Starting phenix.real_space_refine on Sat Sep 12 03:32:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6omv_20132/09_2026/6omv_20132.cif Found real_map, /net/cci-nas-00/data/ceres_data/6omv_20132/09_2026/6omv_20132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6omv_20132/09_2026/6omv_20132.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6omv_20132/09_2026/6omv_20132.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6omv_20132/09_2026/6omv_20132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6omv_20132/09_2026/6omv_20132.map" model { file = "/net/cci-nas-00/data/ceres_data/6omv_20132/09_2026/6omv_20132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6omv_20132/09_2026/6omv_20132.cif" } resolution = 3.9 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= 0.000 sd= 0.002 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 57 5.49 5 Mg 2 5.21 5 S 41 5.16 5 C 8199 2.51 5 N 2171 2.21 5 O 2627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13097 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 349 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "F" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 242 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 951 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "B" Number of atoms: 9985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9985 Classifications: {'peptide': 1208} Link IDs: {'PTRANS': 26, 'TRANS': 1181} Chain breaks: 2 Chain: "G" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 620 Classifications: {'RNAv2': 29} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 9, 'rna3p': 19} Chain: "C" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 942 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 2.96, per 1000 atoms: 0.23 Number of scatterers: 13097 At special positions: 0 Unit cell: (132.184, 106.6, 127.92, 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 41 16.00 P 57 15.00 Mg 2 11.99 O 2627 8.00 N 2171 7.00 C 8199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 566.5 milliseconds 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 13 sheets defined 45.2% alpha, 10.6% beta 19 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 123 through 126 Processing helix chain 'A' and resid 127 through 148 removed outlier: 3.599A pdb=" N ILE A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE A 146 " --> pdb=" O GLN A 142 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.640A pdb=" N ARG A 155 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.644A pdb=" N ARG A 203 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.597A pdb=" N HIS A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 34 Processing helix chain 'B' and resid 36 through 66 removed outlier: 4.247A pdb=" N ASP B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LYS B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY B 49 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 73 through 81 removed outlier: 3.555A pdb=" N TYR B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 90 through 112 removed outlier: 3.524A pdb=" N LEU B 94 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE B 109 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.823A pdb=" N GLU B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 147 through 150 removed outlier: 3.711A pdb=" N ALA B 150 " --> pdb=" O PHE B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 150' Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 171 through 178 Processing helix chain 'B' and resid 179 through 193 removed outlier: 3.603A pdb=" N VAL B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 230 through 242 Processing helix chain 'B' and resid 254 through 260 Processing helix chain 'B' and resid 296 through 308 removed outlier: 3.796A pdb=" N VAL B 300 " --> pdb=" O SER B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 327 Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.501A pdb=" N LYS B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 370 Processing helix chain 'B' and resid 378 through 392 Processing helix chain 'B' and resid 397 through 404 Processing helix chain 'B' and resid 410 through 431 Processing helix chain 'B' and resid 452 through 472 removed outlier: 4.043A pdb=" N ALA B 472 " --> pdb=" O ASN B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 498 removed outlier: 4.047A pdb=" N ASP B 489 " --> pdb=" O SER B 485 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 512 removed outlier: 4.116A pdb=" N HIS B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 588 through 598 Proline residue: B 594 - end of helix removed outlier: 3.595A pdb=" N PHE B 598 " --> pdb=" O PRO B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 606 Processing helix chain 'B' and resid 610 through 619 Processing helix chain 'B' and resid 630 through 643 removed outlier: 3.920A pdb=" N LEU B 635 " --> pdb=" O ASP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 646 No H-bonds generated for 'chain 'B' and resid 644 through 646' Processing helix chain 'B' and resid 666 through 676 Processing helix chain 'B' and resid 687 through 697 Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 786 through 790 Processing helix chain 'B' and resid 811 through 823 removed outlier: 3.802A pdb=" N ARG B 817 " --> pdb=" O ASN B 813 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS B 822 " --> pdb=" O VAL B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 885 removed outlier: 3.580A pdb=" N GLU B 885 " --> pdb=" O LYS B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 919 removed outlier: 3.700A pdb=" N GLU B 894 " --> pdb=" O TRP B 890 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN B 895 " --> pdb=" O THR B 891 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE B 896 " --> pdb=" O SER B 892 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 897 " --> pdb=" O ILE B 893 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER B 905 " --> pdb=" O ALA B 901 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN B 906 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 907 " --> pdb=" O TYR B 903 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 908 " --> pdb=" O ILE B 904 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N HIS B 909 " --> pdb=" O SER B 905 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS B 910 " --> pdb=" O GLN B 906 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU B 916 " --> pdb=" O CYS B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 955 removed outlier: 3.942A pdb=" N LYS B 945 " --> pdb=" O GLN B 941 