Starting phenix.real_space_refine on Wed Mar 4 11:58:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6omv_20132/03_2026/6omv_20132.cif Found real_map, /net/cci-nas-00/data/ceres_data/6omv_20132/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6omv_20132/03_2026/6omv_20132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6omv_20132/03_2026/6omv_20132.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6omv_20132/03_2026/6omv_20132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6omv_20132/03_2026/6omv_20132.map" } 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-dev-5986/lib/python3.9/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: {'RNA': 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: 3.13, per 1000 atoms: 0.24 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: 1.10 Conformation dependent library (CDL) restraints added in 447.0 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: 1.72 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: 2.71 Time building geometry restraints manager: 1.40 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 1.50e-02 4.44e+03 2.09e+01 bond pdb=" N LEU B 132 " pdb=" CA LEU B 132 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.73e+00 bond pdb=" N ASP B 572 " pdb=" CA ASP B 572 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.01e+00 bond pdb=" N GLU B 479 " pdb=" CA GLU B 479 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.29e-02 6.01e+03 7.90e+00 bond pdb=" N LYS B 265 " pdb=" CA LYS B 265 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.27e-02 6.20e+03 7.75e+00 ... (remaining 13475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 17406 2.08 - 4.16: 869 4.16 - 6.24: 100 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 - 35.20: 7717 35.20 - 70.41: 385 70.41 - 105.61: 19 105.61 - 140.82: 0 140.82 - 176.02: 1 Dihedral angle restraints: 8122 sinusoidal: 3849 harmonic: 4273 Sorted by residual: dihedral pdb=" O4' U G 16 " pdb=" C1' U G 16 " pdb=" N1 U G 16 " pdb=" C2 U G 16 " ideal model delta sinusoidal sigma weight residual -128.00 48.02 -176.02 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA GLU B 221 " pdb=" C GLU B 221 " pdb=" N GLY B 222 " pdb=" CA GLY B 222 " ideal model delta harmonic sigma weight residual 180.00 150.67 29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA LYS B 84 " pdb=" C LYS B 84 " pdb=" N THR B 85 " pdb=" CA THR B 85 " ideal model delta harmonic sigma weight residual 180.00 -151.76 -28.24 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 8119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1392 0.055 - 0.111: 472 0.111 - 0.166: 108 0.166 - 0.221: 23 0.221 - 0.277: 6 Chirality restraints: 2001 Sorted by residual: chirality pdb=" CA ILE B1034 " pdb=" N ILE B1034 " pdb=" C ILE B1034 " pdb=" CB ILE B1034 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C3' C G 11 " pdb=" C4' C G 11 " pdb=" O3' C G 11 " pdb=" C2' C G 11 " both_signs ideal model delta sigma weight residual False -2.48 -2.73 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL B 936 " pdb=" CA VAL B 936 " pdb=" CG1 VAL B 936 " pdb=" CG2 VAL B 936 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.820 Find NCS groups from input model: 0.080 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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= 0.385 Angle : 1.053 10.406 18411 Z= 0.627 Chirality : 0.060 0.277 2001 Planarity : 0.006 0.075 2148 Dihedral : 18.637 176.023 5368 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 covalent geometry : bond 0.00758 (13480) covalent geometry : angle 1.05348 (18411) hydrogen bonds : bond 0.18847 ( 496) hydrogen bonds : angle 8.23253 ( 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 : 0.510 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: 0.1406 time to fit residues: 54.8718 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 : 0.471 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 797 HIS B 861 ASN B 873 HIS B 889 ASN B 895 ASN B 978 ASN B 989 GLN ** B1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1118 GLN C 168 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.107809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.079110 restraints weight = 44868.