Starting phenix.real_space_refine on Thu Sep 18 03:13:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rz7_19605/09_2025/8rz7_19605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rz7_19605/09_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_19605/09_2025/8rz7_19605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rz7_19605/09_2025/8rz7_19605.map" model { file = "/net/cci-nas-00/data/ceres_data/8rz7_19605/09_2025/8rz7_19605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rz7_19605/09_2025/8rz7_19605.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.53, per 1000 atoms: 0.19 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: 1.14 Conformation dependent library (CDL) restraints added in 584.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.46 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: 2.60 Time building geometry restraints manager: 1.52 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.740 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.510 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.042 0.002 ARG A 737 TYR 0.032 0.005 TYR A 299 PHE 0.034 0.004 PHE B1052 TRP 0.045 0.006 TRP B1111 HIS 0.014 0.002 HIS B 781 Details of bonding type rmsd covalent geometry : bond 0.01161 (13844) covalent geometry : angle 1.44676 (18837) hydrogen bonds : bond 0.16344 ( 720) hydrogen bonds : angle 7.06587 ( 2016) *********************** 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 : 0.511 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: 0.1344 time to fit residues: 78.2283 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 : 0.500 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.0070 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 662 HIS B 852 GLN B 880 ASN B 908 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.164304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.127677 restraints weight = 20928.824| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.46 r_work: 0.3523 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13844 Z= 0.153 Angle : 0.665 8.881 18837 Z= 0.343 Chirality : 0.042 0.220 2172 Planarity : 0.004 0.045 2249 Dihedral : 17.940 173.055 2159 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.02 % Allowed : 22.07 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.22), residues: 1551 helix: 0.88 (0.18), residues: 809 sheet: -1.20 (0.37), residues: 201 loop : -1.18 (0.29), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 938 TYR 0.020 0.002 TYR B 236 PHE 0.021 0.002 PHE B 784 TRP 0.014 0.001 TRP B 768 HIS 0.006 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00334 (13844) covalent geometry : angle 0.66485 (18837) hydrogen bonds : bond 0.04591 ( 720) hydrogen bonds : angle 5.23782 ( 2016) *********************** 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 433 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 362 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 LYS cc_start: 0.8141 (mttt) cc_final: 0.7724 (mmmt) REVERT: A 334 LYS cc_start: 0.7629 (mmtm) cc_final: 0.7259 (mmtm) REVERT: A 409 GLN cc_start: 0.8235 (mt0) cc_final: 0.7525 (mp10) REVERT: A 416 ASN cc_start: 0.8349 (t0) cc_final: 0.8137 (t0) REVERT: A 613 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8127 (t0) REVERT: A 658 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6967 (mm-30) REVERT: A 691 ILE cc_start: 0.8189 (tt) cc_final: 0.7864 (tp) REVERT: A 707 CYS cc_start: 0.8333 (p) cc_final: 0.8066 (p) REVERT: A 730 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8101 (mm) REVERT: A 738 SER cc_start: 0.8649 (m) cc_final: 0.8177 (t) REVERT: A 743 SER cc_start: 0.7863 (m) cc_final: 0.7619 (t) REVERT: A 757 TYR cc_start: 0.8094 (m-10) cc_final: 0.7699 (m-10) REVERT: A 799 ASN cc_start: 0.7837 (m-40) cc_final: 0.7613 (p0) REVERT: B 275 HIS cc_start: 0.6792 (OUTLIER) cc_final: 0.5386 (p90) REVERT: B 280 PHE cc_start: 0.4946 (OUTLIER) cc_final: 0.4222 (t80) REVERT: B 427 LEU cc_start: 0.7820 (tp) cc_final: 0.7478 (tt) REVERT: B 534 PHE cc_start: 0.8148 (m-10) cc_final: 0.7814 (m-10) REVERT: B 593 ARG cc_start: 0.8498 (mtt180) cc_final: 0.7907 (ttm110) REVERT: B 636 GLN cc_start: 0.8308 (tt0) cc_final: 0.7838 (tm-30) REVERT: B 703 PHE cc_start: 0.6752 (m-10) cc_final: 0.6144 (m-10) REVERT: B 718 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7501 (tt0) REVERT: B 725 GLU cc_start: 0.8139 (pp20) cc_final: 0.7876 (pp20) REVERT: B 796 ARG cc_start: 0.8211 (mmm-85) cc_final: 0.7869 (mmm-85) REVERT: B 848 ARG cc_start: 0.8952 (ttt-90) cc_final: 0.8461 (ttp-170) REVERT: B 1032 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7700 (m-80) outliers start: 71 outliers final: 33 residues processed: 400 average time/residue: 0.1364 time to fit residues: 75.1475 Evaluate side-chains 391 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 353 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 278 GLU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 380 LEU 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 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 500 ILE 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 