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 952 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS B 953 " --> pdb=" O MET B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 1020 through 1030 Processing helix chain 'B' and resid 1091 through 1103 Processing helix chain 'B' and resid 1111 through 1116 Processing helix chain 'B' and resid 1120 through 1135 removed outlier: 3.860A pdb=" N TYR B1124 " --> pdb=" O ASP B1120 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B1126 " --> pdb=" O ALA B1122 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B1129 " --> pdb=" O SER B1125 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B1130 " --> pdb=" O SER B1126 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B1135 " --> pdb=" O MET B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1169 removed outlier: 4.425A pdb=" N ALA B1169 " --> pdb=" O ARG B1165 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1201 removed outlier: 3.756A pdb=" N GLY B1183 " --> pdb=" O ALA B1179 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS B1190 " --> pdb=" O ASN B1186 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B1191 " --> pdb=" O ILE B1187 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B1199 " --> pdb=" O ILE B1195 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B1200 " --> pdb=" O GLY B1196 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B1201 " --> pdb=" O GLN B1197 " (cutoff:3.500A) Processing helix chain 'B' and resid 1205 through 1209 removed outlier: 3.902A pdb=" N VAL B1209 " --> pdb=" O LEU B1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 1214 through 1224 Processing helix chain 'C' and resid 123 through 149 removed outlier: 3.585A pdb=" N LEU C 127 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ILE C 146 " --> pdb=" O GLN C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 155 removed outlier: 3.577A pdb=" N ARG C 155 " --> pdb=" O TYR C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 removed outlier: 3.616A pdb=" N ARG C 203 " --> pdb=" O SER C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 207 removed outlier: 6.143A pdb=" N TYR A 197 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 removed outlier: 3.622A pdb=" N ARG A 187 " --> pdb=" O VAL B 758 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 783 " --> pdb=" O HIS B 759 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 520 through 522 removed outlier: 3.723A pdb=" N HIS B 797 " --> pdb=" O GLU B 743 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR B 794 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 704 " --> pdb=" O TYR B 553 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TYR B 553 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE B 546 " --> pdb=" O ILE B 581 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 581 " --> pdb=" O ILE B 546 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 520 through 522 removed outlier: 3.723A pdb=" N HIS B 797 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 339 removed outlier: 3.655A pdb=" N PHE B 395 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 764 through 766 Processing sheet with id=AA7, first strand: chain 'B' and resid 850 through 855 removed outlier: 7.035A pdb=" N VAL B 843 " --> pdb=" O VAL B 851 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLN B 853 " --> pdb=" O ILE B 841 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE B 841 " --> pdb=" O GLN B 853 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 858 through 863 Processing sheet with id=AA9, first strand: chain 'B' and resid 1031 through 1037 removed outlier: 6.681A pdb=" N PHE B1031 " --> pdb=" O ASP B1048 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASP B1048 " --> pdb=" O PHE B1031 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1070 through 1073 Processing sheet with id=AB2, first strand: chain 'B' and resid 1139 through 1140 Processing sheet with id=AB3, first strand: chain 'C' and resid 157 through 158 removed outlier: 4.547A pdb=" N ASN C 157 " --> pdb=" O VAL C 213 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 182 through 187 removed outlier: 5.371A pdb=" N TYR C 197 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N CYS C 185 " --> pdb=" O CYS C 195 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS C 195 " --> pdb=" O CYS C 185 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 2.60 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2861 1.33 - 1.45: 3263 1.45 - 1.57: 7178 1.57 - 1.69: 111 1.69 - 1.81: 67 Bond restraints: 13480 Sorted by residual: bond pdb=" O3' U G 9 " pdb=" P A G 10 " ideal model delta sigma weight residual 1.607 1.538 0.069 1.20e-02 6.94e+03 3.26e+01 bond pdb=" C3' DT F -3 " pdb=" O3' DT F -3 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.10e+01 bond pdb=" C3' DT F -2 " pdb=" O3' DT F -2 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.02e+01 bond pdb=" C3' DC F -6 " pdb=" C2' DC F -6 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.50e+00 bond pdb=" C2 DT F -3 " pdb=" N3 DT F -3 " ideal model delta sigma weight residual 1.373 1.349 0.024 8.00e-03 1.56e+04 9.29e+00 ... (remaining 13475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 17284 2.08 - 4.16: 970 4.16 - 6.24: 121 6.24 - 8.32: 22 8.32 - 10.41: 14 Bond angle restraints: 18411 Sorted by residual: angle pdb=" C TYR B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta sigma weight residual 120.89 112.52 8.37 1.50e+00 4.44e-01 3.11e+01 angle pdb=" N PRO B 608 " pdb=" CA PRO B 608 " pdb=" CB PRO B 608 " ideal model delta sigma weight residual 102.36 98.11 4.25 7.80e-01 1.64e+00 2.96e+01 angle pdb=" N SER B 609 " pdb=" CA SER B 609 " pdb=" C SER B 609 " ideal model delta sigma weight residual 110.97 105.10 5.87 1.09e+00 8.42e-01 2.90e+01 angle pdb=" N GLY B 624 " pdb=" CA GLY B 624 " pdb=" C GLY B 624 " ideal model delta sigma weight residual 114.69 108.51 6.18 1.19e+00 7.06e-01 2.70e+01 angle pdb=" C ASN C 169 " pdb=" N LEU C 170 " pdb=" CA LEU C 170 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.66e+01 ... (remaining 18406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 6699 17.62 - 35.25: 925 35.25 - 52.87: 286 52.87 - 70.49: 106 70.49 - 88.12: 22 Dihedral angle restraints: 8038 sinusoidal: 3765 harmonic: 4273 Sorted by residual: dihedral pdb=" C4' G G 23 " pdb=" C3' G G 23 " pdb=" C2' G G 23 " pdb=" C1' G G 23 " ideal model delta sinusoidal sigma weight residual 36.34 -37.89 74.23 1 3.10e+00 1.04e-01 7.28e+02 dihedral pdb=" C4' A G 13 " pdb=" C3' A G 13 " pdb=" C2' A G 13 " pdb=" C1' A G 13 " ideal