : 66.76 % 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: -0.01 (0.22), residues: 1551 helix: 1.13 (0.18), residues: 804 sheet: -1.27 (0.39), residues: 189 loop : -1.15 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 764 HIS 0.009 0.001 HIS B 467 PHE 0.039 0.002 PHE B 784 TYR 0.050 0.002 TYR B 236 ARG 0.009 0.001 ARG A 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6861.64 seconds wall clock time: 122 minutes 28.67 seconds (7348.67 seconds total)