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.081683 restraints weight = 19984.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.083211 restraints weight = 12566.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.084113 restraints weight = 9758.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.084475 restraints weight = 8547.094| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13480 Z= 0.135 Angle : 0.658 11.676 18411 Z= 0.353 Chirality : 0.043 0.280 2001 Planarity : 0.004 0.062 2148 Dihedral : 16.997 177.908 2333 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.29 % Favored : 92.64 % Rotamer: Outliers : 2.75 % Allowed : 16.09 % Favored : 81.16 % 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: -3.16 (0.20), residues: 1427 helix: -1.45 (0.19), residues: 602 sheet: -1.82 (0.42), residues: 132 loop : -2.77 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 18 TYR 0.025 0.002 TYR C 209 PHE 0.020 0.001 PHE C 196 TRP 0.007 0.001 TRP B 602 HIS 0.005 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00282 (13480) covalent geometry : angle 0.65758 (18411) hydrogen bonds : bond 0.04358 ( 496) hydrogen bonds : angle 5.59018 ( 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 260 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 0.482 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: 0.2340 (mtp) cc_final: 0.1573 (mmt) REVERT: A 133 ILE cc_start: 0.9141 (mt) cc_final: 0.8793 (mm) REVERT: A 135 GLU cc_start: 0.8824 (tp30) cc_final: 0.8611 (tp30) REVERT: A 142 GLN cc_start: 0.8700 (tt0) cc_final: 0.8444 (tp-100) REVERT: A 144 TYR cc_start: 0.7665 (t80) cc_final: 0.6825 (t80) REVERT: A 154 LYS cc_start: 0.9434 (mttp) cc_final: 0.9027 (mtmt) REVERT: A 181 GLN cc_start: 0.8369 (tt0) cc_final: 0.7893 (tp-100) REVERT: A 193 GLN cc_start: 0.8567 (tt0) cc_final: 0.8343 (tm-30) REVERT: A 202 LYS cc_start: 0.8043 (mmtp) cc_final: 0.7563 (ptpp) REVERT: A 227 GLU cc_start: 0.9109 (mp0) cc_final: 0.8858 (mp0) REVERT: A 230 ARG cc_start: 0.8828 (ttm110) cc_final: 0.8609 (ttm110) REVERT: A 232 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8051 (mt) REVERT: B 28 GLN cc_start: 0.9019 (tp40) cc_final: 0.8804 (tm-30) REVERT: B 495 ASP cc_start: 0.6661 (p0) cc_final: 0.6354 (p0) REVERT: B 603 MET cc_start: 0.9308 (mpp) cc_final: 0.9087 (pmm) REVERT: B 815 GLU cc_start: 0.8518 (tp30) cc_final: 0.8225 (tp30) REVERT: B 840 TYR cc_start: 0.8874 (t80) cc_final: 0.8555 (t80) REVERT: B 895 ASN cc_start: 0.7837 (m110) cc_final: 0.7608 (m-40) REVERT: B 940 LYS cc_start: 0.8912 (tttt) cc_final: 0.8348 (ptmm) REVERT: B 941 GLN cc_start: 0.8467 (tp40) cc_final: 0.7996 (tp40) REVERT: B 944 GLN cc_start: 0.8244 (mt0) cc_final: 0.7892 (mt0) REVERT: B 949 MET cc_start: 0.7998 (ttm) cc_final: 0.7699 (ttm) REVERT: B 1003 LYS cc_start: 0.9249 (mttt) cc_final: 0.8959 (mttm) REVERT: B 1216 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8271 (tppt) REVERT: C 133 ILE cc_start: 0.8764 (mm) cc_final: 0.8437 (tp) REVERT: C 137 ASP cc_start: 0.9236 (m-30) cc_final: 0.8968 (m-30) REVERT: C 186 MET cc_start: 0.7529 (tpp) cc_final: 0.7292 (ttt) REVERT: C 209 TYR cc_start: 0.8115 (m-80) cc_final: 0.7828 (m-80) REVERT: C 222 ARG cc_start: 0.9115 (tpp-160) cc_final: 0.8829 (tpp80) outliers start: 36 outliers final: 16 residues processed: 245 average time/residue: 0.1204 time