843 GLN Chi-restraints excluded: chain B residue 870 LEU 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 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 89 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 46 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN B 309 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 = 0.4111 r_free = 0.4111 target = 0.161996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.126803 restraints weight = 21075.819| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.37 r_work: 0.3472 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 13844 Z= 0.281 Angle : 0.696 12.170 18837 Z= 0.360 Chirality : 0.045 0.269 2172 Planarity : 0.005 0.055 2249 Dihedral : 17.781 169.680 2131 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.94 % Allowed : 23.27 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.22), residues: 1551 helix: 0.78 (0.18), residues: 809 sheet: -1.13 (0.39), residues: 189 loop : -1.21 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 621 TYR 0.035 0.002 TYR A 563 PHE 0.019 0.002 PHE A 551 TRP 0.012 0.002 TRP B 768 HIS 0.006 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00601 (13844) covalent geometry : angle 0.69621 (18837) hydrogen bonds : bond 0.04998 ( 720) hydrogen bonds : angle 5.22175 ( 2016) *********************** 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 454 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 370 time to evaluate : 0.508 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: 0.6986 (OUTLIER) cc_final: 0.6763 (pm20) REVERT: A 347 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8151 (ttmm) REVERT: A 380 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7462 (mp) REVERT: A 607 SER cc_start: 0.8613 (OUTLIER) cc_final: 0.8331 (t) REVERT: A 658 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7091 (mm-30) REVERT: A 691 ILE cc_start: 0.8341 (tt) cc_final: 0.8027 (tp) REVERT: A 730 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8045 (mm) REVERT: A 738 SER cc_start: 0.8791 (m) cc_final: 0.8291 (t) REVERT: A 799 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7628 (p0) REVERT: B 262 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7239 (m-30) REVERT: B 275 HIS cc_start: 0.6733 (OUTLIER) cc_final: 0.5376 (p90) REVERT: B 280 PHE cc_start: 0.4993 (OUTLIER) cc_final: 0.4282 (t80) REVERT: B 336 LYS cc_start: 0.8150 (tptp) cc_final: 0.7895 (tptp) REVERT: B 427 LEU cc_start: 0.7816 (tp) cc_final: 0.7442 (tt) REVERT: B 565 ASP cc_start: 0.7705 (t0) cc_final: 0.7276 (t0) REVERT: B 636 GLN cc_start: 0.8286 (tt0) cc_final: 0.7847 (tm-30) REVERT: B 687 LYS cc_start: 0.8341 (mmtt) cc_final: 0.8012 (mmtp) REVERT: B 725 GLU cc_start: 0.8239 (pp20) cc_final: 0.7974 (pp20) REVERT: B 726 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8889 (mp) REVERT: B 796 ARG cc_start: 0.8241 (mmm-85) cc_final: 0.7869 (mmm-85) REVERT: B 852 GLN cc_start: 0.8026 (tt0) cc_final: 0.7611 (tm-30) REVERT: B 1053 VAL cc_start: 0.7974 (t) cc_final: 0.7642 (p) REVERT: B 1063 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8012 (pt) outliers start: 84 outliers final: 45 residues processed: 411 average time/residue: 0.1330 time to fit residues: 76.2007 Evaluate side-chains 409 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 353 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 293 THR 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 347 LYS Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 419 GLN 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 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 835 ASN Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 262 ASP 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 368 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 713 LYS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 830 THR 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 Chi-restraints excluded: chain B residue 1063 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 97 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 0.0040 chunk 144 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 4 optimal weight: 40.0000 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN ** 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 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4151 r_free = 0.4151 target = 0.166148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130283 restraints weight = 20983.307| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.46 r_work: 0.3507 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13844 Z= 0.158 Angle : 0.644 12.543 18837 Z= 0.324 Chirality : 0.041 0.199 2172 Planarity : 0.004 0.073 2249 Dihedral : 17.587 178.920 2129 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.73 % Allowed : 24.89 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.22), residues: 1551 helix: 1.06 (0.18), residues: 810 sheet: -1.20 (0.37), residues: 211 loop : -1.12 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 848 TYR 0.024 0.001 TYR B 744 PHE 0.019 0.002 PHE A 551 TRP 0.012 0.001 TRP B 768 HIS 0.005 