Starting phenix.real_space_refine on Wed Aug 5 20:40:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oj6_16906/08_2026/8oj6_16906.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oj6_16906/08_2026/8oj6_16906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oj6_16906/08_2026/8oj6_16906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oj6_16906/08_2026/8oj6_16906.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oj6_16906/08_2026/8oj6_16906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oj6_16906/08_2026/8oj6_16906.map" } resolution = 2.41 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= 0.003 sd= 0.047 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 51 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 7271 2.51 5 N 2055 2.21 5 O 2224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11650 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8550 Classifications: {'peptide': 1085} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1031} Chain breaks: 2 Chain: "B" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2049 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 14, 'TRANS': 251} Chain breaks: 1 Chain: "C" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 455 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 590 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2, 'water': 4} Link IDs: {None: 5} Time building chain proxies: 1.91, per 1000 atoms: 0.16 Number of scatterers: 11650 At special positions: 0 Unit cell: (87.87, 115.14, 148.47, 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 47 16.00 P 51 15.00 Mg 2 11.99 O 2224 8.00 N 2055 7.00 C 7271 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: 0.96 Conformation dependent library (CDL) restraints added in 456.7 milliseconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2510 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 16 sheets defined 40.3% alpha, 22.8% beta 19 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 168 through 175 removed outlier: 3.647A pdb=" N ALA A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 220 through 234 Processing helix chain 'A' and resid 235 through 239 removed outlier: 4.608A pdb=" N SER A 239 " --> pdb=" O PRO A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.662A pdb=" N ASN A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 420 through 430 Processing helix chain 'A' and resid 442 through 458 Processing helix chain 'A' and resid 470 through 482 Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 559 through 565 Processing helix chain 'A' and resid 567 through 593 Processing helix chain 'A' and resid 593 through 606 Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 617 through 632 removed outlier: 3.631A pdb=" N VAL A 621 " --> pdb=" O GLN A 617 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A 631 " --> pdb=" O ARG A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 732 through 734 No H-bonds generated for 'chain 'A' and resid 732 through 734' Processing helix chain 'A' and resid 739 through 744 removed outlier: 3.596A pdb=" N ALA A 744 " --> pdb=" O ASP A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 790 Processing helix chain 'A' and resid 796 through 823 removed outlier: 3.852A pdb=" N LEU A 802 " --> pdb=" O GLU A 798 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 817 " --> pdb=" O VAL A 813 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TYR A 818 " --> pdb=" O CYS A 814 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY A 819 " --> pdb=" O ASN A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 Processing helix chain 'A' and resid 858 through 866 removed outlier: 3.536A pdb=" N ASP A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 870 Processing helix chain 'A' and resid 898 through 918 removed outlier: 3.578A pdb=" N LEU A 902 " --> pdb=" O THR A 898 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ALA A 904 " --> pdb=" O ALA A 900 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 959 Processing helix chain 'A' and resid 963 through 980 Processing helix chain 'A' and resid 980 through 991 removed outlier: 4.065A pdb=" N ALA A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 993 No H-bonds generated for 'chain 'A' and resid 992 through 993' Processing helix chain 'A' and resid 994 through 1000 Processing helix chain 'A' and resid 1004 through 1006 No H-bonds generated for 'chain 'A' and resid 1004 through 1006' Processing helix chain 'A' and resid 1007 through 1022 removed outlier: 3.687A pdb=" N THR A1022 " --> pdb=" O HIS A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1032 removed outlier: 3.509A pdb=" N VAL A1032 " --> pdb=" O GLN A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1044 removed outlier: 3.646A pdb=" N TYR A1044 " --> pdb=" O PRO A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1061 Processing helix chain 'A' and resid 1080 through 1089 removed outlier: 3.629A pdb=" N ALA A1088 " --> pdb=" O GLU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1141 Processing helix chain 'A' and resid 1145 through 1152 Processing helix chain 'A' and resid 1157 through 1174 Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1180 through 1190 Processing helix chain 'A' and resid 1199 through 1209 Processing helix chain 'A' and resid 1219 through 1235 removed outlier: 4.245A pdb=" N ASP A1232 " --> pdb=" O HIS A1228 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 48 Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 153 through 156 Processing helix chain 'B' and resid 181 through 192 Processing helix chain 'B' and resid 273 through 278 Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 79 Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 107 Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 329 removed outlier: 3.578A pdb=" N ASP A 151 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU A 187 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL A 149 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 293 removed outlier: 7.926A pdb=" N ILE A 635 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR A 256 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 436 through 440 removed outlier: 8.613A pdb=" N VAL A 436 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 409 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU A 438 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU A 411 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N PHE A 440 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER A 413 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 398 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL A 409 " --> pdb=" O CYS A 396 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N CYS A 396 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU A 411 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 394 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER A 413 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE A 392 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL A 391 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS A 372 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LYS A 363 " --> pdb=" O PHE A 461 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N THR A 463 " --> pdb=" O LYS A 363 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N MET A 365 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL A 462 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 499 through 502 Processing sheet with id=AA8, first strand: chain 'A' and resid 707 through 709 removed outlier: 5.176A pdb=" N CYS A 926 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASP A 717 " --> pdb=" O CYS A 926 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS A 928 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 884 " --> pdb=" O PHE A 891 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU A 893 " --> pdb=" O ILE A 882 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE A 882 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ARG A 895 " --> pdb=" O MET A 880 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N MET A 880 " --> pdb=" O ARG A 895 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 707 through 709 removed outlier: 3.851A pdb=" N LYS A 932 " --> pdb=" O VAL A 944 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS A 940 " --> pdb=" O ILE A 936 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AB2, first strand: chain 'A' and resid 1033 through 1036 Processing sheet with id=AB3, first strand: chain 'A' and resid 1212 through 1215 Processing sheet with id=AB4, first strand: chain 'B' and resid 31 through 36 removed outlier: 3.945A pdb=" N CYS B 31 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 31 through 36 removed outlier: 3.945A pdb=" N CYS B 31 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.683A pdb=" N VAL B 176 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR B 257 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 256 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ALA B 222 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLY B 258 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG B 224 " --> pdb=" O GLY B 258 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 101 through 102 529 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2636 