model delta sinusoidal sigma weight residual 36.34 -37.14 73.49 1 3.10e+00 1.04e-01 7.15e+02 dihedral pdb=" C4' U G 5 " pdb=" C3' U G 5 " pdb=" C2' U G 5 " pdb=" C1' U G 5 " ideal model delta sinusoidal sigma weight residual 36.35 -36.65 73.00 1 3.10e+00 1.04e-01 7.07e+02 ... (remaining 8035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1530 0.071 - 0.142: 375 0.142 - 0.214: 70 0.214 - 0.285: 19 0.285 - 0.356: 7 Chirality restraints: 2001 Sorted by residual: chirality pdb=" P A G 3 " pdb=" OP1 A G 3 " pdb=" OP2 A G 3 " pdb=" O5' A G 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.53 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C3' G G 23 " pdb=" C4' G G 23 " pdb=" O3' G G 23 " pdb=" C2' G G 23 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C2' G G 23 " pdb=" C3' G G 23 " pdb=" O2' G G 23 " pdb=" C1' G G 23 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 1998 not shown) Planarity restraints: 2148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 128 " -0.050 5.00e-02 4.00e+02 7.50e-02 9.00e+00 pdb=" N PRO B 129 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 600 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.53e+00 pdb=" C LYS B 600 " 0.050 2.00e-02 2.50e+03 pdb=" O LYS B 600 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS B 601 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 482 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.10e+00 pdb=" C ARG B 482 " 0.046 2.00e-02 2.50e+03 pdb=" O ARG B 482 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP B 483 " -0.015 2.00e-02 2.50e+03 ... (remaining 2145 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 284 2.62 - 3.19: 11456 3.19 - 3.76: 22166 3.76 - 4.33: 28838 4.33 - 4.90: 44475 Nonbonded interactions: 107219 Sorted by model distance: nonbonded pdb="MG MG A 301 " pdb=" O HOH G 102 " model vdw 2.054 2.170 nonbonded pdb="MG MG A 301 " pdb=" O HOH A 402 " model vdw 2.070 2.170 nonbonded pdb="MG MG A 301 " pdb=" O HOH G 103 " model vdw 2.076 2.170 nonbonded pdb=" O GLN B1108 " pdb=" NE2 GLN B1108 " model vdw 2.079 3.120 nonbonded pdb=" O LYS B 571 " pdb=" OD1 ASP B 572 " model vdw 2.101 3.040 ... (remaining 107214 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 120 through 233) selection = chain 'C' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.520 Find NCS groups from input model: 0.090 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.008 0.069 13480 Z= 0.427 Angle : 1.090 10.406 18411 Z= 0.659 Chirality : 0.069 0.356 2001 Planarity : 0.006 0.075 2148 Dihedral : 18.834 88.116 5284 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.18 % Favored : 90.19 % Rotamer: Outliers : 1.60 % Allowed : 10.91 % Favored : 87.49 % Cbeta Deviations : 0.07 % 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: -4.46 (0.17), residues: 1427 helix: -2.84 (0.15), residues: 590 sheet: -2.41 (0.35), residues: 173 loop : -3.18 (0.20), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 102 TYR 0.039 0.003 TYR A 188 PHE 0.020 0.003 PHE B 19 TRP 0.013 0.002 TRP B 999 HIS 0.010 0.002 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00767 / 0.43 (13480) covalent geometry : angle 1.09001 / 0.66 (18411) hydrogen bonds : bond 0.18847 / 21.65 ( 496) hydrogen bonds : angle 8.23253 / 9.03 ( 1389) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 268 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.2068 (mtp) cc_final: 0.1293 (mmt) REVERT: A 133 ILE cc_start: 0.9188 (mt) cc_final: 0.8798 (mm) REVERT: A 135 GLU cc_start: 0.8960 (tp30) cc_final: 0.8615 (tp30) REVERT: A 137 ASP cc_start: 0.9155 (m-30) cc_final: 0.8902 (m-30) REVERT: A 142 GLN cc_start: 0.8795 (tt0) cc_final: 0.8369 (tp-100) REVERT: A 144 TYR cc_start: 0.7947 (t80) cc_final: 0.7063 (t80) REVERT: A 154 LYS cc_start: 0.9545 (mttp) cc_final: 0.9157 (mtpt) REVERT: A 157 ASN cc_start: 0.9159 (m110) cc_final: 0.8859 (t0) REVERT: A 193 GLN cc_start: 0.8780 (tt0) cc_final: 0.8309 (tm-30) REVERT: A 202 LYS cc_start: 0.8312 (mmtp) cc_final: 0.7858 (ptpp) REVERT: A 232 LEU cc_start: 0.8681 (tt) cc_final: 0.8176 (mt) REVERT: B 167 LYS cc_start: 0.7531 (pttt) cc_final: 0.7321 (pttt) REVERT: B 308 LEU cc_start: 0.9038 (mm) cc_final: 0.8832 (mp) REVERT: B 558 MET cc_start: 0.7673 (mpp) cc_final: 0.7426 (mpp) REVERT: B 815 GLU cc_start: 0.8790 (tp30) cc_final: 0.8426 (tp30) REVERT: B 840 TYR cc_start: 0.8986 (t80) cc_final: 0.8665 (t80) REVERT: B 927 LEU cc_start: 0.8557 (mt) cc_final: 0.8116 (tt) REVERT: B 940 LYS cc_start: 0.9211 (tttt) cc_final: 0.8778 (tttp) REVERT: B 941 GLN cc_start: 0.8572 (tp40) cc_final: 0.8294 (tp40) REVERT: B 944 GLN cc_start: 0.8407 (mt0) cc_final: 0.8023 (mt0) REVERT: B 945 LYS cc_start: 0.9030 (tptm) cc_final: 0.8726 (ttpt) REVERT: B 1003 LYS cc_start: 0.9350 (mttt) cc_final: 0.9026 (mttm) REVERT: B 1128 MET cc_start: 0.8920 (tpt) cc_final: 0.8671 (tpp) REVERT: B 1167 TYR cc_start: 0.8380 (m-80) cc_final: 0.7987 (m-80) REVERT: C 142 GLN cc_start: 0.9200 (mt0) cc_final: 0.8978 (tm-30) REVERT: C 154 LYS cc_start: 0.8758 (mttm) cc_final: 0.8493 (ttmm) REVERT: C 165 LEU cc_start: 0.9299 (tp) cc_final: 0.9098 (tp) REVERT: C 187 ARG cc_start: 0.7834 (tpp80) cc_final: 0.6979 (tpp80) REVERT: C 192 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8517 (p0) REVERT: C 217 ARG cc_start: 0.6127 (tpt170) cc_final: 0.5808 (tpt170) REVERT: C 219 GLU cc_start: 0.8754 (mp0) cc_final: 0.8387 (mp0) REVERT: C 230 ARG cc_start: 0.7565 (mtt-85) cc_final: 0.7322 (mtt-85) outliers start: 21 outliers final: 4 residues processed: 283 average time/residue: 0.1328 time to fit residues: 52.2078 Evaluate side-chains 198 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 193 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain C residue 192 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN A 145 ASN A 157 ASN A 168 ASN A 181 GLN A 231 ASN B 100 ASN B 160 ASN B 203 GLN B 263 ASN ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN B 613 GLN B 706 ASN B 803 ASN B 861 ASN B 873 HIS B 889 ASN B 895 ASN B 978 ASN B 989 GLN B1118 GLN C 168 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.107439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.078658 restraints weight = 45192.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.081217 restraints weight = 20171.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.082789 restraints weight = 12785.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.083644 restraints weight = 9918.