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00349 (13844) covalent geometry : angle 0.64443 (18837) hydrogen bonds : bond 0.04266 ( 720) hydrogen bonds : angle 4.95511 ( 2016) *********************** 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 437 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 356 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7382 (mp) REVERT: A 451 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7965 (mm-40) REVERT: A 467 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8695 (mp0) REVERT: A 599 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.7917 (tt) REVERT: A 691 ILE cc_start: 0.8304 (tt) cc_final: 0.8015 (tp) REVERT: A 730 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8033 (mm) REVERT: A 738 SER cc_start: 0.8770 (m) cc_final: 0.8288 (t) REVERT: A 757 TYR cc_start: 0.8118 (m-10) cc_final: 0.7819 (m-10) REVERT: A 799 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7583 (p0) REVERT: A 842 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7586 (mm-30) REVERT: B 236 TYR cc_start: 0.6132 (t80) cc_final: 0.5921 (t80) REVERT: B 265 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8324 (mp) REVERT: B 275 HIS cc_start: 0.6713 (OUTLIER) cc_final: 0.5320 (p90) REVERT: B 280 PHE cc_start: 0.4906 (OUTLIER) cc_final: 0.4276 (t80) REVERT: B 336 LYS cc_start: 0.8187 (tptp) cc_final: 0.7803 (tptm) REVERT: B 421 LEU cc_start: 0.7633 (mt) cc_final: 0.7393 (mt) REVERT: B 427 LEU cc_start: 0.7858 (tp) cc_final: 0.7486 (tt) REVERT: B 534 PHE cc_start: 0.8100 (m-80) cc_final: 0.7757 (m-10) REVERT: B 565 ASP cc_start: 0.7770 (t0) cc_final: 0.7308 (t0) REVERT: B 613 ASN cc_start: 0.7609 (m-40) cc_final: 0.7204 (m-40) REVERT: B 616 ARG cc_start: 0.7748 (mtm110) cc_final: 0.7358 (mtm110) REVERT: B 636 GLN cc_start: 0.8262 (tt0) cc_final: 0.7760 (tm-30) REVERT: B 687 LYS cc_start: 0.8337 (mmtt) cc_final: 0.7963 (mmtm) REVERT: B 725 GLU cc_start: 0.8226 (pp20) cc_final: 0.7936 (pp20) REVERT: B 726 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8692 (mp) REVERT: B 752 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7103 (p90) REVERT: B 796 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7963 (mmt90) REVERT: B 877 TYR cc_start: 0.7141 (t80) cc_final: 0.6925 (t80) REVERT: B 889 GLU cc_start: 0.7220 (tt0) cc_final: 0.6771 (tt0) REVERT: B 915 MET cc_start: 0.8245 (mtm) cc_final: 0.8045 (mtm) outliers start: 81 outliers final: 45 residues processed: 399 average time/residue: 0.1528 time to fit residues: 84.3930 Evaluate side-chains 397 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 342 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 460 MET 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 594 THR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 835 ASN Chi-restraints excluded: chain B residue 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 625 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 713 LYS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 806 GLU Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 830 THR Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 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 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 1 optimal weight: 50.0000 chunk 151 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 152 optimal weight: 0.4980 chunk 139 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 HIS A 681 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.165869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.130054 restraints weight = 21110.843| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.49 r_work: 0.3504 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2669 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= 0.163 Angle : 0.644 13.688 18837 Z= 0.323 Chirality : 0.041 0.179 2172 Planarity : 0.004 0.059 2249 Dihedral : 17.260 165.065 2129 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.66 % Allowed : 25.39 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.22), residues: 1551 helix: 1.16 (0.18), residues: 811 sheet: -1.19 (0.36), residues: 211 loop : -1.08 (0.29), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 621 TYR 0.019 0.001 TYR B 744 PHE 0.022 0.002 PHE B 258 TRP 0.009 0.001 TRP B 807 HIS 0.005 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00361 (13844) covalent geometry : angle 0.64414 (18837) hydrogen bonds : bond 0.04209 ( 720) hydrogen bonds : angle 4.84323 ( 2016) *********************** 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 433 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 353 time to evaluate : 0.539 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 353 LYS cc_start: 0.8534 (tttp) cc_final: 0.8212 (ttpp) REVERT: A 451 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8176 (mm-40) REVERT: A 599 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.7873 (tt) REVERT: A 658 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7176 (mm-30) REVERT: A 681 GLN cc_start: 0.7562 (tt0) cc_final: 0.7358 (tt0) REVERT: A 691 ILE cc_start: 0.8348 (tt) cc_final: 0.8026 (tp) REVERT: A 738 SER