1.33 - 1.46: 4109 1.46 - 1.59: 5107 1.59 - 1.72: 86 1.72 - 1.85: 70 Bond restraints: 12008 Sorted by residual: bond pdb=" N1 DC D 32 " pdb=" C6 DC D 32 " ideal model delta sigma weight residual 1.367 1.333 0.034 6.00e-03 2.78e+04 3.15e+01 bond pdb=" CG HIS A 912 " pdb=" CD2 HIS A 912 " ideal model delta sigma weight residual 1.354 1.302 0.052 1.10e-02 8.26e+03 2.24e+01 bond pdb=" CG HIS A 386 " pdb=" CD2 HIS A 386 " ideal model delta sigma weight residual 1.354 1.303 0.051 1.10e-02 8.26e+03 2.19e+01 bond pdb=" N1 DC D 35 " pdb=" C6 DC D 35 " ideal model delta sigma weight residual 1.367 1.341 0.026 6.00e-03 2.78e+04 1.88e+01 bond pdb=" C5 DG C 17 " pdb=" C6 DG C 17 " ideal model delta sigma weight residual 1.419 1.378 0.041 1.00e-02 1.00e+04 1.66e+01 ... (remaining 12003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 15492 2.58 - 5.15: 955 5.15 - 7.72: 51 7.72 - 10.30: 6 10.30 - 12.87: 4 Bond angle restraints: 16508 Sorted by residual: angle pdb=" N PRO A 920 " pdb=" CA PRO A 920 " pdb=" C PRO A 920 " ideal model delta sigma weight residual 110.70 123.57 -12.87 1.22e+00 6.72e-01 1.11e+02 angle pdb=" O2 DT D 33 " pdb=" C2 DT D 33 " pdb=" N3 DT D 33 " ideal model delta sigma weight residual 122.30 117.68 4.62 6.00e-01 2.78e+00 5.92e+01 angle pdb=" C ARG A 170 " pdb=" CA ARG A 170 " pdb=" CB ARG A 170 " ideal model delta sigma weight residual 110.68 100.37 10.31 1.70e+00 3.46e-01 3.68e+01 angle pdb=" CA PRO A 920 " pdb=" C PRO A 920 " pdb=" N PRO A 921 " ideal model delta sigma weight residual 117.93 125.08 -7.15 1.20e+00 6.94e-01 3.55e+01 angle pdb=" C PRO A 177 " pdb=" CA PRO A 177 " pdb=" CB PRO A 177 " ideal model delta sigma weight residual 111.56 121.35 -9.79 1.65e+00 3.67e-01 3.52e+01 ... (remaining 16503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 6762 35.87 - 71.74: 244 71.74 - 107.61: 12 107.61 - 143.48: 0 143.48 - 179.35: 3 Dihedral angle restraints: 7021 sinusoidal: 3116 harmonic: 3905 Sorted by residual: dihedral pdb=" CA ARG B 113 " pdb=" C ARG B 113 " pdb=" N ALA B 114 " pdb=" CA ALA B 114 " ideal model delta harmonic sigma weight residual -180.00 -149.34 -30.66 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA CYS B 272 " pdb=" C CYS B 272 " pdb=" N SER B 273 " pdb=" CA SER B 273 " ideal model delta harmonic sigma weight residual -180.00 -149.62 -30.38 0 5.00e+00 4.00e-02 3.69e+01 dihedral pdb=" CA VAL A 517 " pdb=" C VAL A 517 " pdb=" N ASN A 518 " pdb=" CA ASN A 518 " ideal model delta harmonic sigma weight residual -180.00 -152.39 -27.61 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 7018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1656 0.129 - 0.257: 194 0.257 - 0.386: 11 0.386 - 0.515: 0 0.515 - 0.643: 2 Chirality restraints: 1863 Sorted by residual: chirality pdb=" P DC D 20 " pdb=" OP1 DC D 20 " pdb=" OP2 DC D 20 " pdb=" O5' DC D 20 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P DC C 1 " pdb=" OP1 DC C 1 " pdb=" OP2 DC C 1 " pdb=" O5' DC C 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA PRO A 920 " pdb=" N PRO A 920 " pdb=" C PRO A 920 " pdb=" CB PRO A 920 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 1860 not shown) Planarity restraints: 1951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 330 " 0.411 9.50e-02 1.11e+02 1.84e-01 2.12e+01 pdb=" NE ARG A 330 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 330 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 330 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 330 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 611 " -0.369 9.50e-02 1.11e+02 1.66e-01 2.00e+01 pdb=" NE ARG A 611 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 611 " 0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG A 611 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 611 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA C 18 " -0.063 2.00e-02 2.50e+03 2.67e-02 1.95e+01 pdb=" N9 DA C 18 " 0.010 2.00e-02 2.50e+03 pdb=" C8 DA C 18 " 0.017 2.00e-02 2.50e+03 pdb=" N7 DA C 18 " 0.016 2.00e-02 2.50e+03 pdb=" C5 DA C 18 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DA C 18 " -0.007 2.00e-02 2.50e+03 pdb=" N6 DA C 18 " -0.032 2.00e-02 2.50e+03 pdb=" N1 DA C 18 " -0.014 2.00e-02 2.50e+03 pdb=" C2 DA C 18 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA C 18 " 0.033 2.00e-02 2.50e+03 pdb=" C4 DA C 18 " 0.027 2.00e-02 2.50e+03 ... (remaining 1948 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 284 2.69 - 3.24: 11192 3.24 - 3.79: 19080 3.79 - 4.35: 26050 4.35 - 4.90: 40937 Nonbonded interactions: 97543 Sorted by model distance: nonbonded pdb=" OE2 GLU A 370 " pdb=" CD1 ILE A 560 " model vdw 2.137 3.460 nonbonded pdb=" OD2 ASP A 888 " pdb=" O HOH A1401 " model vdw 2.168 3.040 nonbonded pdb=" N2 DG C 19 " pdb=" O2 DC D 30 " model vdw 2.282 3.120 nonbonded pdb=" N2 DG C 17 " pdb=" N3 DC D 32 " model vdw 2.339 2.560 nonbonded pdb=" NZ LYS B 289 " pdb=" OG1 THR B 302 " model vdw 2.349 3.120 ... (remaining 97538 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=1.00 max=1.00 mean=1.00 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: 2.300 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.980 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:8.