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.084021 restraints weight = 8684.513| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13480 Z= 0.185 Angle : 0.985 24.232 18411 Z= 0.472 Chirality : 0.089 1.328 2001 Planarity : 0.004 0.060 2148 Dihedral : 16.405 125.927 2249 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.78 % Favored : 92.15 % Rotamer: Outliers : 2.90 % Allowed : 16.48 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.35 (0.19), residues: 1427 helix: -1.62 (0.18), residues: 589 sheet: -2.02 (0.39), residues: 150 loop : -2.83 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 230 TYR 0.025 0.002 TYR B1102 PHE 0.020 0.002 PHE C 196 TRP 0.006 0.001 TRP B 534 HIS 0.005 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (13480) covalent geometry : angle 0.98501 / 0.47 (18411) hydrogen bonds : bond 0.05264 / 5.80 ( 496) hydrogen bonds : angle 5.99652 / 6.66 ( 1389) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.2296 (mtp) cc_final: 0.1452 (mmt) REVERT: A 133 ILE cc_start: 0.9188 (mt) cc_final: 0.8826 (mm) REVERT: A 135 GLU cc_start: 0.8820 (tp30) cc_final: 0.8568 (tp30) REVERT: A 142 GLN cc_start: 0.8808 (tt0) cc_final: 0.8437 (tp-100) REVERT: A 144 TYR cc_start: 0.7668 (t80) cc_final: 0.6747 (t80) REVERT: A 154 LYS cc_start: 0.9450 (mttp) cc_final: 0.9062 (mtmt) REVERT: A 157 ASN cc_start: 0.9055 (m-40) cc_final: 0.8821 (t0) REVERT: A 193 GLN cc_start: 0.8653 (tt0) cc_final: 0.8326 (tm-30) REVERT: A 202 LYS cc_start: 0.8041 (mmtp) cc_final: 0.7613 (ptpp) REVERT: A 227 GLU cc_start: 0.9130 (mp0) cc_final: 0.8865 (mp0) REVERT: A 230 ARG cc_start: 0.8846 (ttm110) cc_final: 0.8552 (ttm110) REVERT: A 232 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8086 (mt) REVERT: B 110 LYS cc_start: 0.8640 (pttm) cc_final: 0.8383 (pttm) REVERT: B 495 ASP cc_start: 0.6739 (p0) cc_final: 0.6452 (p0) REVERT: B 815 GLU cc_start: 0.8508 (tp30) cc_final: 0.8227 (tp30) REVERT: B 840 TYR cc_start: 0.8928 (t80) cc_final: 0.8436 (t80) REVERT: B 895 ASN cc_start: 0.7990 (m110) cc_final: 0.7575 (m-40) REVERT: B 927 LEU cc_start: 0.8351 (mt) cc_final: 0.7772 (tt) REVERT: B 940 LYS cc_start: 0.9040 (tttt) cc_final: 0.8439 (tttm) REVERT: B 941 GLN cc_start: 0.8440 (tp40) cc_final: 0.7884 (tp40) REVERT: B 944 GLN cc_start: 0.8172 (mt0) cc_final: 0.7875 (mt0) REVERT: B 1003 LYS cc_start: 0.9254 (mttt) cc_final: 0.8986 (mttm) REVERT: B 1054 ARG cc_start: 0.8708 (ttm170) cc_final: 0.8272 (mtp85) REVERT: C 142 GLN cc_start: 0.9141 (mt0) cc_final: 0.8895 (tm-30) REVERT: C 148 LYS cc_start: 0.8951 (ttmm) cc_final: 0.8382 (mtmm) REVERT: C 209 TYR cc_start: 0.7757 (m-80) cc_final: 0.7499 (m-80) REVERT: C 217 ARG cc_start: 0.6173 (tpt170) cc_final: 0.5967 (tpt170) REVERT: C 222 ARG cc_start: 0.9081 (tpp-160) cc_final: 0.8837 (tpp80) outliers start: 38 outliers final: 18 residues processed: 246 average time/residue: 0.1249 time to fit residues: 44.2205 Evaluate side-chains 212 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 127 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN A 168 ASN B 76 ASN B 264 GLN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 GLN B 449 ASN ** B1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.103653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.074819 restraints weight = 46138.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.077337 restraints weight = 20980.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.078687 restraints weight = 13346.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.079654 restraints weight = 10540.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.080057 restraints weight = 9184.761| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 13480 Z= 0.280 Angle : 0.895 17.653 18411 Z= 0.446 Chirality : 0.069 0.931 2001 Planarity : 0.004 0.055 2148 Dihedral : 16.437 143.103 2241 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.62 % Favored : 91.31 % Rotamer: Outliers : 3.66 % Allowed : 19.15 % Favored : 77.19 % 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: -2.89 (0.21), residues: 1427 helix: -1.12 (0.19), residues: 609 sheet: -1.84 (0.39), residues: 168 loop : -2.72 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 86 TYR 0.019 0.002 TYR B 956 PHE 0.019 0.002 PHE B 946 TRP 0.010 0.001 TRP A 178 HIS 0.011 0.002 HIS B 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.28 (13480) covalent geometry : angle 0.89480 / 0.45 (18411) hydrogen bonds : bond 0.04938 / 5.49 ( 496) hydrogen bonds : angle 5.81981 / 6.64 ( 1389) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.1923 (mtp) cc_final: 0.1124 (mmt) REVERT: A 135 GLU cc_start: 0.8970 (tp30) cc_final: 0.8661 (tp30) REVERT: A 142 GLN cc_start: 0.8990 (tt0) cc_final: 0.8598 (tp-100) REVERT: A 154 LYS cc_start: 0.9484 (mttp) cc_final: 0.9104 (mtpt) REVERT: A 157 ASN cc_start: 0.9191 (m-40) cc_final: 0.8908 (t0) REVERT: A 193 GLN cc_start: 0.8653 (tt0) cc_final: 0.8326 (tm-30) REVERT: A 202 LYS cc_start: 0.8255 (mmtp) cc_final: 0.7743 (ptpp) REVERT: A 230 ARG cc_start: 0.9047 (ttm110) cc_final: 0.8808 (ttm110) REVERT: A 232 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8200 (mt) REVERT: B 187 MET cc_start: 0.4808 (tmm) cc_final: 0.4565 (tmm) REVERT: B 614 LYS cc_start: 0.9709 (mmmt) cc_final: 0.9349 (mmmm) REVERT: B 815 GLU cc_start: 0.8704 (tp30) cc_final: 0.8387 (tp30) REVERT: B 840 TYR cc_start: 0.8989 (t80) cc_final: 0.8672 (t80) REVERT: B 895 ASN cc_start: 0.8066 (m110) cc_final: 0.7738 (m-40) REVERT: B 919 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.7979 (t0) REVERT: B 927 LEU cc_start: 0.8565 (mt) cc_final: 0.7999 (tt) REVERT: B 941 GLN cc_start: 0.8541 (tp40) cc_final: 0.7873 (tp40) REVERT: B 949 MET cc_start: 0.8094 (ttm) cc_final: 0.7826 (ttm) REVERT: B 957 MET cc_start: 0.8265 (tpp) cc_final: 0.7977 (tpp) REVERT: B 1003 LYS cc_start: 0.9322 (mttt) cc_final: 0.9017 (mttm) REVERT: B 1054 ARG cc_start: 0.8889 (ttm170) cc_final: 0.8399 (mtm-85) REVERT: B 1216 LYS cc_start: 0.9024 (ttmm) cc_final: 0.8646 (tppt) REVERT: C 134 LYS cc_start: 0.8545 (mttt) cc_final: 0.8341 (mttt) REVERT: C 148 LYS cc_start: 0.9016 (ttmm) cc_final: 0.8497 (mtmm) REVERT: C 209 TYR cc_start: 0.8118 (m-80) cc_final: 0.7884 (m-80) REVERT: C 217 ARG cc_start: 0.6214 (tpt170) cc_final: 0.5876 (tpt170) REVERT: C 222 ARG cc_start: 0.9094 (tpp-160) cc_final: 0.8834 (tpp80) outliers start: 48 outliers final: 32 residues processed: 214 average time/residue: 0.1144 time to fit residues: 35.5668 Evaluate side-chains 214 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 859 ILE Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 60 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 90 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 138 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** B1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.105286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.076402 restraints weight = 45395.