Starting phenix.real_space_refine on Sat Aug 23 11:15:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oj6_16906/08_2025/8oj6_16906.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oj6_16906/08_2025/8oj6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8oj6_16906/08_2025/8oj6_16906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oj6_16906/08_2025/8oj6_16906.map" model { file = "/net/cci-nas-00/data/ceres_data/8oj6_16906/08_2025/8oj6_16906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oj6_16906/08_2025/8oj6_16906.cif" } 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-2.0-5787/lib/python3.9/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: 2.91, per 1000 atoms: 0.25 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: 0.91 Conformation dependent library (CDL) restraints added in 574.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.69 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: 2.96 Time building geometry restraints manager: 1.27 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=" 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=" C ASN A 307 " pdb=" O ASN A 307 " ideal model delta sigma weight residual 1.246 1.211 0.035 9.20e-03 1.18e+04 1.44e+01 bond pdb=" CA SER A 513 " pdb=" CB SER A 513 " ideal model delta sigma weight residual 1.529 1.466 0.062 1.66e-02 3.63e+03 1.42e+01 bond pdb=" CA ALA A1035 " pdb=" CB ALA A1035 " ideal model delta sigma weight residual 1.534 1.473 0.061 1.78e-02 3.16e+03 1.16e+01 ... (remaining 12003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 15470 2.58 - 5.15: 977 5.15 - 7.72: 52 7.72 - 10.30: 5 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=" O3' DC D 35 " pdb=" P DA D 36 " pdb=" O5' DA D 36 " ideal model delta sigma weight residual 104.00 94.22 9.78 1.50e+00 4.44e-01 4.25e+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 - 0.127: 1654 0.127 - 0.253: 195 0.253 - 0.380: 12 0.380 - 0.506: 0 0.506 - 0.633: 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 2.35 -2.98 -0.63 2.00e-01 2.50e+01 1.00e+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 2.35 -2.97 -0.63 2.00e-01 2.50e+01 9.87e+00 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: 2.010 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.620 Find NCS groups from input model: 0.050 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 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 : 0.009 0.076 12008 Z= 0.600 Angle : 1.351 12.875 16508 Z= 0.888 Chirality : 0.084 0.633 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 aren 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 covalent geometry : bond 0.00938 (12008) covalent geometry : angle 1.35139 (16508) hydrogen bonds : bond 0.18837 ( 559) hydrogen bonds : angle 7.85865 ( 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 : 0.261 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: 0.7407 time to fit residues: 144.1384 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 : 0.430 ------------------------------------------------------------------------------- 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: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4028 r_free = 0.4028 target = 0.140769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.108190 restraints weight = 17579.717| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.72 r_work: 0.3354 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12008 Z= 0.183 Angle : 0.664 8.041 16508 Z= 0.365 Chirality : 0.044 0.204 1863 Planarity : 0.005 0.040 1951 Dihedral : 18.612 175.699 2040 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.43 % Allowed : 10.17 % Favored : 88.40 % 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: 0.04 (0.22), residues: 1341 helix: 0.60 (0.23), residues: 481 sheet: -0.37 (0.29), residues: 259 loop : -0.11 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 182 TYR 0.017 0.002 TYR A 483 PHE 0.023 0.002 PHE A 444 TRP 0.012 0.002 TRP A 502 HIS 0.007 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00403 (12008) covalent geometry : angle 0.66386 (16508) hydrogen bonds : bond 0.05701 ( 559) hydrogen bonds : angle 5.52718 ( 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 139 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8650 (tt0) cc_final: 0.8353 (mp0) REVERT: A 228 MET cc_start: 0.8405 (mtm) cc_final: 0.8193 (mtm) REVERT: A 496 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7595 (mtm-85) REVERT: A 525 MET cc_start: 0.9233 (mmm) cc_final: 0.9033 (mmm) REVERT: A 552 LYS cc_start: 0.8186 (mmmt) cc_final: 0.7772 (pptt) REVERT: A 700 ARG cc_start: 0.8000 (mtp85) cc_final: 0.7729 (mtt-85) REVERT: A 771 GLU cc_start: 0.8404 (tt0) cc_final: 0.7923 (pm20) REVERT: A 923 LYS cc_start: 0.8995 (tttp) cc_final: 0.8763 (tptp) REVERT: A 1156 LEU cc_start: 0.8446 (mm) cc_final: 0.8047 (mt) REVERT: B 85 GLN cc_start: 0.7239 (mm-40) cc_final: 