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.076 12008 Z= 0.651 Angle : 1.347 12.875 16508 Z= 0.920 Chirality : 0.085 0.643 1863 Planarity : 0.014 0.184 1951 Dihedral : 17.113 179.345 4511 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 are not related in a simple way. whole: -1.01 (0.21), residues: 1341 helix: -0.89 (0.21), residues: 470 sheet: -0.45 (0.29), residues: 251 loop : -0.40 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG A 611 TYR 0.059 0.010 TYR A 490 PHE 0.050 0.008 PHE A1031 TRP 0.040 0.008 TRP A 502 HIS 0.027 0.004 HIS A 729 Details of bonding type rmsd/Z covalent geometry : bond 0.00950 / 0.65 (12008) covalent geometry : angle 1.34666 / 0.92 (16508) hydrogen bonds : bond 0.18837 / 13.07 ( 559) hydrogen bonds : angle 7.85865 / 5.61 ( 1522) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8927 (tt0) cc_final: 0.8241 (mp0) REVERT: A 228 MET cc_start: 0.8542 (mtm) cc_final: 0.8293 (mtm) REVERT: A 426 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8333 (tt0) REVERT: A 525 MET cc_start: 0.9197 (mmm) cc_final: 0.8908 (mmm) REVERT: A 552 LYS cc_start: 0.8226 (mmmt) cc_final: 0.7120 (pptt) REVERT: A 581 ASP cc_start: 0.8570 (m-30) cc_final: 0.8323 (t0) REVERT: A 700 ARG cc_start: 0.8243 (mtp85) cc_final: 0.8003 (mtt-85) REVERT: A 711 ASN cc_start: 0.9026 (m110) cc_final: 0.8822 (m110) REVERT: A 771 GLU cc_start: 0.8774 (tt0) cc_final: 0.8112 (pm20) REVERT: A 799 GLU cc_start: 0.7989 (tt0) cc_final: 0.7543 (tp30) REVERT: A 860 GLU cc_start: 0.7929 (tp30) cc_final: 0.7407 (mp0) REVERT: A 923 LYS cc_start: 0.9034 (tttp) cc_final: 0.8753 (tptp) REVERT: A 925 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8590 (mt-10) REVERT: A 927 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7498 (mp0) REVERT: A 950 MET cc_start: 0.8700 (tpp) cc_final: 0.8389 (ttm) REVERT: A 981 ASP cc_start: 0.8155 (m-30) cc_final: 0.7763 (t0) REVERT: A 1025 GLU cc_start: 0.8907 (tt0) cc_final: 0.8635 (tm-30) REVERT: A 1156 LEU cc_start: 0.8431 (mm) cc_final: 0.8109 (mt) REVERT: A 1185 GLU cc_start: 0.8287 (tt0) cc_final: 0.7755 (tp30) REVERT: B 85 GLN cc_start: 0.7495 (mm110) cc_final: 0.6993 (mt0) REVERT: B 101 LEU cc_start: 0.7937 (mt) cc_final: 0.7733 (mp) REVERT: B 121 ARG cc_start: 0.8528 (mmm-85) cc_final: 0.8144 (mmm160) REVERT: B 282 GLN cc_start: 0.6281 (mp10) cc_final: 0.6035 (mp-120) REVERT: B 313 PHE cc_start: 0.6783 (m-80) cc_final: 0.6258 (m-80) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.7582 time to fit residues: 148.0543 Evaluate side-chains 125 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN B 69 HIS B 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.140646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.108173 restraints weight = 17582.008| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.72 r_work: 0.3350 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12008 Z= 0.187 Angle : 0.707 8.417 16508 Z= 0.389 Chirality : 0.049 0.346 1863 Planarity : 0.005 0.059 1951 Dihedral : 18.745 168.156 2040 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.69 % Allowed : 10.17 % Favored : 88.14 % 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 are not related in a simple way. whole: -0.07 (0.22), residues: 1341 helix: 0.49 (0.23), residues: 481 sheet: -0.40 (0.30), residues: 251 loop : -0.16 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 182 TYR 0.019 0.002 TYR A 483 PHE 0.025 0.002 PHE A 444 TRP 0.017 0.002 TRP A 502 HIS 0.007 0.001 HIS A 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (12008) covalent geometry : angle 0.70682 / 0.39 (16508) hydrogen bonds : bond 0.05985 / 4.19 ( 559) hydrogen bonds : angle 5.67530 / 3.98 ( 1522) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8608 (tt0) cc_final: 0.8350 (mp0) REVERT: A 525 MET cc_start: 0.9213 (mmm) cc_final: 0.9012 (mmm) REVERT: A 700 ARG cc_start: 0.7890 (mtp85) cc_final: 0.7657 (mtt-85) REVERT: A 711 ASN cc_start: 0.8975 (m110) cc_final: 0.8772 (m110) REVERT: A 771 GLU cc_start: 0.8392 (tt0) cc_final: 0.7937 (pm20) REVERT: A 799 GLU cc_start: 0.7596 (tt0) cc_final: 0.7331 (tp30) REVERT: A 925 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8195 (mt-10) REVERT: A 1156 LEU cc_start: 0.8468 (mm) cc_final: 0.8060 (mt) REVERT: B 81 LEU cc_start: 0.6712 (mt) cc_final: 0.6457 (mp) REVERT: B 85 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6653 (mt0) REVERT: B 108 LEU cc_start: 0.7184 (mt) cc_final: 0.6973 (mt) REVERT: B 122 ARG cc_start: 0.6141 (OUTLIER) cc_final: 0.5908 (ttp-170) outliers start: 19 outliers final: 4 residues processed: 139 average time/residue: 0.7867 time to fit residues: 116.5471 Evaluate side-chains 115 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain B residue 122 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.141170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.108856 restraints weight = 17789.087| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.73 r_work: 0.3366 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12008 Z= 0.152 Angle : 0.627 7.852 16508 Z= 0.346 Chirality : 0.045 0.314 1863 Planarity : 0.005 0.057 1951 Dihedral : 18.575 156.405 2040 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.25 % Allowed : 11.95 % Favored : 86.80 % 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 are not related in a simple way. whole: 0.15 (0.22), residues: 1341 helix: 0.90 (0.24), residues: 481 sheet: -0.54 (0.30), residues: 255 loop : -0.11 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 182 TYR 0.016 0.002 TYR A 281 PHE 0.020 0.002 PHE A 444 TRP 0.015 0.002 TRP A 502 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (12008) covalent geometry : angle 0.62668 / 0.35 (16508) hydrogen bonds : bond 0.05255 / 3.61 ( 559) hydrogen bonds : angle 5.27630 / 3.69 ( 1522) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8670 (tt0) cc_final: 0.8381 (mp0) REVERT: A 234 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7648 (pm20) REVERT: A 552 LYS cc_start: 0.8228 (mmmt) cc_final: 0.7768 (pptt) REVERT: A 771 GLU cc_start: 0.8435 (tt0) cc_final: 0.7895 (pm20) REVERT: B 85 GLN cc_start: 0.7377 (mm-40) cc_final: 0.6872 (mt0) REVERT: B 159 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8511 (tptp) outliers start: 14 outliers final: 3 residues processed: 127 average time/residue: 0.7541 time to fit residues: 102.7025 Evaluate side-chains 106 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 314 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 118 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 711 ASN B 69 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.139622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.107874 restraints weight = 17688.564| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.93 r_work: 0.3321 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12008 Z= 0.212 Angle : 0.656 7.200 16508 Z= 0.360 Chirality : 0.046 0.314 1863 Planarity : 0.005 0.056 1951 Dihedral : 18.612 156.548 2040 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.68 % Allowed : 12.40 % Favored : 84.92 % 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 are not related in a simple way. whole: 0.12 (0.22), residues: 1341 helix: 0.94 (0.24), residues: 481 sheet: -0.57 (0.30), residues: 250 loop : -0.20 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 126 TYR 0.019 0.002 TYR A 483 PHE 0.021 0.002 PHE B 213 TRP 0.019 0.002 TRP A 502 HIS 0.006 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (12008) covalent geometry : angle 0.65597 / 0.36 (16508) hydrogen bonds : bond 0.05605 / 3.87 ( 559) hydrogen bonds : angle 5.26520 / 3.69 ( 1522) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8285 (mmmt) REVERT: A 210 GLU cc_start: 0.8801 (tt0) cc_final: 0.8420 (mp0) REVERT: A 234 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7603 (pm20) REVERT: A 291 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8495 (ttpt) REVERT: A 552 LYS cc_start: 0.8225 (mmmt) cc_final: 0.7789 (pptt) REVERT: A 771 GLU cc_start: 0.8502 (tt0) cc_final: 0.7934 (pm20) REVERT: B 36 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7060 (pt0) REVERT: B 85 GLN cc_start: 0.7419 (mm-40) cc_final: 0.6812 (mt0) outliers start: 30 outliers final: 11 residues processed: 123 average time/residue: 0.7556 time to fit residues: 99.7431 Evaluate side-chains 115 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1170 CYS Chi-restraints excluded: chain A residue 1188 LEU Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 274 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 137 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 745 HIS B 69 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.137882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104963 restraints weight = 