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.078970 restraints weight = 20714.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.080497 restraints weight = 13208.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.081283 restraints weight = 10283.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.081558 restraints weight = 9091.147| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13480 Z= 0.156 Angle : 0.764 11.563 18411 Z= 0.383 Chirality : 0.058 0.665 2001 Planarity : 0.004 0.053 2148 Dihedral : 16.395 138.074 2241 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.57 % Favored : 92.36 % Rotamer: Outliers : 3.59 % Allowed : 20.44 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.46 (0.21), residues: 1427 helix: -0.65 (0.20), residues: 597 sheet: -1.54 (0.42), residues: 142 loop : -2.59 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 230 TYR 0.019 0.002 TYR B 678 PHE 0.014 0.001 PHE B 173 TRP 0.010 0.001 TRP B 602 HIS 0.006 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (13480) covalent geometry : angle 0.76364 / 0.38 (18411) hydrogen bonds : bond 0.04216 / 4.77 ( 496) hydrogen bonds : angle 5.43032 / 6.11 ( 1389) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.1622 (mtp) cc_final: 0.0908 (mmt) REVERT: A 135 GLU cc_start: 0.8935 (tp30) cc_final: 0.8683 (tp30) REVERT: A 142 GLN cc_start: 0.8979 (tt0) cc_final: 0.8553 (tp-100) REVERT: A 154 LYS cc_start: 0.9479 (mttp) cc_final: 0.8973 (mtmt) REVERT: A 157 ASN cc_start: 0.9129 (m-40) cc_final: 0.8848 (t0) REVERT: A 181 GLN cc_start: 0.8394 (tt0) cc_final: 0.8119 (tt0) REVERT: A 186 MET cc_start: 0.7523 (mmm) cc_final: 0.6993 (mmm) REVERT: A 193 GLN cc_start: 0.8648 (tt0) cc_final: 0.8276 (tm-30) REVERT: A 202 LYS cc_start: 0.8139 (mmtp) cc_final: 0.7560 (ptpp) REVERT: A 232 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8066 (mt) REVERT: B 110 LYS cc_start: 0.8686 (pttm) cc_final: 0.8267 (pttm) REVERT: B 247 GLU cc_start: 0.3819 (OUTLIER) cc_final: 0.2994 (mp0) REVERT: B 590 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8056 (p0) REVERT: B 614 LYS cc_start: 0.9679 (mmmt) cc_final: 0.9323 (mmmm) REVERT: B 815 GLU cc_start: 0.8793 (tp30) cc_final: 0.8407 (tp30) REVERT: B 840 TYR cc_start: 0.8949 (t80) cc_final: 0.8554 (t80) REVERT: B 895 ASN cc_start: 0.7699 (m110) cc_final: 0.7438 (m-40) REVERT: B 927 LEU cc_start: 0.8404 (mt) cc_final: 0.8081 (tp) REVERT: B 941 GLN cc_start: 0.8725 (tp40) cc_final: 0.7948 (tp40) REVERT: B 1003 LYS cc_start: 0.9311 (mttt) cc_final: 0.8975 (mttm) REVERT: B 1216 LYS cc_start: 0.9060 (ttmm) cc_final: 0.8373 (tppt) REVERT: C 133 ILE cc_start: 0.8760 (mm) cc_final: 0.8436 (tp) REVERT: C 137 ASP cc_start: 0.9192 (m-30) cc_final: 0.8858 (m-30) REVERT: C 148 LYS cc_start: 0.9054 (ttmm) cc_final: 0.8570 (mtmm) REVERT: C 209 TYR cc_start: 0.8190 (m-80) cc_final: 0.7902 (m-80) REVERT: C 230 ARG cc_start: 0.7540 (mtt-85) cc_final: 0.6991 (ptp-170) outliers start: 47 outliers final: 28 residues processed: 234 average time/residue: 0.1084 time to fit residues: 37.6078 Evaluate side-chains 220 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 34 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 65 optimal weight: 0.0020 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN A 168 ASN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN B1108 GLN B1186 ASN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.107686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.079584 restraints weight = 45671.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.082113 restraints weight = 20517.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.083677 restraints weight = 12973.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.084565 restraints weight = 10005.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.084929 restraints weight = 8701.974| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13480 Z= 0.140 Angle : 0.730 11.432 18411 Z= 0.366 Chirality : 0.055 0.568 2001 Planarity : 0.003 0.054 2148 Dihedral : 16.303 137.341 2241 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.43 % Allowed : 21.51 % Favored : 75.06 % 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: -2.23 (0.21), residues: 1427 helix: -0.39 (0.21), residues: 598 sheet: -1.50 (0.44), residues: 132 loop : -2.52 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1189 TYR 0.017 0.001 TYR B1102 PHE 0.012 0.001 PHE B 490 TRP 0.007 0.001 TRP B 602 HIS 0.005 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (13480) covalent geometry : angle 0.72964 / 0.37 (18411) hydrogen bonds : bond 0.03990 / 4.51 ( 496) hydrogen bonds : angle 5.28225 / 5.94 ( 1389) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.2000 (mtp) cc_final: 0.1328 (mmt) REVERT: A 134 LYS cc_start: 0.8954 (mttm) cc_final: 0.8291 (mtpt) REVERT: A 135 GLU cc_start: 0.8784 (tp30) cc_final: 0.8542 (tp30) REVERT: A 154 LYS cc_start: 0.9456 (mttp) cc_final: 0.9015 (mtmt) REVERT: A 157 ASN cc_start: 0.9173 (m-40) cc_final: 0.8845 (t0) REVERT: A 186 MET cc_start: 0.7744 (mmm) cc_final: 0.7147 (mmm) REVERT: A 193 GLN cc_start: 0.8615 (tt0) cc_final: 0.8401 (tm-30) REVERT: A 202 LYS cc_start: 0.7727 (mmtp) cc_final: 0.7243 (ptpp) REVERT: A 232 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8072 (mt) REVERT: B 590 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7801 (p0) REVERT: B 614 LYS cc_start: 0.9667 (mmmt) cc_final: 0.9409 (pttp) REVERT: B 815 GLU cc_start: 0.8511 (tp30) cc_final: 0.8234 (tp30) REVERT: B 840 TYR cc_start: 0.8867 (t80) cc_final: 0.8545 (t80) REVERT: B 919 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8080 (t0) REVERT: B 927 LEU cc_start: 0.8257 (mt) cc_final: 0.7941 (tp) REVERT: B 941 GLN cc_start: 0.8584 (tp40) cc_final: 0.7887 (tp40) REVERT: B 1003 LYS cc_start: 0.9231 (mttt) cc_final: 0.8944 (mttm) REVERT: B 1054 ARG cc_start: 0.8647 (ttm170) cc_final: 0.8356 (mmt-90) REVERT: B 1216 LYS cc_start: 0.8903 (ttmm) cc_final: 0.8297 (tppt) REVERT: C 133 ILE cc_start: 0.8880 (mm) cc_final: 0.8486 (tp) REVERT: C 137 ASP cc_start: 0.9235 (m-30) cc_final: 0.8772 (m-30) REVERT: C 148 LYS cc_start: 0.9053 (ttmm) cc_final: 0.8567 (mtmm) REVERT: C 192 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8569 (m-30) REVERT: C 209 TYR cc_start: 0.8354 (m-80) cc_final: 0.8050 (m-80) outliers start: 45 outliers final: 31 residues processed: 226 average time/residue: 0.1145 time to fit residues: 37.8737 Evaluate side-chains 218 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 13 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 64 optimal weight: 0.0970 chunk 116 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 0.0770 chunk 31 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 89 optimal weight: 0.0670 overall best weight: 0.3674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN A 168 ASN A 181 GLN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 ASN B 895 ASN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.109228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.081108 restraints weight = 45093.