Starting phenix.real_space_refine on Thu Jul 31 15:31:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rz7_19605/07_2025/8rz7_19605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rz7_19605/07_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_19605/07_2025/8rz7_19605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rz7_19605/07_2025/8rz7_19605.map" model { file = "/net/cci-nas-00/data/ceres_data/8rz7_19605/07_2025/8rz7_19605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rz7_19605/07_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-5711/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: 9.09, per 1000 atoms: 0.67 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: 3.81 Conformation dependent library (CDL) restraints added in 1.7 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: 5.26 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: 5.71 Time building geometry restraints manager: 4.22 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: 3.640 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 39.600 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.500 ------------------------------------------------------------------------------- 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= 0.624 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 Details of bonding type rmsd hydrogen bonds : bond 0.16344 ( 720) hydrogen bonds : angle 7.06587 ( 2016) covalent geometry : bond 0.01161 (13844) covalent geometry : angle 1.44676 (18837) *********************** 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 : 1.433 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: 0.3012 time to fit residues: 174.2143 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 : 1.437 ------------------------------------------------------------------------------- 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 = 0.164537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.127892 restraints weight = 20956.635| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.47 r_work: 0.3530 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 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= 0.152 Angle : 0.661 9.005 18837 Z= 0.340 Chirality : 0.042 0.210 2172 Planarity : 0.004 0.045 2249 Dihedral : 17.885 172.297 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 Details of bonding type rmsd hydrogen bonds : bond 0.04455 ( 720) hydrogen bonds : angle 5.17883 ( 2016) covalent geometry : bond 0.00334 (13844) covalent geometry : angle 0.66081 (18837) *********************** 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 : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7172 (tm-30) REVERT: A 301 LYS cc_start: 0.8134 (mttt) cc_final: 0.7667 (mmtt) REVERT: A 334 LYS cc_start: 0.7669 (mmtm) cc_final: 0.7378 (mmtm) REVERT: A 409 GLN cc_start: 0.8179 (mt0) cc_final: 0.7505 (mp10) REVERT: A 613 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8103 (t0) REVERT: A 691 ILE cc_start: 0.8183 (tt) cc_final: 0.7857 (tp) REVERT: A 707 CYS cc_start: 0.8346 (p) cc_final: 0.8094 (p) REVERT: A 730 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8144 (mm) REVERT: A 738 SER cc_start: 0.8652 (m) cc_final: 0.8173 (t) REVERT: A 743 SER cc_start: 0.7861 (m) cc_final: 0.7618 (t) REVERT: A 757 TYR cc_start: 0.8094 (m-10) cc_final: 0.7716 (m-10) REVERT: A 799 ASN cc_start: 0.7814 (m-40) cc_final: 0.7613 (p0) REVERT: B 275 HIS cc_start: 0.6805 (OUTLIER) cc_final: 0.5370 (p90) REVERT: B 280 PHE cc_start: 0.4959 (OUTLIER) cc_final: 0.4241 (t80) REVERT: B 427 LEU cc_start: 0.7823 (tp) cc_final: 0.7477 (tt) REVERT: B 534 PHE cc_start: 0.8124 (m-10) cc_final: 0.7774 (m-10) REVERT: B 593 ARG cc_start: 0.8511 (mtt180) cc_final: 0.7891 (ttm-80) REVERT: B 636 GLN cc_start: 0.8286 (tt0) cc_final: 0.7823 (tm-30) REVERT: B 703 PHE cc_start: 0.6730 (m-10) cc_final: 0.6119 (m-10) REVERT: B 718 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7520 (tt0) REVERT: B 725 GLU cc_start: 0.8143 (pp20) cc_final: 0.7875 (pp20) REVERT: B 796 ARG cc_start: 0.8205 (mmm-85) cc_final: 0.7862 (mmm-85) REVERT: B 848 ARG cc_start: 0.8940 (ttt-90) cc_final: 0.8472 (ttt180) REVERT: B 1032 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7728 (m-80) outliers start: 72 outliers final: 30 residues processed: 403 average time/residue: 0.3189 time to fit residues: 174.9780 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 : 1.387 ------------------------------------------------------------------------------- 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: 0.7980 chunk 3 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 90 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 145 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.163328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.126761 restraints weight = 21037.591| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.47 r_work: 0.3507 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13844 Z= 0.179 Angle : 0.639 10.529 18837 Z= 0.328 Chirality : 0.042 0.241 2172 Planarity : 0.004 0.065 2249 Dihedral : 17.667 176.534 2131 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.45 % Allowed : 23.27 % Favored : 71.29 % 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: -0.04 (0.22), residues: 1551 helix: 1.00 (0.18), residues: 810 sheet: -1.05 (0.38), residues: 201 loop : -1.10 (0.29), residues: 540 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 0.029 0.002 TYR A 563 ARG 0.007 0.000 ARG B 938 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 720) hydrogen bonds : angle 5.02403 ( 2016) covalent geometry : bond 0.00391 (13844) covalent geometry : angle 0.63913 (18837) *********************** 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 441 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 364 time to evaluate : 1.359 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 301 LYS cc_start: 0.8066 (mttt) cc_final: 0.7671 (mmmt) REVERT: A 409 GLN cc_start: 0.8209 (mt0) cc_final: 0.7812 (tm-30) REVERT: A 459 ASP cc_start: 0.6477 (m-30) cc_final: 0.6208 (m-30) REVERT: A 607 SER cc_start: 0.8566 (OUTLIER) cc_final: 0.8309 (t) REVERT: A 691 ILE cc_start: 0.8281 (tt) cc_final: 0.7969 (tp) REVERT: A 707 CYS cc_start: 0.8295 (p) cc_final: 0.8042 (p) REVERT: A 730 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8064 (mm) REVERT: A 738 SER cc_start: 0.8772 (m) cc_final: 0.8286 (t) REVERT: A 743 SER cc_start: 0.8126 (m) cc_final: 0.7785 (t) REVERT: A 757 TYR cc_start: 0.8103 (m-10) cc_final: 0.7762 (m-10) REVERT: A 799 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7612 (p0) REVERT: B 275 HIS cc_start: 0.6708 (OUTLIER) cc_final: 0.5348 (p90) REVERT: B 280 PHE cc_start: 0.5054 (OUTLIER) cc_final: 0.4363 (t80) REVERT: B 336 LYS cc_start: 0.8131 (tptp) cc_final: 0.7902 (tptp) REVERT: B 427 LEU cc_start: 0.7881 (tp) cc_final: 0.7498 (tt) REVERT: B 508 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8327 (ttmm) REVERT: B 534 PHE cc_start: 0.8189 (m-80) cc_final: 0.7828 (m-10) REVERT: B 549 GLN cc_start: 0.8369 (pt0) cc_final: 0.8117 (pt0) REVERT: B 565 ASP cc_start: 0.7652 (t0) cc_final: 0.7401 (t0) REVERT: B 584 LEU cc_start: 0.8183 (mt) cc_final: 0.7973 (mm) REVERT: B 613 ASN cc_start: 0.7676 (m-40) cc_final: 0.7304 (m-40) REVERT: B 616 ARG cc_start: 0.7784 (mtm110) cc_final: 0.7526 (mtm110) REVERT: B 687 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7957 (mmtm) REVERT: B 699 LYS cc_start: 0.8727 (mttp) cc_final: 0.8513 (mtpp) REVERT: B 703 PHE cc_start: 0.6880 (m-10) cc_final: 0.6251 (m-10) REVERT: B 725 GLU cc_start: 0.8226 (pp20) cc_final: 0.7982 (pp20) REVERT: B 726 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8917 (mp) REVERT: B 796 ARG cc_start: 0.8211 (mmm-85) cc_final: 0.7893 (mmm-85) REVERT: B 890 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7744 (ttp-110) REVERT: B 1024 GLN cc_start: 0.8416 (mt0) cc_final: 0.8092 (mt0) REVERT: B 1027 ASN cc_start: 0.8159 (m-40) cc_final: 0.7860 (m110) REVERT: B 1028 TYR cc_start: 0.8341 (m-80) cc_final: 0.8108 (m-80) outliers start: 77 outliers final: 42 residues processed: 406 average time/residue: 0.3028 time to fit residues: 168.9251 Evaluate side-chains 408 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 359 time to evaluate : 1.523 ------------------------------------------------------------------------------- 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 300 MET 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 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 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 388 ILE 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 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 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 817 HIS Chi-restraints excluded: chain B residue 830 THR Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 890 ARG 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 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 1016 GLU Chi-restraints excluded: chain B residue 1032 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 87 optimal weight: 0.9980 chunk 129 optimal weight: 0.1980 chunk 74 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 645 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.167012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131085 restraints weight = 20888.676| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.46 r_work: 0.3521 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13844 Z= 0.165 Angle : 0.634 11.138 18837 Z= 0.321 Chirality : 0.041 0.193 2172 Planarity : 0.004 0.069 2249 Dihedral : 17.492 169.574 2129 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.66 % Allowed : 24.05 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1551 helix: 1.17 (0.18), residues: 811 sheet: -1.12 (0.37), residues: 211 loop : -1.07 (0.29), residues: 529 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 0.029 0.002 PHE B 258 TYR 0.023 0.002 TYR B 236 ARG 0.009 0.001 ARG A 737 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 720) hydrogen bonds : angle 4.85998 ( 2016) covalent geometry : bond 0.00368 (13844) covalent geometry : angle 0.63407 (18837) *********************** 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 434 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 354 