cc_start: 0.8792 (m) cc_final: 0.8306 (t) REVERT: A 799 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7621 (p0) REVERT: A 842 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7594 (mm-30) REVERT: B 265 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.8028 (mp) REVERT: B 275 HIS cc_start: 0.6714 (OUTLIER) cc_final: 0.5271 (p90) REVERT: B 280 PHE cc_start: 0.4967 (OUTLIER) cc_final: 0.4362 (t80) REVERT: B 336 LYS cc_start: 0.8180 (tptp) cc_final: 0.7787 (tptm) REVERT: B 421 LEU cc_start: 0.7642 (mt) cc_final: 0.7428 (mt) REVERT: B 427 LEU cc_start: 0.7872 (tp) cc_final: 0.7504 (tt) REVERT: B 565 ASP cc_start: 0.7849 (t0) cc_final: 0.7340 (t0) REVERT: B 595 ASP cc_start: 0.6879 (p0) cc_final: 0.6629 (p0) REVERT: B 636 GLN cc_start: 0.8264 (tt0) cc_final: 0.7769 (tm-30) REVERT: B 687 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7949 (mmtm) REVERT: B 699 LYS cc_start: 0.8765 (mttp) cc_final: 0.8510 (mtpp) REVERT: B 725 GLU cc_start: 0.8237 (pp20) cc_final: 0.8000 (pp20) REVERT: B 726 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8627 (mp) REVERT: B 752 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7231 (p90) REVERT: B 796 ARG cc_start: 0.8210 (mmm-85) cc_final: 0.7988 (mmt90) REVERT: B 830 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.7508 (p) REVERT: B 877 TYR cc_start: 0.7220 (t80) cc_final: 0.6902 (t80) REVERT: B 1015 CYS cc_start: 0.8519 (t) cc_final: 0.8261 (t) REVERT: B 1053 VAL cc_start: 0.7914 (t) cc_final: 0.7574 (p) outliers start: 80 outliers final: 44 residues processed: 402 average time/residue: 0.1505 time to fit residues: 83.7821 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 : 0.501 ------------------------------------------------------------------------------- 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 339 GLN 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 599 LEU Chi-restraints excluded: chain A residue 642 VAL 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 826 PHE Chi-restraints excluded: chain A residue 835 ASN Chi-restraints excluded: chain A residue 849 LEU 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 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 601 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 713 LYS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 806 GLU Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 830 THR Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 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 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 55 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN ** 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 = 0.4101 r_free = 0.4101 target = 0.160679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.124398 restraints weight = 21005.905| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.46 r_work: 0.3474 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 13844 Z= 0.262 Angle : 0.701 14.345 18837 Z= 0.354 Chirality : 0.044 0.199 2172 Planarity : 0.005 0.062 2249 Dihedral : 17.137 159.694 2126 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.52 % Allowed : 26.45 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.22), residues: 1551 helix: 1.01 (0.18), residues: 810 sheet: -1.32 (0.36), residues: 211 loop : -1.13 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 616 TYR 0.034 0.002 TYR B 236 PHE 0.036 0.002 PHE B 952 TRP 0.010 0.001 TRP B 807 HIS 0.006 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00566 (13844) covalent geometry : angle 0.70057 (18837) hydrogen bonds : bond 0.04653 ( 720) hydrogen bonds : angle 4.95372 ( 2016) *********************** 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 429 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 351 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 LYS cc_start: 0.8173 (mttm) cc_final: 0.7965 (mmmt) REVERT: A 337 GLN cc_start: 0.6981 (OUTLIER) cc_final: 0.6688 (pm20) REVERT: A 353 LYS cc_start: 0.8654 (tttp) cc_final: 0.8319 (tttp) REVERT: A 362 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8158 (mt) REVERT: A 388 ASN cc_start: 0.7290 (OUTLIER) cc_final: 0.7062 (t160) REVERT: A 451 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8097 (mm-40) REVERT: A 658 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7210 (mm-30) REVERT: A 691 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8145 (tp) REVERT: A 730 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8068 (mm) REVERT: A 738 SER cc_start: 0.8796 (m) cc_final: 0.8253 (p) REVERT: A 799 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7638 (p0) REVERT: A 842 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 265 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8092 (mp) REVERT: B 275 HIS cc_start: 0.6878 (OUTLIER) cc_final: 0.5388 (p90) REVERT: B 280 PHE cc_start: 0.5157 (OUTLIER) cc_final: 0.4482 (t80) REVERT: B 336 LYS cc_start: 0.8179 (tptp) cc_final: 0.7815 (tptm) REVERT: B 534 PHE cc_start: 0.8057 (m-80) cc_final: 0.7595 (m-80) REVERT: B 565 ASP cc_start: 0.7902 (t0) cc_final: 0.7247 (t0) REVERT: B 595 ASP cc_start: 0.6793 (p0) cc_final: 0.6555 (p0) REVERT: B 632 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8325 (mtpp) REVERT: B 636 GLN cc_start: 0.8288 (tt0) cc_final: 0.7793 (tm-30) REVERT: B 687 LYS cc_start: 0.8331 (mmtt) cc_final: 0.8016 (mmtm) REVERT: B 725 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7967 (pp20) REVERT: B 726 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8590 (mp) REVERT: B 752 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.7392 (p90) REVERT: B 796 ARG cc_start: 0.8257 (mmm-85) cc_final: 0.8008 (mmt90) REVERT: B 1053 VAL cc_start: 0.7978 (t) cc_final: 0.7649 (p) outliers start: 78 outliers final: 52 residues processed: 397 average time/residue: 0.1543 time to fit residues: 84.1341 Evaluate side-chains 413 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 349 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 339 GLN Chi-restraints excluded: chain A residue 362 LEU 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 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 633 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 835 ASN Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 262 ASP 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 515 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 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 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 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 Chi-restraints excluded: chain B residue 1063 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 60 optimal weight: 0.2980 chunk 20 optimal weight: 7.9990 chunk 126 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 157 optimal weight: 40.0000 chunk 85 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.165785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130155 restraints weight = 20980.768| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.48 r_work: 0.3517 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13844 Z= 0.156 Angle : 0.652 14.036 18837 Z= 0.325 Chirality : 0.041 0.171 2172 Planarity : 0.005 0.139 2249 Dihedral : 16.980 164.325 2126 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.45 % Allowed : 27.02 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.22), residues: 1551 helix: 1.16 (0.18), residues: 817 sheet: -1.23 (0.37), residues: 211 loop : -1.12 (0.29), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 938 TYR 0.039 0.002 TYR B 236 PHE 0.029 0.002 PHE B 952 TRP 0.010 0.001 TRP B 807 HIS 0.005 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00345 (13844) covalent geometry : angle 0.65156 (18837) hydrogen bonds : bond 0.04161 ( 720) hydrogen bonds : angle 4.78345 ( 2016) *********************** 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 438 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 361 time to evaluate : 0.531 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: 0.8102 (mttm) cc_final: 0.7878 (mmmt) REVERT: A 416 ASN cc_start: 0.8566 (t0) cc_final: 0.8350 (t0) REVERT: A 599 LEU cc_start: 0.8541 (tp) cc_final: 0.7984 (tt) REVERT: A 621 ARG cc_start: 0.8557 (ttm-80) cc_final: 0.7949 (ttm-80) REVERT: A 658 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7098 (mm-30) REVERT: A 730 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7982 (mm) REVERT: A 737 ARG cc_start: 0.8439 (ttt-90) cc_final: 0.8168 (mtp85) REVERT: A 738 SER cc_start: 0.8834 (m) cc_final: 0.8297 (p) REVERT: A 757 TYR cc_start: 0.8127 (m-10) cc_final: 0.7749 (m-10) REVERT: A 799 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7558 (p0) REVERT: A 842 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7561 (mm-30) REVERT: B 265 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8069 (mp) REVERT: B 275 HIS cc_start: 0.6635 (OUTLIER) cc_final: 0.5112 (p90) REVERT: B 280 PHE cc_start: 0.4970 (OUTLIER) cc_final: 0.4285 (t80) REVERT: B 336 LYS cc_start: 0.8130 (tptp) cc_final: 0.7766 (tptm) REVERT: B 427 LEU cc_start: 0.7845 (tp) cc_final: 0.7493 (tt) REVERT: B 432 LEU cc_start: 0.3789 (OUTLIER) cc_final: 0.3511 (pp) REVERT: B 534 PHE cc_start: 0.7995 (m-80) cc_final: 0.7730 (m-80) REVERT: B 565 ASP cc_start: 0.7907 (t0) cc_final: 0.7243 (t0) REVERT: B 584 LEU cc_start: 0.8080 (mm) cc_final: 0.7768 (mm) REVERT: B 632 LYS cc_start: 0.8519 (mmmt) cc_final: 0.8279 (mtpp) REVERT: B 636 GLN cc_start: 0.8245 (tt0) cc_final: 0.7695 (tm-30) REVERT: B 687 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7964 (mmtm) REVERT: B 699 LYS cc_start: 0.8757 (mttp) cc_final: 0.8510 (mtpp) REVERT: B 725 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7925 (pp20) REVERT: B 726 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8546 (mp) REVERT: B 752 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7436 (p90) REVERT: B 796 ARG cc_start: 0.8187 (mmm-85) cc_final: 0.7981 (mmt90) REVERT: B 830 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7504 (p) REVERT: B 889 GLU cc_start: 0.7253 (tt0) cc_final: 0.6782 (tt0) REVERT: B 917 GLN cc_start: 0.8251 (mt0) cc_final: 0.8030 (mt0) REVERT: B 1053 VAL cc_start: 0.7923 (t) cc_final: 0.7584 (p) REVERT: B 1094 