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.083677 restraints weight = 20330.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.085260 restraints weight = 12800.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.086054 restraints weight = 9862.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.086597 restraints weight = 8653.513| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13480 Z= 0.130 Angle : 0.735 12.324 18411 Z= 0.364 Chirality : 0.053 0.494 2001 Planarity : 0.004 0.085 2148 Dihedral : 16.165 134.816 2241 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.28 % Allowed : 22.58 % Favored : 74.14 % 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: -2.15 (0.21), residues: 1427 helix: -0.32 (0.21), residues: 597 sheet: -1.58 (0.42), residues: 136 loop : -2.43 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 230 TYR 0.017 0.001 TYR B 516 PHE 0.012 0.001 PHE B 490 TRP 0.005 0.001 TRP B 602 HIS 0.005 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (13480) covalent geometry : angle 0.73493 / 0.36 (18411) hydrogen bonds : bond 0.03914 / 4.45 ( 496) hydrogen bonds : angle 5.15110 / 5.76 ( 1389) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.2322 (mtp) cc_final: 0.1775 (mmt) REVERT: A 135 GLU cc_start: 0.8696 (tp30) cc_final: 0.8460 (tp30) REVERT: A 154 LYS cc_start: 0.9437 (mttp) cc_final: 0.8728 (mtmt) REVERT: A 181 GLN cc_start: 0.8295 (tt0) cc_final: 0.8028 (tt0) REVERT: A 186 MET cc_start: 0.7701 (mmm) cc_final: 0.7113 (mmm) REVERT: A 193 GLN cc_start: 0.8566 (tt0) cc_final: 0.8358 (tm-30) REVERT: B 247 GLU cc_start: 0.3941 (OUTLIER) cc_final: 0.3313 (mp0) REVERT: B 386 ARG cc_start: -0.1579 (OUTLIER) cc_final: -0.2124 (ptt90) REVERT: B 590 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7729 (p0) REVERT: B 614 LYS cc_start: 0.9660 (mmmt) cc_final: 0.9391 (pttp) REVERT: B 815 GLU cc_start: 0.8530 (tp30) cc_final: 0.8219 (tp30) REVERT: B 840 TYR cc_start: 0.8808 (t80) cc_final: 0.8470 (t80) REVERT: B 941 GLN cc_start: 0.8573 (tp40) cc_final: 0.7868 (tp40) REVERT: B 1003 LYS cc_start: 0.9231 (mttt) cc_final: 0.8987 (mttm) REVERT: B 1068 TYR cc_start: 0.9236 (t80) cc_final: 0.8777 (t80) REVERT: B 1216 LYS cc_start: 0.8907 (ttmm) cc_final: 0.8320 (tppt) REVERT: C 133 ILE cc_start: 0.8876 (mm) cc_final: 0.8457 (tp) REVERT: C 137 ASP cc_start: 0.9219 (m-30) cc_final: 0.8779 (m-30) REVERT: C 148 LYS cc_start: 0.9097 (ttmm) cc_final: 0.8607 (mtmm) REVERT: C 186 MET cc_start: 0.7428 (tpp) cc_final: 0.7175 (tmm) REVERT: C 209 TYR cc_start: 0.8449 (m-80) cc_final: 0.8154 (m-80) outliers start: 43 outliers final: 26 residues processed: 231 average time/residue: 0.1123 time to fit residues: 38.3425 Evaluate side-chains 219 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 118 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 136 optimal weight: 0.4980 chunk 79 optimal weight: 0.0370 chunk 65 optimal weight: 0.8980 overall best weight: 1.0660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.108386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.080198 restraints weight = 45140.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.082745 restraints weight = 20557.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.084305 restraints weight = 12967.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.085185 restraints weight = 9990.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.085568 restraints weight = 8693.743| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13480 Z= 0.141 Angle : 0.736 12.642 18411 Z= 0.364 Chirality : 0.052 0.488 2001 Planarity : 0.003 0.049 2148 Dihedral : 16.108 133.832 2241 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.81 % Allowed : 23.04 % Favored : 73.15 % 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: -1.94 (0.22), residues: 1427 helix: -0.16 (0.21), residues: 594 sheet: -1.62 (0.41), residues: 142 loop : -2.27 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 222 TYR 0.015 0.001 TYR B 516 PHE 0.021 0.001 PHE C 196 TRP 0.006 0.001 TRP B 602 HIS 0.005 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (13480) covalent geometry : angle 0.73573 / 0.36 (18411) hydrogen bonds : bond 0.03836 / 4.31 ( 496) hydrogen bonds : angle 5.08760 / 5.72 ( 1389) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 198 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.2405 (mtp) cc_final: 0.1914 (mmt) REVERT: A 134 LYS cc_start: 0.9089 (mttm) cc_final: 0.7967 (mtmt) REVERT: A 137 ASP cc_start: 0.9152 (m-30) cc_final: 0.8873 (p0) REVERT: A 154 LYS cc_start: 0.9413 (mttp) cc_final: 0.8854 (mtmt) REVERT: A 186 MET cc_start: 0.7722 (mmm) cc_final: 0.7121 (mmm) REVERT: A 202 LYS cc_start: 0.8221 (mmtp) cc_final: 0.7732 (mtmm) REVERT: A 230 ARG cc_start: 0.9028 (ttm110) cc_final: 0.8442 (ttm110) REVERT: B 110 LYS cc_start: 0.8702 (pttm) cc_final: 0.8343 (pttm) REVERT: B 247 GLU cc_start: 0.3908 (OUTLIER) cc_final: 0.3247 (mp0) REVERT: B 386 ARG cc_start: -0.1345 (OUTLIER) cc_final: -0.1870 (ptt180) REVERT: B 456 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8737 (mpp) REVERT: B 614 LYS cc_start: 0.9670 (mmmt) cc_final: 0.9254 (mmmm) REVERT: B 659 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7514 (mp0) REVERT: B 815 GLU cc_start: 0.8558 (tp30) cc_final: 0.8242 (tp30) REVERT: B 840 TYR cc_start: 0.8876 (t80) cc_final: 0.8519 (t80) REVERT: B 941 GLN cc_start: 0.8555 (tp40) cc_final: 0.7876 (tp40) REVERT: B 1003 LYS cc_start: 0.9224 (mttt) cc_final: 0.8988 (mttm) REVERT: B 1068 TYR cc_start: 0.9238 (t80) cc_final: 0.8706 (t80) REVERT: B 1131 MET cc_start: 0.9294 (tpp) cc_final: 0.8848 (mmm) REVERT: B 1216 LYS cc_start: 0.8929 (ttmm) cc_final: 0.8330 (tppt) REVERT: C 133 ILE cc_start: 0.8870 (mm) cc_final: 0.8419 (tp) REVERT: C 137 ASP cc_start: 0.9244 (m-30) cc_final: 0.8721 (m-30) REVERT: C 138 LEU cc_start: 0.8880 (tp) cc_final: 0.8645 (tt) REVERT: C 148 LYS cc_start: 0.9159 (ttmm) cc_final: 0.8674 (mtmm) REVERT: C 186 MET cc_start: 0.7440 (tpp) cc_final: 0.7087 (ttt) REVERT: C 192 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8022 (m-30) REVERT: C 209 TYR cc_start: 0.8492 (m-80) cc_final: 0.8180 (m-80) outliers start: 50 outliers final: 34 residues processed: 228 average time/residue: 0.1180 time to fit residues: 39.4624 Evaluate side-chains 228 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 882 GLU Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 107 optimal weight: 0.8980 chunk 87 optimal weight: 0.0980 chunk 1 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN C 233 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.108558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.080407 restraints weight = 45007.