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6726 (pm20) REVERT: A 409 GLN cc_start: 0.8239 (mt0) cc_final: 0.7733 (tm-30) REVERT: A 413 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7965 (mm-40) REVERT: A 599 LEU cc_start: 0.8557 (tp) cc_final: 0.7983 (tt) REVERT: A 691 ILE cc_start: 0.8323 (tt) cc_final: 0.7997 (tp) REVERT: A 707 CYS cc_start: 0.8254 (p) cc_final: 0.8004 (p) REVERT: A 730 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8018 (mm) REVERT: A 738 SER cc_start: 0.8787 (m) cc_final: 0.8309 (t) REVERT: A 743 SER cc_start: 0.8134 (m) cc_final: 0.7794 (t) REVERT: A 757 TYR cc_start: 0.8099 (m-10) cc_final: 0.7852 (m-10) REVERT: A 799 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7639 (p0) REVERT: A 842 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7588 (mm-30) REVERT: B 265 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7980 (mp) REVERT: B 275 HIS cc_start: 0.6619 (OUTLIER) cc_final: 0.5173 (p90) REVERT: B 280 PHE cc_start: 0.4939 (OUTLIER) cc_final: 0.4292 (t80) REVERT: B 336 LYS cc_start: 0.8164 (tptp) cc_final: 0.7777 (tptm) REVERT: B 421 LEU cc_start: 0.7669 (mt) cc_final: 0.7426 (mt) REVERT: B 427 LEU cc_start: 0.7858 (tp) cc_final: 0.7477 (tt) REVERT: B 457 ARG cc_start: 0.7787 (tpp80) cc_final: 0.7584 (tpp80) REVERT: B 534 PHE cc_start: 0.8148 (m-80) cc_final: 0.7830 (m-10) REVERT: B 565 ASP cc_start: 0.7714 (t0) cc_final: 0.7468 (t0) REVERT: B 584 LEU cc_start: 0.8185 (mt) cc_final: 0.7934 (mm) REVERT: B 636 GLN cc_start: 0.8195 (tt0) cc_final: 0.7766 (tm-30) REVERT: B 687 LYS cc_start: 0.8335 (mmtt) cc_final: 0.7937 (mmtm) REVERT: B 703 PHE cc_start: 0.6952 (m-10) cc_final: 0.6265 (m-10) REVERT: B 726 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8945 (mp) REVERT: B 796 ARG cc_start: 0.8217 (mmm-85) cc_final: 0.7898 (mmt90) REVERT: B 830 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.7467 (p) REVERT: B 852 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: B 989 ILE cc_start: 0.7963 (mm) cc_final: 0.7727 (mt) REVERT: B 996 TYR cc_start: 0.8256 (t80) cc_final: 0.7935 (t80) REVERT: B 1027 ASN cc_start: 0.8113 (m-40) cc_final: 0.7840 (m110) REVERT: B 1094 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7971 (tm-30) outliers start: 80 outliers final: 43 residues processed: 399 average time/residue: 0.3202 time to fit residues: 175.7382 Evaluate side-chains 397 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 345 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 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 799 ASN Chi-restraints excluded: chain A residue 826 PHE 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 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 1016 GLU Chi-restraints excluded: chain B residue 1032 PHE 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: 0.9990 chunk 76 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 147 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN B 880 ASN ** 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 = 0.4155 r_free = 0.4155 target = 0.166647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131020 restraints weight = 21036.116| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.48 r_work: 0.3510 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2662 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= 0.170 Angle : 0.632 13.039 18837 Z= 0.319 Chirality : 0.041 0.176 2172 Planarity : 0.005 0.066 2249 Dihedral : 17.304 168.034 2125 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.23 % Allowed : 25.18 % Favored : 69.59 % 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: 0.17 (0.22), residues: 1551 helix: 1.24 (0.18), residues: 811 sheet: -1.10 (0.37), residues: 211 loop : -1.07 (0.29), residues: 529 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 0.019 0.001 PHE B 784 TYR 0.034 0.001 TYR B 236 ARG 0.008 0.000 ARG A 737 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 720) hydrogen bonds : angle 4.79025 ( 2016) covalent geometry : bond 0.00376 (13844) covalent geometry : angle 0.63201 (18837) *********************** 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 431 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 357 time to evaluate : 1.192 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 337 GLN cc_start: 0.6977 (OUTLIER) cc_final: 0.6668 (pm20) REVERT: A 409 GLN cc_start: 0.8227 (mt0) cc_final: 0.7744 (tm-30) REVERT: A 413 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7941 (mm-40) REVERT: A 596 ASN cc_start: 0.7608 (t0) cc_final: 0.7225 (t0) REVERT: A 658 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7024 (mm-30) REVERT: A 691 ILE cc_start: 0.8354 (tt) cc_final: 0.8027 (tp) REVERT: A 707 CYS cc_start: 0.8268 (p) cc_final: 0.8039 (p) REVERT: A 730 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7982 (mm) REVERT: A 738 SER cc_start: 0.8772 (m) cc_final: 0.8301 (t) REVERT: A 743 SER cc_start: 0.8182 (m) cc_final: 0.7838 (t) REVERT: A 757 TYR cc_start: 0.8113 (m-10) cc_final: 0.7754 (m-10) REVERT: A 799 ASN cc_start: 0.7897 (m-40) cc_final: 0.7626 (p0) REVERT: A 841 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8121 (mm) REVERT: A 842 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7560 (mm-30) REVERT: B 265 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7534 (mp) REVERT: B 275 HIS cc_start: 0.6671 (OUTLIER) cc_final: 0.5202 (p90) REVERT: B 280 PHE cc_start: 0.4951 (OUTLIER) cc_final: 0.4305 (t80) REVERT: B 336 LYS cc_start: 0.8149 (tptp) cc_final: 0.7784 (tptm) REVERT: B 427 LEU cc_start: 0.7835 (tp) cc_final: 0.7459 (tt) REVERT: B 534 PHE cc_start: 0.8129 (m-80) cc_final: 0.7806 (m-10) REVERT: B 565 ASP cc_start: 0.7791 (t0) cc_final: 0.7304 (t0) REVERT: B 584 LEU cc_start: 0.8174 (mt) cc_final: 0.7920 (mm) REVERT: B 595 ASP cc_start: 0.6881 (p0) cc_final: 0.6578 (p0) REVERT: B 636 GLN cc_start: 0.8202 (tt0) cc_final: 0.7773 (tm-30) REVERT: B 687 LYS cc_start: 0.8357 (mmtt) cc_final: 0.7947 (mmtm) REVERT: B 703 PHE cc_start: 0.6981 (m-10) cc_final: 0.6331 (m-10) REVERT: B 725 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7957 (pp20) REVERT: B 726 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8682 (mp) REVERT: B 796 ARG cc_start: 0.8214 (mmm-85) cc_final: 0.7987 (mmt90) REVERT: B 830 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.7476 (p) REVERT: B 989 ILE cc_start: 0.7990 (mm) cc_final: 0.7744 (mt) REVERT: B 996 TYR cc_start: 0.8284 (t80) cc_final: 0.7912 (t80) REVERT: B 1027 ASN cc_start: 0.8073 (m-40) cc_final: 0.7818 (m110) outliers start: 74 outliers final: 51 residues processed: 401 average time/residue: 0.3150 time to fit residues: 174.9743 Evaluate side-chains 406 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 346 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL 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 387 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 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 826 PHE 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 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 725 GLU 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 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 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: 0.7980 chunk 16 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 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 = 0.4146 r_free = 0.4146 target = 0.165541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.129580 restraints weight = 21109.302| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.49 r_work: 0.3504 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13844 Z= 0.178 Angle : 0.649 14.082 18837 Z= 0.325 Chirality : 0.041 0.174 2172 Planarity : 0.005 0.061 2249 Dihedral : 17.198 172.477 2124 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.37 % Allowed : 25.53 % Favored : 69.09 % 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: 1.29 (0.18), residues: 811 sheet: -1.18 (0.36), residues: 213 loop : -1.09 (0.29), residues: 527 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 0.022 0.002 PHE B 784 TYR 0.021 0.001 TYR B 744 ARG 0.008 0.000 ARG A 737 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 720) hydrogen bonds : angle 4.77401 ( 2016) covalent geometry : bond 0.00392 (13844) covalent geometry : angle 0.64941 (18837) *********************** 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 428 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 352 time to evaluate : 1.430 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 301 LYS cc_start: 0.8281 (mttt) cc_final: 0.7861 (mmmt) REVERT: A 337 GLN cc_start: 0.6941 (OUTLIER) cc_final: 0.6712 (pm20) REVERT: A 353 LYS cc_start: 0.8602 (tttm) cc_final: 0.8393 (tttm) REVERT: A 409 GLN cc_start: 0.8213 (mt0) cc_final: 0.7724 (tm-30) REVERT: A 413 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7921 (mm-40) REVERT: A 658 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7011 (mm-30) REVERT: A 691 ILE cc_start: 0.8352 (tt) cc_final: 0.8038 (tp) REVERT: A 707 CYS cc_start: 0.8246 (p) cc_final: 0.8003 (p) REVERT: A 730 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8019 (mm) REVERT: A 738 SER cc_start: 0.8792 (m) cc_final: 0.8258 (p) REVERT: A 743 SER cc_start: 0.8248 (m) cc_final: 0.7861 (t) REVERT: A 757 TYR cc_start: 0.8111 (m-10) cc_final: 0.7707 (m-10) REVERT: A 799 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7662 (p0) REVERT: A 841 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8198 (mm) REVERT: A 842 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7589 (mm-30) REVERT: B 265 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7649 (mp) REVERT: B 275 HIS cc_start: 0.6693 (OUTLIER) cc_final: 0.5137 (p90) REVERT: B 280 PHE cc_start: 0.4885 (OUTLIER) cc_final: 0.4265 (t80) REVERT: B 336 LYS cc_start: 0.8172 (tptp) cc_final: 0.7787 (tptm) REVERT: B 407 ASP cc_start: 0.7605 (t70) cc_final: 0.7384 (t70) REVERT: B 427 LEU cc_start: 0.7836 (tp) cc_final: 0.7450 (tt) REVERT: B 565 ASP cc_start: 0.7826 (t0) cc_final: 0.7160 (t0) REVERT: B 584 LEU cc_start: 0.8159 (mt) cc_final: 0.7951 (mm) REVERT: B 595 ASP cc_start: 0.6855 (p0) cc_final: 0.6573 (p0) REVERT: B 636 GLN cc_start: 0.8188 (tt0) cc_final: 0.7762 (tm-30) REVERT: B 687 LYS cc_start: 0.8271 (mmtt) cc_final: 0.7955 (mmtm) REVERT: B 703 PHE