17616.267| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.73 r_work: 0.3298 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 12008 Z= 0.311 Angle : 0.759 8.196 16508 Z= 0.409 Chirality : 0.051 0.314 1863 Planarity : 0.006 0.078 1951 Dihedral : 18.746 162.219 2040 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.48 % Allowed : 12.49 % Favored : 84.03 % 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 are not related in a simple way. whole: -0.11 (0.22), residues: 1341 helix: 0.65 (0.24), residues: 487 sheet: -0.66 (0.30), residues: 251 loop : -0.26 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 126 TYR 0.022 0.003 TYR A 483 PHE 0.024 0.003 PHE A 590 TRP 0.022 0.003 TRP A 502 HIS 0.009 0.002 HIS A 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00713 / 0.31 (12008) covalent geometry : angle 0.75908 / 0.41 (16508) hydrogen bonds : bond 0.06564 / 4.57 ( 559) hydrogen bonds : angle 5.48731 / 3.86 ( 1522) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7655 (tpm170) REVERT: A 228 MET cc_start: 0.8422 (mtm) cc_final: 0.8209 (mtm) REVERT: A 234 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: A 512 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.6904 (ptm-80) REVERT: A 552 LYS cc_start: 0.8287 (mmmt) cc_final: 0.7646 (pptt) REVERT: A 739 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8036 (mtp85) REVERT: A 771 GLU cc_start: 0.8453 (tt0) cc_final: 0.7970 (pm20) REVERT: A 882 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8596 (mt) REVERT: A 950 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7541 (ttm) REVERT: B 85 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7015 (mt0) REVERT: B 88 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6368 (ttm170) outliers start: 39 outliers final: 14 residues processed: 139 average time/residue: 0.7181 time to fit residues: 106.9452 Evaluate side-chains 126 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 739 ARG Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1170 CYS Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 314 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 861 GLN B 69 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.139646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.107016 restraints weight = 17556.490| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.71 r_work: 0.3337 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12008 Z= 0.177 Angle : 0.629 6.969 16508 Z= 0.346 Chirality : 0.045 0.323 1863 Planarity : 0.005 0.040 1951 Dihedral : 18.569 161.401 2040 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.59 % Allowed : 13.92 % Favored : 83.50 % 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 are not related in a simple way. whole: 0.08 (0.22), residues: 1341 helix: 0.97 (0.24), residues: 482 sheet: -0.66 (0.30), residues: 250 loop : -0.25 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1026 TYR 0.017 0.002 TYR A 281 PHE 0.017 0.002 PHE A 444 TRP 0.018 0.002 TRP A 502 HIS 0.004 0.001 HIS A 729 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (12008) covalent geometry : angle 0.62939 / 0.35 (16508) hydrogen bonds : bond 0.05115 / 3.55 ( 559) hydrogen bonds : angle 5.24908 / 3.67 ( 1522) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8386 (mmmt) cc_final: 0.8177 (mmmm) REVERT: A 222 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7484 (tpm170) REVERT: A 234 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7603 (pm20) REVERT: A 552 LYS cc_start: 0.8299 (mmmt) cc_final: 0.7713 (pptt) REVERT: A 739 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7946 (mtp85) REVERT: A 771 GLU cc_start: 0.8436 (tt0) cc_final: 0.7882 (pm20) REVERT: A 950 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7540 (ttm) REVERT: B 85 GLN cc_start: 0.7640 (mm-40) cc_final: 0.6980 (mt0) REVERT: B 88 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.6238 (ttm110) outliers start: 29 outliers final: 12 residues processed: 134 average time/residue: 0.6502 time to fit residues: 93.4794 Evaluate side-chains 122 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 739 ARG Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1170 CYS Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 313 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 16 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 861 GLN B 69 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.139113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.106508 restraints weight = 17601.071| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.71 r_work: 0.3327 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12008 Z= 0.202 Angle : 0.647 7.246 