to fit residues: 42.4454 Evaluate side-chains 213 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 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 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 1089 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 127 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 44 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 105 optimal weight: 0.0980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 HIS B 808 ASN B1108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.107715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.079024 restraints weight = 45609.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.081556 restraints weight = 20368.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.083131 restraints weight = 12937.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.083888 restraints weight = 10032.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.084217 restraints weight = 8891.846| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2698 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= 0.142 Angle : 0.629 10.565 18411 Z= 0.335 Chirality : 0.042 0.183 2001 Planarity : 0.004 0.053 2148 Dihedral : 16.723 177.993 2325 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.64 % Favored : 92.29 % Rotamer: Outliers : 3.20 % Allowed : 18.46 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.21), residues: 1427 helix: -0.73 (0.20), residues: 601 sheet: -1.59 (0.44), residues: 130 loop : -2.55 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 155 TYR 0.023 0.001 TYR B 510 PHE 0.012 0.001 PHE B 490 TRP 0.009 0.001 TRP B 602 HIS 0.005 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00301 (13480) covalent geometry : angle 0.62878 (18411) hydrogen bonds : bond 0.03840 ( 496) hydrogen bonds : angle 5.19988 ( 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 263 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 0.517 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: 0.2397 (mtp) cc_final: 0.2002 (mmt) REVERT: A 135 GLU cc_start: 0.8773 (tp30) cc_final: 0.8544 (tp30) REVERT: A 142 GLN cc_start: 0.8794 (tt0) cc_final: 0.8540 (tp-100) REVERT: A 144 TYR cc_start: 0.7753 (t80) cc_final: 0.6826 (t80) REVERT: A 154 LYS cc_start: 0.9456 (mttp) cc_final: 0.8994 (mtmt) REVERT: A 181 GLN cc_start: 0.8321 (tt0) cc_final: 0.8028 (tp40) REVERT: A 193 GLN cc_start: 0.8556 (tt0) cc_final: 0.8337 (tm-30) REVERT: A 202 LYS cc_start: 0.7912 (mmtp) cc_final: 0.7349 (ptpp) REVERT: A 232 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8033 (mt) REVERT: B 110 LYS cc_start: 0.8566 (pttm) cc_final: 0.8075 (pttm) REVERT: B 167 LYS cc_start: 0.7509 (pttt) cc_final: 0.7301 (pttt) REVERT: B 510 TYR cc_start: 0.7579 (t80) cc_final: 0.6606 (t80) REVERT: B 513 GLN cc_start: 0.6044 (OUTLIER) cc_final: 0.4296 (pp30) REVERT: B 614 LYS cc_start: 0.9687 (mmmt) cc_final: 0.9435 (pttp) REVERT: B 815 GLU cc_start: 0.8556 (tp30) cc_final: 0.8278 (tp30) REVERT: B 840 TYR cc_start: 0.8892 (t80) cc_final: 0.8604 (t80) REVERT: B 940 LYS cc_start: 0.8963 (tttt) cc_final: 0.8399 (ptmm) REVERT: B 941 GLN cc_start: 0.8372 (tp40) cc_final: 0.7732 (tp40) REVERT: B 944 GLN cc_start: 0.8300 (mt0) cc_final: 0.8074 (mt0) REVERT: B 1003 LYS cc_start: 0.9243 (mttt) cc_final: 0.8987 (mttm) REVERT: B 1068 TYR cc_start: 0.9301 (t80) cc_final: 0.9059 (t80) REVERT: B 1108 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7712 (mp10) REVERT: B 1216 LYS cc_start: 0.8902 (ttmm) cc_final: 0.8333 (tppt) REVERT: C 133 ILE cc_start: 0.8899 (mm) cc_final: 0.8563 (tp) REVERT: C 137 ASP cc_start: 0.9280 (m-30) cc_final: 0.8958 (m-30) REVERT: C 148 LYS cc_start: 0.8997 (ttmm) cc_final: 0.8396 (mtmm) REVERT: C 192 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8590 (m-30) REVERT: C 209 TYR cc_start: 0.8358 (m-80) cc_final: 0.8030 (m-80) REVERT: C 222 ARG cc_start: 0.9154 (tpp-160) cc_final: 0.8875 (tpp80) REVERT: C 230 ARG cc_start: 0.7296 (mtt-85) cc_final: 0.6724 (ptp-170) outliers start: 42 outliers final: 24 residues processed: 242 average time/residue: 0.1212 time to fit residues: 42.3625 Evaluate side-chains 227 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 232 LEU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 513 GLN 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 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 951 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 B residue 1108 GLN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 60 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 168 ASN B 76 ASN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN B 895 ASN ** B1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 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 = 0.3881 r_free = 0.3881 target = 0.104351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.080159 restraints weight = 45778.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.079444 restraints weight = 26034.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.080398 restraints weight = 20696.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.080376 restraints weight = 15524.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.081498 restraints weight = 13964.441| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13480 Z= 0.197 Angle : 0.660 9.499 18411 Z= 0.352 Chirality : 0.044 0.193 2001 Planarity : 0.004 0.046 2148 Dihedral : 16.723 177.843 2325 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.62 % Favored : 91.31 % Rotamer: Outliers : 3.74 % Allowed : 20.06 % Favored : 76.20 % 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: -2.11 (0.22), residues: 1427 helix: -0.35 (0.21), residues: 608 sheet: -1.41 (0.44), residues: 133 loop : -2.41 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 155 TYR 0.026 0.002 TYR B 562 PHE 0.016 0.001 PHE B 946 TRP 0.014 0.001 TRP B 602 HIS 0.005 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00419 (13480) covalent geometry : angle 0.66008 (18411) hydrogen bonds : bond 0.03906 ( 496) hydrogen bonds : angle 5.16243 ( 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 241 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 192 time to evaluate : 0.482 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: 0.1966 (mtp) cc_final: 0.1433 (mmt) REVERT: A 142 GLN cc_start: 0.8945 (tt0) cc_final: 0.8557 (tp-100) REVERT: A 154 LYS cc_start: 0.9499 (mttp) cc_final: 0.9019 (mtmt) REVERT: A 186 MET cc_start: 0.7486 (mmm) cc_final: 0.6840 (mmm) REVERT: A 193 GLN cc_start: 0.8624 (tt0) cc_final: 0.8381 (tm-30) REVERT: A 202 LYS cc_start: 0.8374 (mmtp) cc_final: 0.7885 (mtmm) REVERT: A 227 GLU cc_start: 0.9173 (mp0) cc_final: 0.8961 (mp0) REVERT: A 232 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8025 (mt) REVERT: B 116 LYS cc_start: 0.9069 (mmtp) cc_final: 0.8266 (pttm) REVERT: B 510 TYR cc_start: 0.7581 (t80) cc_final: 0.6417 (t80) REVERT: B 513 GLN cc_start: 0.6325 (OUTLIER) cc_final: 0.4508 (pp30) REVERT: B 614 LYS cc_start: 0.9689 (mmmt) cc_final: 0.9325 (mmmm) REVERT: B 659 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7627 (mp0) REVERT: B 815 GLU cc_start: 0.8699 (tp30) cc_final: 0.8402 (tp30) REVERT: B 840 TYR cc_start: 0.8984 (t80) cc_final: 0.8603 (t80) REVERT: B 895 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7731 (t0) REVERT: B 919 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8131 (t0) REVERT: B 940 LYS cc_start: 0.9079 (tttt) cc_final: 0.8401 (ptmm) REVERT: B 941 GLN cc_start: 0.8498 (tp40) cc_final: 0.7886 (tp40) REVERT: B 944 GLN cc_start: 0.8370 (mt0) cc_final: 0.8132 (mt0) REVERT: B 949 MET cc_start: 0.8013 (ttm) cc_final: 0.7678 (ttm) REVERT: B 1003 LYS cc_start: 0.9267 (mttt) cc_final: 0.9003 (mttm) REVERT: B 1131 MET cc_start: 0.8921 (mmm) cc_final: 0.8522 (mmm) REVERT: B 1216 LYS cc_start: 0.8907 (ttmm) cc_final: 0.8352 (tppt) REVERT: C 133 ILE cc_start: 0.8905 (mm) cc_final: 0.8463 (tp) REVERT: C 137 ASP cc_start: 0.9298 (m-30) cc_final: 0.8823 (m-30) REVERT: C 138 LEU cc_start: 0.8686 (tt) cc_final: 0.7341 (tp) REVERT: C 148 LYS cc_start: 0.9055 (ttmm) cc_final: 0.8549 (mtmm) REVERT: C 209 TYR cc_start: 0.8191 (m-80) cc_final: 0.7902 (m-80) REVERT: C 222 ARG cc_start: 0.9164 (tpp-160) cc_final: 0.8896 (tpp80) outliers start: 49 outliers final: 29 residues processed: 221 average time/residue: 0.1103 time to fit residues: 35.8241 Evaluate side-chains 212 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 158 VAL Chi-restraints excluded: chain A residue 166 ASP 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 132 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 513 GLN 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 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 951 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 150 LEU Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 34 optimal weight: 0.4980 chunk 116 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 168 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN B 268 GLN B 895 ASN B1108 GLN ** C 193 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 = 0.3997 r_free = 0.3997 target = 0.108951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.079981 restraints weight = 45695.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.082535 restraints weight = 20565.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.084122 restraints weight = 13008.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.084975 restraints weight = 10116.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.085365 restraints weight = 8875.897| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13480 Z= 0.118 Angle : 0.613 9.656 18411 Z= 0.321 Chirality : 0.042 0.198 2001 Planarity : 0.003 0.044 2148 Dihedral : 16.521 176.563 2325 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.20 % Allowed : 21.51 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.78 (0.22), residues: 1427 helix: -0.05 (0.21), residues: 596 sheet: -1.43 (0.42), residues: 136 loop : -2.19 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1189 TYR 0.018 0.001 TYR B 562 PHE 0.016 0.001 PHE B 173 TRP 0.009 0.001 TRP B 602 HIS 0.005 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00249 (13480) covalent geometry : angle 0.61312 (18411) hydrogen bonds : bond 0.03537 ( 496) hydrogen bonds : angle 4.86690 ( 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 262 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 0.501 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: 0.2076 (mtp) cc_final: 0.1514 (mmt) REVERT: A 142 GLN cc_start: 0.8926 (tt0) cc_final: 0.8608 (tp-100) REVERT: A 144 TYR cc_start: 0.7745 (t80) cc_final: 0.6866 (t80) REVERT: A 154 LYS cc_start: 0.9457 (mttp) cc_final: 0.8774 (mtmt) REVERT: A 181 GLN cc_start: 0.8440 (tt0) cc_final: 0.8209 (tt0) REVERT: A 184 GLU cc_start: 0.5441 (OUTLIER) cc_final: 0.5128 (mt-10) REVERT: A 186 MET cc_start: 0.7433 (mmm) cc_final: 0.6818 (mmm) REVERT: A 193 GLN cc_start: 0.8562 (tt0) cc_final: 0.8356 (tm-30) REVERT: A 202 LYS cc_start: 0.7994 (mmtp) cc_final: 0.7470 (mtmm) REVERT: B 110 LYS cc_start: 0.8670 (pttm) cc_final: 0.8368 (pttm) REVERT: B 116 LYS cc_start: 0.8974 (mmtp) cc_final: 0.8169 (pttm) REVERT: B 167 LYS cc_start: 0.7500 (pttt) cc_final: 0.7259 (pttt) REVERT: B 219 PHE cc_start: 0.7895 (m-80) cc_final: 0.7693 (m-80) REVERT: B 386 