cc_start: 0.7017 (m-10) cc_final: 0.6413 (m-10) REVERT: B 726 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8597 (mp) REVERT: B 730 LEU cc_start: 0.8457 (tp) cc_final: 0.8253 (tp) REVERT: B 744 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.6498 (m-80) REVERT: B 796 ARG cc_start: 0.8181 (mmm-85) cc_final: 0.7956 (mmt90) REVERT: B 830 THR cc_start: 0.8223 (m) cc_final: 0.7498 (p) REVERT: B 852 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: B 989 ILE cc_start: 0.8005 (mm) cc_final: 0.7761 (mt) REVERT: B 996 TYR cc_start: 0.8279 (t80) cc_final: 0.7866 (t80) REVERT: B 1027 ASN cc_start: 0.8086 (m-40) cc_final: 0.7877 (m110) REVERT: B 1053 VAL cc_start: 0.7881 (t) cc_final: 0.7527 (p) outliers start: 76 outliers final: 55 residues processed: 397 average time/residue: 0.3169 time to fit residues: 174.2059 Evaluate side-chains 416 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 351 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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 300 MET Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 368 GLU 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 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 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 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 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 823 LYS 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 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 1032 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 90 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 124 optimal weight: 0.0170 chunk 123 optimal weight: 5.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- 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 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 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 = 0.4157 r_free = 0.4157 target = 0.166325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.130680 restraints weight = 21034.049| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.46 r_work: 0.3513 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2924 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= 0.190 Angle : 0.659 14.172 18837 Z= 0.331 Chirality : 0.042 0.173 2172 Planarity : 0.005 0.087 2249 Dihedral : 17.023 162.920 2123 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.66 % Allowed : 26.59 % Favored : 67.75 % 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: 0.17 (0.22), residues: 1551 helix: 1.31 (0.18), residues: 811 sheet: -1.19 (0.36), residues: 213 loop : -1.14 (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 B 630 PHE 0.021 0.001 PHE B 784 TYR 0.042 0.002 TYR B 236 ARG 0.007 0.001 ARG A 737 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 720) hydrogen bonds : angle 4.76112 ( 2016) covalent geometry : bond 0.00418 (13844) covalent geometry : angle 0.65925 (18837) *********************** 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 433 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 353 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6657 (pm20) REVERT: A 351 MET cc_start: 0.8074 (tpt) cc_final: 0.7643 (mmm) REVERT: A 353 LYS cc_start: 0.8585 (tttm) cc_final: 0.8353 (tttm) REVERT: A 409 GLN cc_start: 0.8264 (mt0) cc_final: 0.7740 (tm-30) REVERT: A 413 GLN cc_start: 0.8321 (mm-40) cc_final: 0.7915 (mm-40) REVERT: A 596 ASN cc_start: 0.7625 (t0) cc_final: 0.7218 (t0) REVERT: A 658 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7116 (mm-30) REVERT: A 691 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8039 (tp) REVERT: A 707 CYS cc_start: 0.8232 (p) cc_final: 0.7972 (p) REVERT: A 730 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8026 (mm) REVERT: A 738 SER cc_start: 0.8815 (m) cc_final: 0.8287 (p) REVERT: A 743 SER cc_start: 0.8247 (m) cc_final: 0.7866 (t) REVERT: A 757 TYR cc_start: 0.8143 (m-10) cc_final: 0.7730 (m-10) REVERT: A 772 THR cc_start: 0.8005 (p) cc_final: 0.7804 (t) REVERT: A 799 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7619 (p0) REVERT: A 842 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7602 (mm-30) REVERT: B 265 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7699 (mp) REVERT: B 275 HIS cc_start: 0.6583 (OUTLIER) cc_final: 0.5099 (p90) REVERT: B 280 PHE cc_start: 0.4938 (OUTLIER) cc_final: 0.4314 (t80) REVERT: B 336 LYS cc_start: 0.8143 (tptp) cc_final: 0.7750 (tptm) REVERT: B 407 ASP cc_start: 0.7653 (t70) cc_final: 0.7418 (t70) REVERT: B 427 LEU cc_start: 0.7836 (tp) cc_final: 0.7475 (tt) REVERT: B 432 LEU cc_start: 0.3942 (OUTLIER) cc_final: 0.3691 (pp) REVERT: B 565 ASP cc_start: 0.7844 (t0) cc_final: 0.7176 (t0) REVERT: B 584 LEU cc_start: 0.8160 (mt) cc_final: 0.7946 (mm) REVERT: B 595 ASP cc_start: 0.6813 (p0) cc_final: 0.6564 (p0) REVERT: B 632 LYS cc_start: 0.8557 (mmmt) cc_final: 0.8303 (mtpp) REVERT: B 636 GLN cc_start: 0.8159 (tt0) cc_final: 0.7679 (tm-30) REVERT: B 687 LYS cc_start: 0.8284 (mmtt) cc_final: 0.7955 (mmtm) REVERT: B 744 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.6564 (m-80) REVERT: B 796 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.8029 (mmt90) REVERT: B 830 