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8091 (tm-30) outliers start: 77 outliers final: 48 residues processed: 404 average time/residue: 0.1633 time to fit residues: 90.8830 Evaluate side-chains 409 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 351 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 836 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 368 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 432 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 813 LYS 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 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 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 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 = 0.4156 r_free = 0.4156 target = 0.166499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.131953 restraints weight = 20766.310| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.39 r_work: 0.3527 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13844 Z= 0.178 Angle : 0.674 13.563 18837 Z= 0.337 Chirality : 0.042 0.243 2172 Planarity : 0.005 0.108 2249 Dihedral : 16.874 161.271 2124 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.88 % Allowed : 27.79 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.22), residues: 1551 helix: 1.15 (0.18), residues: 816 sheet: -1.27 (0.37), residues: 211 loop : -1.14 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 737 TYR 0.033 0.002 TYR B 744 PHE 0.025 0.002 PHE B 952 TRP 0.010 0.001 TRP B 807 HIS 0.004 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00392 (13844) covalent geometry : angle 0.67406 (18837) hydrogen bonds : bond 0.04195 ( 720) hydrogen bonds : angle 4.78851 ( 2016) *********************** 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 416 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 347 time to evaluate : 0.541 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: 0.8159 (mttm) cc_final: 0.7947 (mmmt) REVERT: A 416 ASN cc_start: 0.8571 (t0) cc_final: 0.8345 (t0) REVERT: A 430 LYS cc_start: 0.7820 (mtpp) cc_final: 0.7438 (mmmm) REVERT: A 599 LEU cc_start: 0.8580 (tp) cc_final: 0.8199 (tt) REVERT: A 621 ARG cc_start: 0.8558 (ttm-80) cc_final: 0.7998 (ttm-80) REVERT: A 658 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7119 (mm-30) REVERT: A 681 GLN cc_start: 0.7521 (tt0) cc_final: 0.7169 (tt0) REVERT: A 691 ILE cc_start: 0.8338 (tt) cc_final: 0.8101 (tp) REVERT: A 730 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8046 (mm) REVERT: A 737 ARG cc_start: 0.8457 (ttt-90) cc_final: 0.8222 (mtp85) REVERT: A 738 SER cc_start: 0.8805 (m) cc_final: 0.8237 (p) REVERT: A 747 ILE cc_start: 0.8558 (mt) cc_final: 0.8321 (mm) REVERT: A 757 TYR cc_start: 0.8135 (m-10) cc_final: 0.7765 (m-10) REVERT: A 799 ASN cc_start: 0.7838 (OUTLIER) cc_final: 0.7621 (p0) REVERT: A 842 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7578 (mm-30) REVERT: B 265 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8074 (mp) REVERT: B 280 PHE cc_start: 0.5111 (OUTLIER) cc_final: 0.4454 (t80) REVERT: B 336 LYS cc_start: 0.8189 (tptp) cc_final: 0.7869 (tptm) REVERT: B 427 LEU cc_start: 0.7829 (tp) cc_final: 0.7463 (tt) REVERT: B 534 PHE cc_start: 0.8019 (m-80) cc_final: 0.7742 (m-80) REVERT: B 565 ASP cc_start: 0.7859 (t0) cc_final: 0.7249 (t0) REVERT: B 632 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8286 (mtpp) REVERT: B 636 GLN cc_start: 0.8172 (tt0) cc_final: 0.7668 (tm-30) REVERT: B 687 LYS cc_start: 0.8240 (mmtt) cc_final: 0.7926 (mmtm) REVERT: B 725 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7952 (pp20) REVERT: B 726 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8646 (mp) REVERT: B 796 ARG cc_start: 0.8239 (mmm-85) cc_final: 0.8030 (mmt90) REVERT: B 830 THR cc_start: 0.8218 (m) cc_final: 0.7514 (p) REVERT: B 1053 VAL cc_start: 0.7925 (t) cc_final: 0.7592 (p) REVERT: B 1094 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8027 (tm-30) outliers start: 69 outliers final: 51 residues processed: 385 average time/residue: 0.1557 time to fit residues: 82.1518 Evaluate side-chains 403 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 346 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 339 GLN 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 589 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 851 LEU 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 368 LEU Chi-restraints excluded: chain B residue 388 ILE 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 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 785 ILE Chi-restraints excluded: chain B residue 806 GLU Chi-restraints excluded: chain B residue 813 LYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 47 optimal weight: 3.9990 chunk 132 optimal weight: 0.1980 chunk 130 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 81 optimal weight: 0.0010 chunk 110 optimal weight: 1.9990 chunk 1 optimal weight: 40.0000 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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 460 ASN ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 729 HIS B 852 GLN B 917 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 = 0.4180 r_free = 0.4180 target = 0.168318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.133077 restraints weight = 21093.626| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.49 r_work: 0.3549 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13844 Z= 0.146 Angle : 0.674 12.697 18837 Z= 0.338 Chirality : 0.042 0.372 2172 Planarity : 0.005 0.085 2249 Dihedral : 16.762 163.449 2121 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.38 % Allowed : 28.22 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.22), residues: 1551 helix: 1.27 (0.18), residues: 811 sheet: -0.82 (0.41), residues: 176 loop : -1.16 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 669 TYR 0.032 0.001 TYR B 744 PHE 0.032 0.002 PHE A 276 TRP 0.012 0.001 TRP B 807 HIS 0.006 0.001 HIS B 467 Details of bonding type rmsd covalent geometry : bond 0.00326 (13844) covalent geometry : angle 0.67362 (18837) hydrogen bonds : bond 0.04011 ( 720) hydrogen bonds : angle 4.69452 ( 2016) *********************** 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 423 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 361 time to evaluate : 0.613 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 406 ARG cc_start: 0.8254 (mmm160) cc_final: 0.7932 (mmm-85) REVERT: A 414 LEU cc_start: 0.9006 (tt) cc_final: 0.8750 (tp) REVERT: A 430 LYS cc_start: 0.7828 (mtpp) cc_final: 0.7430 (mmmm) REVERT: A 621 ARG cc_start: 0.8564 (ttm-80) cc_final: 0.7973 (ttm-80) REVERT: A 658 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7141 (mm-30) REVERT: A 691 ILE cc_start: 0.8351 (tt) cc_final: 0.8110 (tp) REVERT: A 730 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8006 (mm) REVERT: A 737 ARG cc_start: 0.8430 (ttt-90) cc_final: 0.8207 (mtp85) REVERT: A 738 SER cc_start: 0.8788 (m) cc_final: 0.8235 (p) REVERT: A 747 ILE cc_start: 0.8582 (mt) cc_final: 0.8322 (mm) REVERT: A 757 TYR cc_start: 0.8112 (m-10) cc_final: 0.7714 (m-10) REVERT: A 799 ASN cc_start: 0.7791 (OUTLIER) cc_final: 0.7572 (p0) REVERT: A 836 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6540 (m-80) REVERT: A 842 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7594 (mm-30) REVERT: B 265 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7926 (mp) REVERT: B 280 PHE cc_start: 0.4964 (OUTLIER) cc_final: 0.4307 (t80) REVERT: B 336 LYS cc_start: 0.8210 (tptp) cc_final: 0.7799 (tptm) REVERT: B 373 GLU cc_start: 0.8208 (mp0) cc_final: 0.7402 (pt0) REVERT: B 415 GLU cc_start: 0.7516 (tp30) cc_final: 0.7135 (tp30) REVERT: B 427 LEU cc_start: 0.7903 (tp) cc_final: 0.7565 (tt) REVERT: B 527 GLN cc_start: 0.7936 (tt0) cc_final: 0.7615 (tp40) REVERT: B 534 PHE cc_start: 0.7980 (m-80) cc_final: 0.7696 (m-80) REVERT: B 565 ASP cc_start: 0.7856 (t0) cc_final: 0.7221 (t0) REVERT: B 632 LYS cc_start: 0.8464 (mmmt) cc_final: 0.8243 (mtpp) REVERT: B 636 GLN cc_start: 0.8144 (tt0) cc_final: 0.7719 (tp-100) REVERT: B 674 GLU cc_start: 0.7638 (tt0) cc_final: 0.7434 (tt0) REVERT: B 687 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7872 (mmtm) REVERT: B 725 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7987 (pp20) REVERT: B 726 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8881 (mp) REVERT: B 796 ARG cc_start: 0.8249 (mmm-85) cc_final: 0.8033 (mmt90) REVERT: B 797 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7609 (mm-30) REVERT: B 830 THR cc_start: 0.8174 (m) cc_final: 0.7477 (p) REVERT: B 969 GLN cc_start: 0.8236 (mt0) cc_final: 0.7871 (pt0) REVERT: B 1053 VAL cc_start: 0.7899 (t) cc_final: 0.7553 (p) REVERT: B 1094 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7994 (tm-30) outliers start: 62 outliers final: 49 residues processed: 393 average time/residue: 0.1511 time to fit residues: 82.2719 Evaluate side-chains 408 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 352 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 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 627 LYS 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 742 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 713 LYS Chi-restraints excluded: chain B residue 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 806 GLU Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1032 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 59 optimal weight: 0.0970 chunk 124 optimal weight: 0.4980 chunk 10 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN ** 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 = 0.4179 r_free = 0.4179 target = 0.168208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.132831 restraints weight = 21001.741| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.48 r_work: 0.3547 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13844 Z= 0.160 Angle : 0.695 12.629 18837 Z= 0.348 Chirality : 0.042 0.339 2172 Planarity : 0.005 0.084 2249 Dihedral : 16.696 162.003 2121 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.03 % Allowed : 28.