0.6724 (mt0) REVERT: B 108 LEU cc_start: 0.7309 (mt) cc_final: 0.7078 (mt) outliers start: 16 outliers final: 3 residues processed: 135 average time/residue: 0.7774 time to fit residues: 111.7343 Evaluate side-chains 113 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain B residue 213 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4008 r_free = 0.4008 target = 0.139315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.106641 restraints weight = 17709.525| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.74 r_work: 0.3327 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12008 Z= 0.234 Angle : 0.668 8.028 16508 Z= 0.363 Chirality : 0.045 0.197 1863 Planarity : 0.005 0.062 1951 Dihedral : 18.627 174.321 2040 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.32 % Allowed : 11.78 % Favored : 85.91 % 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: 0.12 (0.22), residues: 1341 helix: 0.83 (0.24), residues: 481 sheet: -0.48 (0.30), residues: 250 loop : -0.15 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 121 TYR 0.020 0.002 TYR A 483 PHE 0.021 0.002 PHE A 444 TRP 0.018 0.002 TRP A 502 HIS 0.007 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00532 (12008) covalent geometry : angle 0.66838 (16508) hydrogen bonds : bond 0.05749 ( 559) hydrogen bonds : angle 5.37826 ( 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 142 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8750 (tt0) cc_final: 0.8384 (mp0) REVERT: A 222 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7514 (tpm170) REVERT: A 234 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: A 291 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8451 (ttpt) REVERT: A 552 LYS cc_start: 0.8246 (mmmt) cc_final: 0.7642 (pptt) REVERT: A 771 GLU cc_start: 0.8451 (tt0) cc_final: 0.7945 (pm20) REVERT: B 85 GLN cc_start: 0.7477 (mm-40) cc_final: 0.6892 (mt0) REVERT: B 213 PHE cc_start: 0.5815 (p90) cc_final: 0.5456 (p90) outliers start: 26 outliers final: 6 residues processed: 132 average time/residue: 0.8216 time to fit residues: 115.4926 Evaluate side-chains 110 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 291 LYS Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 212 VAL 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: 0.9980 chunk 18 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.140404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.107945 restraints weight = 17627.494| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.70 r_work: 0.3347 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12008 Z= 0.173 Angle : 0.603 8.107 16508 Z= 0.329 Chirality : 0.043 0.199 1863 Planarity : 0.005 0.040 1951 Dihedral : 18.469 172.974 2040 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.05 % Allowed : 12.93 % Favored : 85.01 % 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: 0.25 (0.23), residues: 1341 helix: 1.07 (0.24), residues: 482 sheet: -0.59 (0.29), residues: 257 loop : -0.08 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 179 TYR 0.016 0.002 TYR A 483 PHE 0.018 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 covalent geometry : bond 0.00390 (12008) covalent geometry : angle 0.60317 (16508) hydrogen bonds : bond 0.04863 ( 559) hydrogen bonds : angle 5.14172 ( 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 136 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8742 (tt0) cc_final: 0.8389 (mp0) REVERT: A 234 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: A 496 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7650 (mtm-85) REVERT: A 552 LYS cc_start: 0.8268 (mmmt) cc_final: 0.7666 (pptt) REVERT: A 771 GLU cc_start: 0.8374 (tt0) cc_final: 0.7899 (pm20) REVERT: B 85 GLN cc_start: 0.7448 (mm-40) cc_final: 0.6853 (mt0) REVERT: B 158 MET cc_start: 0.8134 (ttt) cc_final: 0.7882 (tpp) REVERT: B 182 ARG cc_start: 0.5051 (tpt-90) cc_final: 0.4808 (tpt-90) REVERT: B 213 PHE cc_start: 0.5747 (p90) cc_final: 0.5393 (p90) outliers start: 23 outliers final: 7 residues processed: 130 average time/residue: 0.7299 time to fit residues: 101.8650 Evaluate side-chains 115 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 496 ARG Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 1156 LEU 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 313 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 137 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1197 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 = 0.3999 r_free = 0.3999 target = 0.138726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.106918 restraints weight = 17581.016| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.71 r_work: 0.3314 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 12008 Z= 0.255 Angle : 0.672 8.073 16508 Z= 0.363 Chirality : 0.045 0.200 1863 Planarity : 0.005 0.066 1951 Dihedral : 18.590 172.493 2040 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.85 % Allowed : 12.76 % Favored : 84.39 % 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: 0.18 (0.22), residues: 1341 helix: 0.98 (0.24), residues: 482 sheet: -0.61 (0.30), residues: 251 loop : -0.12 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 126 TYR 0.019 0.002 TYR A 483 PHE 0.021 0.002 PHE A 590 TRP 0.019 0.002 TRP A 502 HIS 0.008 0.001 HIS A 386 Details of bonding type rmsd covalent geometry : bond 0.00593 (12008) covalent geometry : angle 0.67204 (16508) hydrogen bonds : bond 0.05631 ( 559) hydrogen bonds : angle 5.28338 ( 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 149 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7728 (tpm170) REVERT: A 234 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: A 291 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8463 (ttpt) REVERT: A 552 LYS cc_start: 0.8305 (mmmt) cc_final: 0.7720 (pptt) REVERT: A 771 GLU cc_start: 0.8474 (tt0) cc_final: 0.7914 (pm20) REVERT: A 950 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7593 (ttm) REVERT: B 85 GLN cc_start: 0.7618 (mm-40) cc_final: 0.6965 (mt0) REVERT: B 213 PHE cc_start: 0.5668 (p90) cc_final: 0.5375 (p90) outliers start: 32 outliers final: 14 residues processed: 142 average time/residue: 0.7227 time to fit residues: 109.9667 Evaluate side-chains 122 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 291 LYS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 801 VAL 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 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 212 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 313 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 GLN ** B 69 HIS ** 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 = 0.4017 r_free = 0.4017 target = 0.139965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.108388 restraints weight = 17544.184| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.72 r_work: 0.3340 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12008 Z= 0.178 Angle : 0.607 8.095 16508 Z= 0.330 Chirality : 0.043 0.200 1863 Planarity : 0.005 0.039 1951 Dihedral : 18.454 170.792 2040 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.94 % Allowed : 13.65 % Favored : 83.41 % 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: 0.25 (0.23), residues: 1341 helix: 1.12 (0.24), residues: 483 sheet: -0.70 (0.30), residues: 256 loop : -0.09 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 179 TYR 0.016 0.002 TYR A 281 PHE 0.017 0.002 PHE A 444 TRP 0.017 0.002 TRP A 502 HIS 0.004 0.001 HIS A 912 Details of bonding type rmsd covalent geometry : bond 0.00405 (12008) covalent geometry : angle 0.60672 (16508) hydrogen bonds : bond 0.04823 ( 559) hydrogen bonds : angle 5.12943 ( 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: 33 poor density : 109 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7568 (pm20) REVERT: A 291 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8439 (ttpt) REVERT: A 330 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8897 (mtt180) REVERT: A 545 GLU cc_start: 0.8091 (tt0) cc_final: 0.7861 (tt0) REVERT: A 552 LYS cc_start: 0.8297 (mmmt) cc_final: 0.7720 (pptt) REVERT: A 771 GLU cc_start: 0.8417 (tt0) cc_final: 0.7860 (pm20) REVERT: A 950 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7565 (ttm) REVERT: B 85 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7026 (mt0) REVERT: B 213 PHE cc_start: 0.5609 (p90) cc_final: 0.5329 (p90) outliers start: 33 outliers final: 14 residues processed: 133 average time/residue: 0.7217 time to fit residues: 102.9797 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 : 0.298 ------------------------------------------------------------------------------- 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 291 LYS Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 801 VAL 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 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 212 VAL Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 314 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 16 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.139893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.108206 restraints weight = 17600.037| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.72 r_work: 0.3337 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12008 Z= 0.182 Angle : 0.608 8.052 16508 Z= 0.329 Chirality : 0.043 0.201 1863 Planarity : 0.005 0.042 1951 Dihedral : 18.419 168.896 2040 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.59 % Allowed : 14.63 % Favored : 82.78 % 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: 0.23 (0.23), residues: 1341 helix: 1.15 (0.24), residues: 483 sheet: -0.89 (0.29), residues: 265 loop : -0.03 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 179 TYR 0.016 0.002 TYR A 281 PHE 0.016 0.002 PHE A 444 TRP 0.017 