THR cc_start: 0.8214 (m) cc_final: 0.7501 (p) REVERT: B 852 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7618 (tm-30) REVERT: B 877 TYR cc_start: 0.7143 (t80) cc_final: 0.6936 (t80) REVERT: B 989 ILE cc_start: 0.7993 (mm) cc_final: 0.7752 (mt) REVERT: B 996 TYR cc_start: 0.8266 (t80) cc_final: 0.7851 (t80) REVERT: B 1053 VAL cc_start: 0.7921 (t) cc_final: 0.7593 (p) outliers start: 80 outliers final: 57 residues processed: 403 average time/residue: 0.3028 time to fit residues: 168.5941 Evaluate side-chains 408 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 341 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 362 LEU 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 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 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 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 370 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 413 GLU 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 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 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 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: 0.9990 chunk 89 optimal weight: 0.0030 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 150 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 630 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.167049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.131817 restraints weight = 20888.033| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.45 r_work: 0.3528 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13844 Z= 0.163 Angle : 0.660 14.083 18837 Z= 0.330 Chirality : 0.042 0.265 2172 Planarity : 0.005 0.062 2249 Dihedral : 16.895 163.672 2123 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.52 % Allowed : 26.66 % Favored : 67.82 % 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: 0.19 (0.22), residues: 1551 helix: 1.36 (0.18), residues: 806 sheet: -1.25 (0.38), residues: 201 loop : -1.15 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 768 HIS 0.006 0.001 HIS B 630 PHE 0.038 0.002 PHE B 952 TYR 0.057 0.002 TYR B 236 ARG 0.007 0.000 ARG A 621 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 720) hydrogen bonds : angle 4.71476 ( 2016) covalent geometry : bond 0.00363 (13844) covalent geometry : angle 0.65974 (18837) *********************** 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: 78 poor density : 352 time to evaluate : 1.428 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 337 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6734 (pm20) REVERT: A 406 ARG cc_start: 0.8306 (mmm160) cc_final: 0.8014 (mmm-85) REVERT: A 409 GLN cc_start: 0.8264 (mt0) cc_final: 0.7715 (tm-30) REVERT: A 413 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7835 (mm-40) REVERT: A 451 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8007 (mm-40) REVERT: A 459 ASP cc_start: 0.6425 (m-30) cc_final: 0.6206 (m-30) REVERT: A 658 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7050 (mm-30) REVERT: A 691 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8078 (tp) REVERT: A 707 CYS cc_start: 0.8227 (p) cc_final: 0.7955 (p) REVERT: A 730 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8021 (mm) REVERT: A 738 SER cc_start: 0.8797 (m) cc_final: 0.8291 (t) REVERT: A 743 SER cc_start: 0.8207 (m) cc_final: 0.7834 (t) REVERT: A 757 TYR cc_start: 0.8127 (m-10) cc_final: 0.7739 (m-10) REVERT: A 772 THR cc_start: 0.7951 (p) cc_final: 0.7740 (t) REVERT: A 799 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7536 (p0) REVERT: A 842 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7603 (mm-30) REVERT: B 265 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7713 (mp) REVERT: B 280 PHE cc_start: 0.4905 (OUTLIER) cc_final: 0.4277 (t80) REVERT: B 336 LYS cc_start: 0.8140 (tptp) cc_final: 0.7757 (tptm) REVERT: B 427 LEU cc_start: 0.7837 (tp) cc_final: 0.7468 (tt) REVERT: B 432 LEU cc_start: 0.3927 (OUTLIER) cc_final: 0.3677 (pp) REVERT: B 516 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7142 (tp30) REVERT: B 565 ASP cc_start: 0.7871 (t0) cc_final: 0.7223 (t0) REVERT: B 584 LEU cc_start: 0.8162 (mt) cc_final: 0.7951 (mm) REVERT: B 595 ASP cc_start: 0.6758 (p0) cc_final: 0.6520 (p0) REVERT: B 632 LYS cc_start: 0.8506 (mmmt) cc_final: 0.8256 (mtpp) REVERT: B 636 GLN cc_start: 0.8114 (tt0) cc_final: 0.7628 (tm-30) REVERT: B 687 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7923 (mmtm) REVERT: B 796 ARG cc_start: 0.8250 (mmm-85) cc_final: 0.8037 (mmt90) REVERT: B 830 THR cc_start: 0.8186 (m) cc_final: 0.7493 (p) REVERT: B 852 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: B 877 TYR cc_start: 0.7143 (t80) cc_final: 0.6916 (t80) REVERT: B 969 GLN cc_start: 0.8340 (mt0) cc_final: 0.7409 (mm110) REVERT: B 989 ILE cc_start: 0.8010 (mm) cc_final: 0.7755 (mt) REVERT: B 1053 VAL cc_start: 0.7921 (t) cc_final: 0.7587 (p) outliers start: 78 outliers final: 57 residues processed: 399 average time/residue: 0.3039 time to fit residues: 166.9091 Evaluate side-chains 408 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 342 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 