16508 Z= 0.353 Chirality : 0.046 0.323 1863 Planarity : 0.005 0.050 1951 Dihedral : 18.568 161.488 2040 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.12 % Allowed : 13.92 % Favored : 82.96 % 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 are not related in a simple way. whole: 0.00 (0.22), residues: 1341 helix: 0.92 (0.24), residues: 488 sheet: -0.85 (0.30), residues: 260 loop : -0.23 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 126 TYR 0.017 0.002 TYR A 483 PHE 0.018 0.002 PHE A 590 TRP 0.018 0.002 TRP A 502 HIS 0.005 0.001 HIS A 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (12008) covalent geometry : angle 0.64667 / 0.35 (16508) hydrogen bonds : bond 0.05352 / 3.70 ( 559) hydrogen bonds : angle 5.22624 / 3.67 ( 1522) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7481 (tpm170) REVERT: A 234 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: A 330 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8177 (mtt180) REVERT: A 552 LYS cc_start: 0.8307 (mmmt) cc_final: 0.7767 (pptt) REVERT: A 771 GLU cc_start: 0.8409 (tt0) cc_final: 0.8003 (pm20) REVERT: A 868 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7064 (pm20) REVERT: A 908 LYS cc_start: 0.8531 (mttt) cc_final: 0.8329 (mmmm) REVERT: A 950 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7490 (ttm) REVERT: B 85 GLN cc_start: 0.7639 (mm-40) cc_final: 0.6994 (mt0) outliers start: 35 outliers final: 14 residues processed: 134 average time/residue: 0.5649 time to fit residues: 81.2799 Evaluate side-chains 125 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1170 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 314 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 123 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 18 optimal weight: 0.0570 chunk 74 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 99 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 861 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.140791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.108507 restraints weight = 17639.757| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.70 r_work: 0.3360 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12008 Z= 0.142 Angle : 0.596 7.890 16508 Z= 0.327 Chirality : 0.044 0.327 1863 Planarity : 0.004 0.040 1951 Dihedral : 18.449 160.247 2040 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.16 % Favored : 97.76 % Rotamer: Outliers : 2.14 % Allowed : 15.43 % Favored : 82.43 % 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 are not related in a simple way. whole: 0.21 (0.23), residues: 1341 helix: 1.17 (0.24), residues: 483 sheet: -0.90 (0.29), residues: 266 loop : -0.08 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 179 TYR 0.017 0.002 TYR A 281 PHE 0.015 0.001 PHE A 444 TRP 0.010 0.001 TRP A 502 HIS 0.004 0.001 HIS A 912 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (12008) covalent geometry : angle 0.59560 / 0.33 (16508) hydrogen bonds : bond 0.04569 / 3.16 ( 559) hydrogen bonds : angle 5.04737 / 3.53 ( 1522) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7567 (pm20) REVERT: A 552 LYS cc_start: 0.8395 (mmmt) cc_final: 0.7720 (pptt) REVERT: A 739 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7864 (mtp85) REVERT: A 771 GLU cc_start: 0.8371 (tt0) cc_final: 0.7946 (pm20) REVERT: A 868 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7137 (pm20) REVERT: A 908 LYS cc_start: 0.8500 (mttt) cc_final: 0.8300 (mmmm) REVERT: A 950 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7529 (ttm) REVERT: B 85 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7067 (mt0) outliers start: 24 outliers final: 16 residues processed: 129 average time/residue: 0.6944 time to fit residues: 96.3622 Evaluate side-chains 131 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 739 ARG Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1170 CYS Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 313 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 109 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.140218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.108610 restraints weight = 17490.116| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.69 r_work: 0.3348 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12008 Z= 0.170 Angle : 0.616 7.836 16508 Z= 0.336 Chirality : 0.045 0.327 1863 Planarity : 0.005 0.041 1951 Dihedral : 18.448 159.778 2040 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.24 % Favored : 97.69 % Rotamer: Outliers : 2.23 % Allowed : 15.43 % Favored : 82.34 % 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 are not related in a simple way. whole: 0.21 (0.23), residues: 1341 helix: 1.20 (0.24), residues: 485 sheet: -1.02 (0.29), residues: 271 loop : -0.02 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 179 TYR 0.017 0.002 TYR A 281 PHE 0.016 0.002 PHE A 444 TRP 0.012 0.002 TRP A 502 HIS 0.004 0.001 HIS A 729 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (12008) covalent geometry : angle 0.61606 / 0.34 (16508) hydrogen bonds : bond 0.04834 / 3.33 ( 559) hydrogen bonds : angle 5.03906 / 3.53 ( 1522) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7601 (pm20) REVERT: A 330 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8136 (mtt180) REVERT: A 552 LYS cc_start: 0.8391 (mmmt) cc_final: 0.7744 (pptt) REVERT: A 771 GLU cc_start: 0.8379 (tt0) cc_final: 0.7972 (pm20) REVERT: A 868 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7142 (pm20) REVERT: A 908 LYS cc_start: 0.8507 (mttt) cc_final: 0.8296 (mmmm) REVERT: A 950 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7518 (ttm) REVERT: B 85 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7143 (mt0) outliers start: 25 outliers final: 14 residues processed: 125 average time/residue: 0.7050 time to fit residues: 94.6610 Evaluate side-chains 125 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1170 CYS Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 313 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 28 optimal weight: 0.3980 chunk 54 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1197 HIS B 282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.139897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.108323 restraints weight = 17719.338| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.72 r_work: 0.3339 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12008 Z= 0.184 Angle : 0.631 8.468 16508 Z= 0.343 Chirality : 0.045 0.328 1863 Planarity : 0.005 0.042 1951 Dihedral : 18.467 159.329 2040 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.39 % Favored : 97.54 % Rotamer: Outliers : 1.87 % Allowed : 15.61 % Favored : 82.52 % 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 are not related in a simple way. whole: 0.21 (0.23), residues: 1341 helix: 1.18 (0.24), residues: 484 sheet: -0.98 (0.29), residues: 267 loop : -0.03 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 179 TYR 0.019 0.002 TYR A 281 PHE 0.016 0.002 PHE A 590 TRP 0.020 0.002 TRP A 502 HIS 0.005 0.001 HIS A 729 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (12008) covalent geometry : angle 0.63137 / 0.34 (16508) hydrogen bonds : bond 0.04974 / 3.43 ( 559) hydrogen bonds : angle 5.05845 / 3.55 ( 1522) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8145 (mtt180) REVERT: A 552 LYS cc_start: 0.8401 (mmmt) cc_final: 0.7750 (pptt) REVERT: A 771 GLU cc_start: 0.8461 (tt0) cc_final: 0.7975 (pm20) REVERT: A 868 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7065 (pm20) REVERT: A 908 LYS cc_start: 0.8541 (mttt) cc_final: 0.8331 (mmmm) REVERT: A 950 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7543 (ttm) REVERT: B 85 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7140 (mt0) outliers start: 21 outliers final: 16 residues processed: 121 average time/residue: 0.6533 time to fit residues: 85.0092 Evaluate side-chains 123 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1170 CYS Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 313 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 94 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.140195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.108601 restraints weight = 17638.585| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.73 r_work: 0.3340 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12008 Z= 0.168 Angle : 0.620 8.264 16508 Z= 0.337 Chirality : 0.045 0.330 1863 Planarity : 0.005 0.041 1951 Dihedral : 18.435 158.546 2040 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.31 % Favored : 97.61 % Rotamer: Outliers : 1.87 % Allowed : 15.97 % Favored : 82.16 % 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 are not related in a simple way. whole: 0.25 (0.23), residues: 1341 helix: 1.22 (0.24), residues: 485 sheet: -0.97 (0.29), residues: 267 loop : -0.02 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 92 TYR 0.019 0.002 TYR A 281 PHE 0.015 0.002 PHE A 444 TRP 0.015 0.002 TRP A 502 HIS 0.004 0.001 HIS A 912 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (12008) covalent geometry : angle 0.62011 / 0.34 (16508) hydrogen bonds : bond 0.04799 / 3.31 ( 559) hydrogen bonds : angle 5.01760 / 3.52 ( 1522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5476.59 seconds wall clock time: 93 minutes 44.91 seconds (5624.91 seconds total)