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.22), residues: 1551 helix: 1.27 (0.18), residues: 811 sheet: -0.96 (0.40), residues: 189 loop : -1.16 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 340 TYR 0.036 0.002 TYR B 236 PHE 0.029 0.002 PHE A 276 TRP 0.011 0.001 TRP B 807 HIS 0.005 0.001 HIS B 467 Details of bonding type rmsd covalent geometry : bond 0.00359 (13844) covalent geometry : angle 0.69472 (18837) hydrogen bonds : bond 0.04079 ( 720) hydrogen bonds : angle 4.71219 ( 2016) ********************** 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 416 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 359 time to evaluate : 0.520 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 406 ARG cc_start: 0.8247 (mmm160) cc_final: 0.7930 (mmm-85) REVERT: A 414 LEU cc_start: 0.9063 (tt) cc_final: 0.8820 (tp) REVERT: A 658 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7093 (mm-30) REVERT: A 672 MET cc_start: 0.7767 (mmm) cc_final: 0.7550 (mmm) REVERT: A 681 GLN cc_start: 0.7498 (tt0) cc_final: 0.7281 (tt0) REVERT: A 691 ILE cc_start: 0.8361 (tt) cc_final: 0.8123 (tp) REVERT: A 730 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8020 (mm) REVERT: A 737 ARG cc_start: 0.8432 (ttt-90) cc_final: 0.8179 (mtp85) REVERT: A 738 SER cc_start: 0.8808 (m) cc_final: 0.8244 (p) REVERT: A 799 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.7581 (p0) REVERT: A 836 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6609 (m-80) REVERT: B 265 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7920 (mp) REVERT: B 280 PHE cc_start: 0.4930 (OUTLIER) cc_final: 0.4292 (t80) REVERT: B 336 LYS cc_start: 0.8179 (tptp) cc_final: 0.7781 (tptm) REVERT: B 373 GLU cc_start: 0.8217 (mp0) cc_final: 0.7390 (pt0) REVERT: B 410 SER cc_start: 0.8371 (t) cc_final: 0.8081 (p) REVERT: B 415 GLU cc_start: 0.7526 (tp30) cc_final: 0.7206 (tp30) REVERT: B 454 ARG cc_start: 0.8164 (ttt-90) cc_final: 0.7772 (ttt90) REVERT: B 527 GLN cc_start: 0.7940 (tt0) cc_final: 0.7619 (tp40) REVERT: B 534 PHE cc_start: 0.8026 (m-80) cc_final: 0.7708 (m-80) REVERT: B 565 ASP cc_start: 0.7852 (t0) cc_final: 0.7238 (t0) REVERT: B 632 LYS cc_start: 0.8452 (mmmt) cc_final: 0.8223 (mtpp) REVERT: B 636 GLN cc_start: 0.8174 (tt0) cc_final: 0.7768 (tp-100) REVERT: B 649 LYS cc_start: 0.8513 (tptt) cc_final: 0.8312 (tptt) REVERT: B 674 GLU cc_start: 0.7626 (tt0) cc_final: 0.7405 (tt0) REVERT: B 687 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7866 (mmtm) REVERT: B 725 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.8011 (pp20) REVERT: B 726 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8883 (mp) REVERT: B 796 ARG cc_start: 0.8269 (mmm-85) cc_final: 0.8065 (mmt90) REVERT: B 830 THR cc_start: 0.8177 (m) cc_final: 0.7477 (p) REVERT: B 1018 GLU cc_start: 0.7882 (tt0) cc_final: 0.7374 (tt0) REVERT: B 1053 VAL cc_start: 0.7905 (t) cc_final: 0.7555 (p) REVERT: B 1094 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8005 (tm-30) outliers start: 57 outliers final: 46 residues processed: 389 average time/residue: 0.1548 time to fit residues: 83.0454 Evaluate side-chains 406 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 353 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 280 PHE 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 601 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 713 LYS Chi-restraints excluded: chain B residue 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 806 GLU Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 972 VAL Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1032 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 2.9990 chunk 124 optimal weight: 0.0070 chunk 104 optimal weight: 0.7980 chunk 107 optimal weight: 0.0670 chunk 161 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 116 optimal weight: 0.0060 chunk 36 optimal weight: 6.9990 overall best weight: 0.3152 ------------------------------------------------------------------------------- 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 681 GLN ** 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 827 HIS B 852 GLN B 917 GLN B 969 GLN B1027 ASN ** 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 = 0.4199 r_free = 0.4199 target = 0.169893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134664 restraints weight = 21143.415| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.52 r_work: 0.3578 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13844 Z= 0.138 Angle : 0.698 14.281 18837 Z= 0.347 Chirality : 0.042 0.289 2172 Planarity : 0.005 0.067 2249 Dihedral : 16.584 163.472 2121 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.89 % Allowed : 29.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.22), residues: 1551 helix: 1.33 (0.18), residues: 806 sheet: -0.66 (0.42), residues: 164 loop : -1.08 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 340 TYR 0.032 0.002 TYR B 236 PHE 0.028 0.002 PHE A 276 TRP 0.010 0.001 TRP B 807 HIS 0.006 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00310 (13844) covalent geometry : angle 0.69763 (18837) hydrogen bonds : bond 0.03950 ( 720) hydrogen bonds : angle 4.69143 ( 2016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3662.29 seconds wall clock time: 63 minutes 31.37 seconds (3811.37 seconds total)