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 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 682 THR 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 275 HIS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 280 PHE 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 413 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 103 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 142 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 781 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 = 0.4141 r_free = 0.4141 target = 0.165169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.129673 restraints weight = 20764.772| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.44 r_work: 0.3511 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 13844 Z= 0.240 Angle : 0.724 14.760 18837 Z= 0.367 Chirality : 0.044 0.249 2172 Planarity : 0.005 0.062 2249 Dihedral : 16.870 159.235 2123 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.30 % Allowed : 27.23 % Favored : 67.47 % 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: 1.14 (0.18), residues: 805 sheet: -1.32 (0.38), residues: 201 loop : -1.13 (0.28), residues: 545 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 0.035 0.002 PHE B 952 TYR 0.052 0.002 TYR B 236 ARG 0.007 0.001 ARG A 621 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 720) hydrogen bonds : angle 4.84213 ( 2016) covalent geometry : bond 0.00527 (13844) covalent geometry : angle 0.72363 (18837) *********************** 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: 75 poor density : 354 time to evaluate : 1.364 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 301 LYS cc_start: 0.8344 (mttt) cc_final: 0.7907 (mmmt) REVERT: A 337 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6753 (pm20) REVERT: A 353 LYS cc_start: 0.8580 (tttm) cc_final: 0.8293 (tttm) REVERT: A 388 ASN cc_start: 0.7102 (OUTLIER) cc_final: 0.6846 (t160) REVERT: A 414 LEU cc_start: 0.9080 (tt) cc_final: 0.8801 (tp) REVERT: A 451 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8007 (mm-40) REVERT: A 658 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7112 (mm-30) REVERT: A 691 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8087 (tp) REVERT: A 730 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8132 (mm) REVERT: A 738 SER cc_start: 0.8789 (m) cc_final: 0.8266 (p) REVERT: A 799 ASN cc_start: 0.7859 (OUTLIER) cc_final: 0.7633 (p0) REVERT: A 842 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7607 (mm-30) REVERT: B 265 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7744 (mp) REVERT: B 275 HIS cc_start: 0.6723 (OUTLIER) cc_final: 0.6362 (p-80) REVERT: B 280 PHE cc_start: 0.5064 (OUTLIER) cc_final: 0.4406 (t80) REVERT: B 336 LYS cc_start: 0.8185 (tptp) cc_final: 0.7837 (tptm) REVERT: B 516 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7152 (tp30) REVERT: B 565 ASP cc_start: 0.7897 (t0) cc_final: 0.7301 (t0) REVERT: B 584 LEU cc_start: 0.8176 (mt) cc_final: 0.7974 (mm) REVERT: B 632 LYS cc_start: 0.8521 (mmmt) cc_final: 0.8275 (mtpp) REVERT: B 636 GLN cc_start: 0.8141 (tt0) cc_final: 0.7727 (tm-30) REVERT: B 687 LYS cc_start: 0.8289 (mmtt) cc_final: 0.7962 (mmtm) REVERT: B 781 HIS cc_start: 0.6907 (OUTLIER) cc_final: 0.6541 (m90) REVERT: B 796 ARG cc_start: 0.8286 (mmm-85) cc_final: 0.8075 (mmt90) REVERT: B 830 THR cc_start: 0.8291 (m) cc_final: 0.7588 (p) REVERT: B 852 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: B 996 TYR cc_start: 0.8314 (t80) cc_final: 0.7902 (t80) REVERT: B 1018 GLU cc_start: 0.7675 (tt0) cc_final: 0.7399 (tt0) REVERT: B 1053 VAL cc_start: 0.7961 (t) cc_final: 0.7652 (p) outliers start: 75 outliers final: 55 residues processed: 401 average time/residue: 0.3397 time to fit residues: 191.1706 Evaluate side-chains 414 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 348 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 231 ASP 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 339 GLN Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 388 ASN 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 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 682 THR 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 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 370 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 413 GLU 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 673 LEU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 744 TYR 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 823 LYS Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 852 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 146 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 154 optimal weight: 0.5980 chunk 69 optimal weight: 0.3980 chunk 130 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 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 630 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.167583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.132886 restraints weight = 21131.502| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.43 r_work: 0.3538 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13844 Z= 0.163 Angle : 0.711 