ARG cc_start: -0.0995 (OUTLIER) cc_final: -0.1454 (ptt180) REVERT: B 510 TYR cc_start: 0.7477 (t80) cc_final: 0.6468 (t80) REVERT: B 513 GLN cc_start: 0.6114 (OUTLIER) cc_final: 0.4589 (pp30) REVERT: B 531 MET cc_start: 0.8806 (mmm) cc_final: 0.8159 (tpp) REVERT: B 614 LYS cc_start: 0.9688 (mmmt) cc_final: 0.9271 (mmmm) REVERT: B 659 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7543 (mp0) REVERT: B 815 GLU cc_start: 0.8568 (tp30) cc_final: 0.8246 (tp30) REVERT: B 840 TYR cc_start: 0.8842 (t80) cc_final: 0.8276 (t80) REVERT: B 853 GLN cc_start: 0.8376 (pm20) cc_final: 0.8093 (pm20) REVERT: B 895 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7458 (t0) REVERT: B 919 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8303 (t0) REVERT: B 940 LYS cc_start: 0.8954 (tttt) cc_final: 0.8299 (ptmm) REVERT: B 941 GLN cc_start: 0.8405 (tp40) cc_final: 0.7924 (tp40) REVERT: B 1003 LYS cc_start: 0.9222 (mttt) cc_final: 0.8880 (mttm) REVERT: B 1054 ARG cc_start: 0.8826 (ttm170) cc_final: 0.8358 (mtt-85) REVERT: B 1068 TYR cc_start: 0.9267 (t80) cc_final: 0.8860 (t80) REVERT: B 1108 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7899 (mp10) REVERT: B 1131 MET cc_start: 0.8864 (mmm) cc_final: 0.8422 (mmm) REVERT: B 1216 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8332 (tppt) REVERT: C 133 ILE cc_start: 0.8888 (mm) cc_final: 0.8384 (tp) REVERT: C 137 ASP cc_start: 0.9247 (m-30) cc_final: 0.8645 (m-30) REVERT: C 148 LYS cc_start: 0.9107 (ttmm) cc_final: 0.8582 (mtmm) REVERT: C 163 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8104 (mm-40) REVERT: C 209 TYR cc_start: 0.8351 (m-80) cc_final: 0.8006 (m-80) outliers start: 42 outliers final: 27 residues processed: 246 average time/residue: 0.1240 time to fit residues: 44.0382 Evaluate side-chains 227 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 161 SER Chi-restraints excluded: chain A residue 177 LEU 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 132 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain B residue 513 GLN 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 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 927 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 1108 GLN Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 13 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 32 optimal weight: 0.0870 chunk 11 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN B 112 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN B 895 ASN ** B1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.108461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.079563 restraints weight = 44940.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.082164 restraints weight = 20085.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.083740 restraints weight = 12617.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.084476 restraints weight = 9770.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.085078 restraints weight = 8616.510| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13480 Z= 0.119 Angle : 0.624 11.253 18411 Z= 0.323 Chirality : 0.042 0.218 2001 Planarity : 0.003 0.050 2148 Dihedral : 16.437 176.909 2325 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.67 % Allowed : 22.73 % Favored : 74.60 % 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: -1.65 (0.22), residues: 1427 helix: 0.12 (0.22), residues: 591 sheet: -1.43 (0.42), residues: 142 loop : -2.14 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1189 TYR 0.025 0.001 TYR B 995 PHE 0.016 0.001 PHE B 521 TRP 0.008 0.001 TRP B 602 HIS 0.004 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00250 (13480) covalent geometry : angle 0.62378 (18411) hydrogen bonds : bond 0.03444 ( 496) hydrogen bonds : angle 4.74943 ( 