0.002 TRP A 502 HIS 0.004 0.001 HIS A 729 Details of bonding type rmsd covalent geometry : bond 0.00416 (12008) covalent geometry : angle 0.60752 (16508) hydrogen bonds : bond 0.04844 ( 559) hydrogen bonds : angle 5.07077 ( 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 134 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: A 291 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8444 (ttpt) REVERT: A 330 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8164 (mtt180) REVERT: A 552 LYS cc_start: 0.8335 (mmmt) cc_final: 0.7686 (pptt) REVERT: A 739 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7913 (mtp85) REVERT: A 771 GLU cc_start: 0.8393 (tt0) cc_final: 0.7947 (pm20) REVERT: A 950 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7591 (ttm) REVERT: B 85 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7169 (mt0) REVERT: B 213 PHE cc_start: 0.5506 (p90) cc_final: 0.5253 (p90) outliers start: 29 outliers final: 13 residues processed: 130 average time/residue: 0.6713 time to fit residues: 93.6038 Evaluate side-chains 119 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 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 A residue 291 LYS Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 739 ARG Chi-restraints excluded: chain A residue 801 VAL 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 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 212 VAL Chi-restraints excluded: chain B residue 267 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 123 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 99 optimal weight: 0.9980 chunk 62 optimal weight: 0.2980 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.140623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.108974 restraints weight = 17599.839| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.73 r_work: 0.3350 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3242 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= 0.156 Angle : 0.588 7.939 16508 Z= 0.318 Chirality : 0.042 0.200 1863 Planarity : 0.005 0.039 1951 Dihedral : 18.329 164.098 2040 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.01 % Favored : 97.91 % Rotamer: Outliers : 2.41 % Allowed : 14.36 % Favored : 83.23 % 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 (0.23), residues: 1341 helix: 1.27 (0.24), residues: 485 sheet: -0.96 (0.29), residues: 267 loop : 0.05 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 179 TYR 0.017 0.002 TYR A 281 PHE 0.015 0.002 PHE A 444 TRP 0.010 0.001 TRP A 502 HIS 0.004 0.001 HIS A 912 Details of bonding type rmsd covalent geometry : bond 0.00354 (12008) covalent geometry : angle 0.58822 (16508) hydrogen bonds : bond 0.04498 ( 559) hydrogen bonds : angle 4.98500 ( 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 134 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7539 (pm20) REVERT: A 291 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8435 (ttpt) REVERT: A 545 GLU cc_start: 0.8073 (tt0) cc_final: 0.7832 (tt0) REVERT: A 552 LYS cc_start: 0.8340 (mmmt) cc_final: 0.7702 (pptt) REVERT: A 739 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7887 (mtp85) REVERT: A 771 GLU cc_start: 0.8408 (tt0) cc_final: 0.7947 (pm20) REVERT: A 868 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6981 (pm20) REVERT: A 950 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7554 (ttm) REVERT: B 85 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7154 (mt0) REVERT: B 158 MET cc_start: 0.8120 (ttt) cc_final: 0.7874 (tpp) REVERT: B 213 PHE cc_start: 0.5412 (p90) cc_final: 0.5196 (p90) outliers start: 27 outliers final: 13 residues processed: 127 average time/residue: 0.6220 time to fit residues: 84.6540 Evaluate side-chains 121 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 291 LYS Chi-restraints excluded: chain A residue 739 ARG Chi-restraints excluded: chain A residue 801 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 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 181 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: 1.9990 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 91 optimal weight: 0.0770 chunk 49 optimal weight: 0.0570 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.141473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.110640 restraints weight = 17574.732| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.69 r_work: 0.3372 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12008 Z= 0.136 Angle : 0.568 7.892 16508 Z= 0.307 Chirality : 0.041 0.207 1863 Planarity : 0.004 0.041 1951 Dihedral : 18.155 152.256 2040 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.01 % Favored : 97.91 % Rotamer: Outliers : 1.87 % Allowed : 15.43 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.43 (0.23), residues: 1341 helix: 1.37 (0.24), residues: 485 sheet: -0.89 (0.29), residues: 267 loop : 0.09 