14.425 18837 Z= 0.356 Chirality : 0.042 0.234 2172 Planarity : 0.005 0.062 2249 Dihedral : 16.809 163.010 2121 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.31 % Allowed : 28.64 % Favored : 67.04 % 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: 0.11 (0.22), residues: 1551 helix: 1.23 (0.18), residues: 804 sheet: -1.10 (0.40), residues: 177 loop : -1.16 (0.28), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 807 HIS 0.004 0.001 HIS B 729 PHE 0.039 0.002 PHE B 784 TYR 0.058 0.002 TYR B 236 ARG 0.007 0.000 ARG A 621 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 720) hydrogen bonds : angle 4.76245 ( 2016) covalent geometry : bond 0.00369 (13844) covalent geometry : angle 0.71125 (18837) ********************** 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 423 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 362 time to evaluate : 1.354 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 301 LYS cc_start: 0.8324 (mttt) cc_final: 0.7874 (mmmt) REVERT: A 406 ARG cc_start: 0.8268 (mmm160) cc_final: 0.7894 (mmm-85) REVERT: A 414 LEU cc_start: 0.9056 (tt) cc_final: 0.8773 (tp) REVERT: A 621 ARG cc_start: 0.8592 (ttm-80) cc_final: 0.8388 (ttm-80) REVERT: A 658 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7017 (mm-30) REVERT: A 691 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8084 (tp) REVERT: A 738 SER cc_start: 0.8785 (m) cc_final: 0.8280 (t) REVERT: A 757 TYR cc_start: 0.8120 (m-10) cc_final: 0.7727 (m-10) REVERT: A 799 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7593 (p0) REVERT: A 842 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7579 (mm-30) REVERT: B 275 HIS cc_start: 0.6598 (OUTLIER) cc_final: 0.5087 (p90) REVERT: B 280 PHE cc_start: 0.4892 (OUTLIER) cc_final: 0.4240 (t80) REVERT: B 336 LYS cc_start: 0.8148 (tptp) cc_final: 0.7761 (tptm) REVERT: B 373 GLU cc_start: 0.8315 (mp0) cc_final: 0.7111 (mt-10) REVERT: B 415 GLU cc_start: 0.7517 (tp30) cc_final: 0.6937 (tp30) REVERT: B 427 LEU cc_start: 0.7825 (tp) cc_final: 0.7514 (tt) REVERT: B 454 ARG cc_start: 0.8165 (ttt-90) cc_final: 0.7760 (ttt90) REVERT: B 565 ASP cc_start: 0.7862 (t0) cc_final: 0.7251 (t0) REVERT: B 584 LEU cc_start: 0.8137 (mt) cc_final: 0.7930 (mm) REVERT: B 632 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8271 (mtpp) REVERT: B 636 GLN cc_start: 0.8106 (tt0) cc_final: 0.7724 (tp-100) REVERT: B 687 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7892 (mmtm) REVERT: B 781 HIS cc_start: 0.6810 (OUTLIER) cc_final: 0.6470 (m90) REVERT: B 796 ARG cc_start: 0.8250 (mmm-85) cc_final: 0.8034 (mmt90) REVERT: B 830 THR cc_start: 0.8191 (m) cc_final: 0.7496 (p) REVERT: B 852 GLN cc_start: 0.8143 (tt0) cc_final: 0.7699 (tm-30) REVERT: B 969 GLN cc_start: 0.8296 (mt0) cc_final: 0.7390 (mm110) REVERT: B 989 ILE cc_start: 0.8052 (mm) cc_final: 0.7798 (mt) REVERT: B 1053 VAL cc_start: 0.7934 (t) cc_final: 0.7614 (p) outliers start: 61 outliers final: 51 residues processed: 399 average time/residue: 0.2970 time to fit residues: 162.9873 Evaluate side-chains 404 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 348 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 231 ASP 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 339 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 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 682 THR 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 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 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 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 413 GLU 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 673 LEU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 744 TYR 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 895 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 22 optimal weight: 0.8980 chunk 59 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 460 ASN ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN B 917 GLN ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4181 r_free = 0.4181 target = 0.168534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.133940 restraints weight = 21035.094| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.43 r_work: 0.3551 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13844 Z= 0.156 Angle : 0.711 14.105 18837 Z= 0.356 Chirality : 0.042 0.224 2172 Planarity : 0.005 0.062 2249 Dihedral : 16.699 161.878 2121 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.53 % Allowed : 28.78 % Favored : 66.69 % 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: 0.17 (0.22), residues: 1551 helix: 1.23 (0.18), residues: 805 sheet: -0.84 (0.43), residues: 156 loop : -1.17 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 768 HIS 0.009 0.001 HIS B 467 PHE 0.045 0.002 PHE B 784 TYR 0.060 0.002 TYR B 236 ARG 0.008 0.001 ARG B 616 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 720) hydrogen bonds : angle 4.77633 ( 2016) covalent geometry : bond 0.00355 (13844) covalent geometry : angle 0.71108 (18837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7304.03 seconds wall clock time: 125 minutes 30.82 seconds (7530.82 seconds total)