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.082934 restraints weight = 20509.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.084497 restraints weight = 12975.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.085223 restraints weight = 10011.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.085831 restraints weight = 8811.134| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13480 Z= 0.143 Angle : 0.735 13.439 18411 Z= 0.365 Chirality : 0.052 0.470 2001 Planarity : 0.003 0.049 2148 Dihedral : 16.052 133.029 2241 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.36 % Allowed : 23.57 % Favored : 73.07 % 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: -1.81 (0.22), residues: 1427 helix: -0.06 (0.21), residues: 592 sheet: -1.53 (0.43), residues: 136 loop : -2.18 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1189 TYR 0.048 0.001 TYR B 995 PHE 0.019 0.001 PHE C 196 TRP 0.008 0.001 TRP B 602 HIS 0.004 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (13480) covalent geometry : angle 0.73461 / 0.37 (18411) hydrogen bonds : bond 0.03871 / 4.39 ( 496) hydrogen bonds : angle 5.02466 / 5.64 ( 1389) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 202 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.2449 (mtp) cc_final: 0.2073 (mmt) REVERT: A 134 LYS cc_start: 0.9113 (mttm) cc_final: 0.8500 (mtmt) REVERT: A 154 LYS cc_start: 0.9426 (mttp) cc_final: 0.9021 (mttt) REVERT: A 186 MET cc_start: 0.7642 (mmm) cc_final: 0.7083 (mmm) REVERT: A 202 LYS cc_start: 0.8212 (mmtp) cc_final: 0.7749 (mtmm) REVERT: B 110 LYS cc_start: 0.8747 (pttm) cc_final: 0.8395 (pttm) REVERT: B 116 LYS cc_start: 0.9016 (mmtp) cc_final: 0.8204 (pttm) REVERT: B 224 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6991 (m-80) REVERT: B 247 GLU cc_start: 0.4052 (OUTLIER) cc_final: 0.3329 (mp0) REVERT: B 386 ARG cc_start: -0.0814 (OUTLIER) cc_final: -0.1356 (ptt180) REVERT: B 456 MET cc_start: 0.9192 (mpp) cc_final: 0.8713 (mpp) REVERT: B 513 GLN cc_start: 0.7617 (mt0) cc_final: 0.5940 (pp30) REVERT: B 514 LYS cc_start: 0.8620 (tptp) cc_final: 0.8332 (tptp) REVERT: B 614 LYS cc_start: 0.9667 (mmmt) cc_final: 0.9244 (mmmm) REVERT: B 659 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7556 (mp0) REVERT: B 755 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: B 815 GLU cc_start: 0.8559 (tp30) cc_final: 0.8248 (tp30) REVERT: B 840 TYR cc_start: 0.8899 (t80) cc_final: 0.8447 (t80) REVERT: B 941 GLN cc_start: 0.8571 (tp40) cc_final: 0.7831 (tp40) REVERT: B 1003 LYS cc_start: 0.9209 (mttt) cc_final: 0.8963 (mttm) REVERT: B 1131 MET cc_start: 0.9283 (tpp) cc_final: 0.8858 (mmm) REVERT: B 1216 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8313 (tppt) REVERT: C 133 ILE cc_start: 0.8874 (mm) cc_final: 0.8427 (tp) REVERT: C 137 ASP cc_start: 0.9212 (m-30) cc_final: 0.8668 (m-30) REVERT: C 148 LYS cc_start: 0.9146 (ttmm) cc_final: 0.8651 (mtmm) REVERT: C 186 MET cc_start: 0.7389 (tpp) cc_final: 0.7017 (ttt) REVERT: C 209 TYR cc_start: 0.8418 (m-80) cc_final: 0.8153 (m-80) outliers start: 44 outliers final: 35 residues processed: 232 average time/residue: 0.1208 time to fit residues: 40.5082 Evaluate side-chains 233 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 747 ARG Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 34 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN C 208 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.106323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.077481 restraints weight = 44923.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.080054 restraints weight = 20579.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.081689 restraints weight = 13050.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.082617 restraints weight = 10023.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.083019 restraints weight = 8697.266| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13480 Z= 0.170 Angle : 0.757 12.675 18411 Z= 0.374 Chirality : 0.053 0.480 2001 Planarity : 0.004 0.049 2148 Dihedral : 16.058 133.138 2241 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 3.51 % Allowed : 23.87 % Favored : 72.62 % 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: -1.83 (0.22), residues: 1427 helix: -0.00 (0.21), residues: 597 sheet: -1.64 (0.42), residues: 142 loop : -2.26 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 230 TYR 0.019 0.001 TYR B 995 PHE 0.015 0.001 PHE B 597 TRP 0.010 0.001 TRP B 602 HIS 0.030 0.002 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (13480) covalent geometry : angle 0.75650 / 0.37 (18411) hydrogen bonds : bond 0.03888 / 4.43 ( 496) hydrogen bonds : angle 4.98553 / 5.61 ( 1389) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.2402 (mtp) cc_final: 0.1794 (mmt) REVERT: A 154 LYS cc_start: 0.9472 (mttp) cc_final: 0.9172 (mttt) REVERT: A 186 MET cc_start: 0.7716 (mmm) cc_final: 0.7103 (mmm) REVERT: A 193 GLN cc_start: 0.8540 (tt0) cc_final: 0.8212 (tm-30) REVERT: A 202 LYS cc_start: 0.8299 (mmtp) cc_final: 0.7792 (mtmm) REVERT: A 230 ARG cc_start: 0.8972 (ttm110) cc_final: 0.8557 (ptp-110) REVERT: A 232 LEU cc_start: 0.8080 (tt) cc_final: 0.7628 (mm) REVERT: B 110 LYS cc_start: 0.8768 (pttm) cc_final: 0.8475 (pttm) REVERT: B 116 LYS cc_start: 0.9054 (mmtp) cc_final: 0.8254 (pttm) REVERT: B 224 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.7123 (m-80) REVERT: B 247 GLU cc_start: 0.3720 (OUTLIER) cc_final: 0.3043 (mp0) REVERT: B 386 ARG cc_start: -0.0962 (OUTLIER) cc_final: -0.1422 (ptt180) REVERT: B 456 MET cc_start: 0.9187 (mpp) cc_final: 0.8765 (mpp) REVERT: B 513 GLN cc_start: 0.7743 (mt0) cc_final: 0.5912 (pp30) REVERT: B 514 LYS cc_start: 0.8782 (tptp) cc_final: 0.8444 (tptp) REVERT: B 614 LYS cc_start: 0.9668 (mmmt) cc_final: 0.9261 (mmmm) REVERT: B 659 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7588 (mp0) REVERT: B 755 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: B 815 GLU cc_start: 0.8763 (tp30) cc_final: 0.8438 (tp30) REVERT: B 840 TYR cc_start: 0.8958 (t80) cc_final: 0.8431 (t80) REVERT: B 919 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8226 (t0) REVERT: B 941 GLN cc_start: 0.8671 (tp40) cc_final: 0.7985 (tp40) REVERT: B 1003 LYS cc_start: 0.9260 (mttt) cc_final: 0.8967 (mttm) REVERT: B 1131 MET cc_start: 0.9400 (tpp) cc_final: 0.8869 (mmm) REVERT: B 1216 LYS cc_start: 0.9017 (ttmm) cc_final: 0.8383 (tppt) REVERT: C 133 ILE cc_start: 0.8844 (mm) cc_final: 0.8401 (tp) REVERT: C 137 ASP cc_start: 0.9202 (m-30) cc_final: 0.8679 (m-30) REVERT: C 148 LYS cc_start: 0.9120 (ttmm) cc_final: 0.8636 (mtmm) REVERT: C 186 MET cc_start: 0.7372 (tpp) cc_final: 0.6989 (ttt) REVERT: C 209 TYR cc_start: 0.8437 (m-80) cc_final: 0.8175 (m-80) outliers start: 46 outliers final: 34 residues processed: 227 average time/residue: 0.1224 time to fit residues: 40.0909 Evaluate side-chains 232 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 747 ARG Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 72 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 34 optimal weight: 0.0270 chunk 59 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.2640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN C 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.106309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.077446 restraints weight = 45471.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.080057 restraints weight = 20667.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.081681 restraints weight = 13081.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.082446 restraints weight = 10059.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.082680 restraints weight = 8827.881| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13480 Z= 0.148 Angle : 0.746 14.271 18411 Z= 0.369 Chirality : 0.052 0.462 2001 Planarity : 0.004 0.056 2148 Dihedral : 16.028 133.072 2241 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.28 % Allowed : 23.95 % Favored : 72.77 % 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: -1.74 (0.22), residues: 1427 helix: 0.10 (0.21), residues: 591 sheet: -1.69 (0.41), residues: 142 loop : -2.19 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 230 TYR 0.025 0.001 TYR B 995 PHE 0.038 0.001 PHE C 196 TRP 0.009 0.001 TRP B 602 HIS 0.017 0.002 HIS C 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (13480) covalent geometry : angle 0.74639 / 0.37 (18411) hydrogen bonds : bond 0.03868 / 4.44 ( 496) hydrogen bonds : angle 4.94059 / 5.56 ( 1389) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.1807 (OUTLIER) cc_final: 0.1312 (mmt) REVERT: A 134 LYS cc_start: 0.9109 (mttm) cc_final: 0.8547 (mtmt) REVERT: A 154 LYS cc_start: 0.9493 (mttp) cc_final: 0.9112 (mttt) REVERT: A 186 MET cc_start: 0.7694 (mmm) cc_final: 0.7100 (mmm) REVERT: A 193 GLN cc_start: 0.8555 (tt0) cc_final: 0.8232 (tm-30) REVERT: A 202 LYS cc_start: 0.8273 (mmtp) cc_final: 0.7788 (mtmm) REVERT: A 230 ARG cc_start: 0.9047 (ttm110) cc_final: 0.8571 (ptp-110) REVERT: B 110 LYS cc_start: 0.8754 (pttm) cc_final: 0.8460 (pttm) REVERT: B 116 LYS cc_start: 0.9050 (mmtp) cc_final: 0.8257 (pttm) REVERT: B 224 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.7131 (m-80) REVERT: B 247 GLU cc_start: 0.4010 (OUTLIER) cc_final: 0.3298 (mp0) REVERT: B 386 ARG cc_start: -0.1101 (OUTLIER) cc_final: -0.1486 (ptt180) REVERT: B 456 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8765 (mpp) REVERT: B 513 GLN cc_start: 0.7822 (mt0) cc_final: 0.6037 (pp30) REVERT: B 514 LYS cc_start: 0.8783 (tptp) cc_final: 0.8417 (tptp) REVERT: B 614 LYS cc_start: 0.9667 (mmmt) cc_final: 0.9274 (mmmm) REVERT: B 659 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7587 (mp0) REVERT: B 755 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: B 815 GLU cc_start: 0.8775 (tp30) cc_final: 0.8412 (tp30) REVERT: B 840 TYR cc_start: 0.8931 (t80) cc_final: 0.8395 (t80) REVERT: B 919 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8238 (t0) REVERT: B 941 GLN cc_start: 0.8681 (tp40) cc_final: 0.7992 (tp40) REVERT: B 1003 LYS cc_start: 0.9255 (mttt) cc_final: 0.8956 (mttm) REVERT: B 1131 MET cc_start: 0.9412 (tpp) cc_final: 0.8869 (mmm) REVERT: B 1216 LYS cc_start: 0.9026 (ttmm) cc_final: 0.8385 (tppt) REVERT: C 133 ILE cc_start: 0.8835 (mm) cc_final: 0.8395 (tp) REVERT: C 137 ASP cc_start: 0.9200 (m-30) cc_final: 0.8647 (m-30) REVERT: C 148 LYS cc_start: 0.9148 (ttmm) cc_final: 0.8759 (mtmm) REVERT: C 209 TYR cc_start: 0.8393 (m-80) cc_final: 0.8153 (m-80) outliers start: 43 outliers final: 34 residues processed: 223 average time/residue: 0.1228 time to fit residues: 40.3409 Evaluate side-chains 232 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 747 ARG Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 882 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 139 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 GLN A 168 ASN ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN C 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.106775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.078057 restraints weight = 44905.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.080682 restraints weight = 20519.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.082208 restraints weight = 12972.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.082775 restraints weight = 10093.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.083616 restraints weight = 9033.486| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13480 Z= 0.141 Angle : 0.753 18.822 18411 Z= 0.369 Chirality : 0.052 0.450 2001 Planarity : 0.004 0.051 2148 Dihedral : 15.985 133.170 2241 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.28 % Allowed : 24.18 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.22), residues: 1427 helix: 0.09 (0.21), residues: 592 sheet: -1.60 (0.43), residues: 132 loop : -2.17 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 230 TYR 0.024 0.001 TYR B 995 PHE 0.033 0.001 PHE C 196 TRP 0.009 0.001 TRP B 602 HIS 0.017 0.001 HIS C 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (13480) covalent geometry : angle 0.75325 / 0.37 (18411) hydrogen bonds : bond 0.03832 / 4.39 ( 496) hydrogen bonds : angle 4.94584 / 5.54 ( 1389) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2822.08 seconds wall clock time: 49 minutes 28.99 seconds (2968.99 seconds total)