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 179 TYR 0.016 0.001 TYR A 281 PHE 0.014 0.001 PHE A 444 TRP 0.008 0.001 TRP A 502 HIS 0.004 0.001 HIS A 912 Details of bonding type rmsd covalent geometry : bond 0.00304 (12008) covalent geometry : angle 0.56772 (16508) hydrogen bonds : bond 0.04182 ( 559) hydrogen bonds : angle 4.86024 ( 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 126 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: A 552 LYS cc_start: 0.8322 (mmmt) cc_final: 0.7724 (pptt) REVERT: A 739 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7976 (mtp85) REVERT: A 771 GLU cc_start: 0.8342 (tt0) cc_final: 0.7949 (pm20) REVERT: A 868 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7000 (pm20) REVERT: A 950 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7548 (ttm) REVERT: B 85 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7272 (mt0) REVERT: B 158 MET cc_start: 0.8134 (ttt) cc_final: 0.7850 (tpp) REVERT: B 213 PHE cc_start: 0.5485 (p90) cc_final: 0.5277 (p90) outliers start: 21 outliers final: 13 residues processed: 119 average time/residue: 0.6133 time to fit residues: 78.3282 Evaluate side-chains 119 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 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 181 THR Chi-restraints excluded: chain B residue 212 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: 5.9990 chunk 86 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 0.0670 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.140574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.108827 restraints weight = 17796.968| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.77 r_work: 0.3347 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3398 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= 0.165 Angle : 0.595 8.306 16508 Z= 0.321 Chirality : 0.042 0.214 1863 Planarity : 0.005 0.042 1951 Dihedral : 18.115 153.261 2040 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.94 % Favored : 97.99 % Rotamer: Outliers : 1.69 % Allowed : 15.52 % Favored : 82.78 % 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: 0.40 (0.23), residues: 1341 helix: 1.32 (0.24), residues: 485 sheet: -0.85 (0.29), residues: 267 loop : 0.08 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 92 TYR 0.017 0.002 TYR A 281 PHE 0.015 0.002 PHE A 444 TRP 0.012 0.001 TRP A 502 HIS 0.004 0.001 HIS A 729 Details of bonding type rmsd covalent geometry : bond 0.00378 (12008) covalent geometry : angle 0.59532 (16508) hydrogen bonds : bond 0.04543 ( 559) hydrogen bonds : angle 4.92046 ( 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 118 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7537 (pm20) REVERT: A 500 ARG cc_start: 0.8783 (ttt-90) cc_final: 0.8554 (ttt-90) REVERT: A 552 LYS cc_start: 0.8311 (mmmt) cc_final: 0.7763 (pptt) REVERT: A 771 GLU cc_start: 0.8440 (tt0) cc_final: 0.7997 (pm20) REVERT: A 868 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6994 (pm20) REVERT: A 950 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7505 (ttm) REVERT: B 85 GLN cc_start: 0.7535 (mm-40) cc_final: 0.7287 (mt0) REVERT: B 158 MET cc_start: 0.8106 (ttt) cc_final: 0.7865 (tpp) REVERT: B 213 PHE cc_start: 0.5463 (p90) cc_final: 0.5256 (p90) outliers start: 19 outliers final: 15 residues processed: 113 average time/residue: 0.6561 time to fit residues: 79.4579 Evaluate side-chains 116 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 639 THR 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 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 181 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 94 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 115 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.140040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.106608 restraints weight = 17687.221| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.86 r_work: 0.3358 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12008 Z= 0.182 Angle : 0.609 8.534 16508 Z= 0.328 Chirality : 0.043 0.211 1863 Planarity : 0.005 0.051 1951 Dihedral : 18.129 154.242 2040 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.16 % Favored : 97.76 % Rotamer: Outliers : 2.14 % Allowed : 15.08 % Favored : 82.78 % 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: 0.37 (0.23), residues: 1341 helix: 1.28 (0.24), residues: 485 sheet: -0.85 (0.29), residues: 267 loop : 0.06 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 179 TYR 0.019 0.002 TYR A 281 PHE 0.015 0.002 PHE A 590 TRP 0.015 0.002 TRP A 502 HIS 0.004 0.001 HIS A 729 Details of bonding type rmsd covalent geometry : bond 0.00419 (12008) covalent geometry : angle 0.60936 (16508) hydrogen bonds : bond 0.04709 ( 559) hydrogen bonds : angle 4.98299 ( 1522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5498.07 seconds wall clock time: 94 minutes 2.26 seconds (5642.26 seconds total)