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 241 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.484 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: 0.2134 (mtp) cc_final: 0.1743 (mmt) REVERT: A 142 GLN cc_start: 0.9076 (tt0) cc_final: 0.8577 (tp-100) REVERT: A 144 TYR cc_start: 0.7673 (t80) cc_final: 0.6748 (t80) REVERT: A 154 LYS cc_start: 0.9453 (mttp) cc_final: 0.9044 (mttt) REVERT: A 181 GLN cc_start: 0.8422 (tt0) cc_final: 0.8165 (tt0) REVERT: A 186 MET cc_start: 0.7493 (mmm) cc_final: 0.6783 (mmm) REVERT: A 202 LYS cc_start: 0.7973 (mmtp) cc_final: 0.7527 (mtmm) REVERT: A 206 ARG cc_start: 0.8309 (ttp80) cc_final: 0.8038 (ttp80) REVERT: A 230 ARG cc_start: 0.9078 (ttm110) cc_final: 0.8562 (ptp-110) REVERT: B 116 LYS cc_start: 0.8875 (mmtp) cc_final: 0.8187 (pttm) REVERT: B 167 LYS cc_start: 0.7481 (pttt) cc_final: 0.7253 (pttt) REVERT: B 219 PHE cc_start: 0.7959 (m-80) cc_final: 0.7667 (m-80) REVERT: B 247 GLU cc_start: 0.3852 (OUTLIER) cc_final: 0.3199 (mp0) REVERT: B 386 ARG cc_start: -0.0845 (OUTLIER) cc_final: -0.1255 (ptt180) REVERT: B 510 TYR cc_start: 0.7454 (t80) cc_final: 0.6436 (t80) REVERT: B 513 GLN cc_start: 0.6113 (OUTLIER) cc_final: 0.4566 (pp30) REVERT: B 531 MET cc_start: 0.8817 (mmm) cc_final: 0.8237 (tpp) REVERT: B 614 LYS cc_start: 0.9676 (mmmt) cc_final: 0.9264 (mmmm) REVERT: B 659 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7468 (mp0) REVERT: B 815 GLU cc_start: 0.8665 (tp30) cc_final: 0.8306 (tp30) REVERT: B 840 TYR cc_start: 0.8862 (t80) cc_final: 0.8295 (t80) REVERT: B 853 GLN cc_start: 0.8387 (pm20) cc_final: 0.8163 (pm20) REVERT: B 895 ASN cc_start: 0.8029 (OUTLIER) cc_final: 0.7661 (t0) REVERT: B 919 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8328 (t0) REVERT: B 941 GLN cc_start: 0.8311 (tp40) cc_final: 0.8041 (tp40) REVERT: B 1003 LYS cc_start: 0.9211 (mttt) cc_final: 0.8936 (mttm) REVERT: B 1131 MET cc_start: 0.8975 (mmm) cc_final: 0.8583 (mmm) REVERT: B 1216 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8333 (tppt) REVERT: C 133 ILE cc_start: 0.8878 (mm) cc_final: 0.8397 (tp) REVERT: C 137 ASP cc_start: 0.9223 (m-30) cc_final: 0.8642 (m-30) REVERT: C 138 LEU cc_start: 0.9033 (tp) cc_final: 0.8792 (tp) REVERT: C 148 LYS cc_start: 0.9147 (ttmm) cc_final: 0.8661 (mtmm) REVERT: C 163 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8110 (mm-40) REVERT: C 209 TYR cc_start: 0.8402 (m-80) cc_final: 0.8065 (m-80) outliers start: 35 outliers final: 26 residues processed: 230 average time/residue: 0.1206 time to fit residues: 40.1701 Evaluate side-chains 230 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE 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 132 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 513 GLN 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 620 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 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 927 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 182 VAL Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 118 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN B 895 ASN B1108 GLN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.105454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.081955 restraints weight = 44820.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.080802 restraints weight = 24980.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.081461 restraints weight = 18274.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.081806 restraints weight = 13979.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.081936 restraints weight = 12987.333| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13480 Z= 0.152 Angle : 0.653 12.844 18411 Z= 0.336 Chirality : 0.043 0.185 2001 Planarity : 0.003 0.045 2148 Dihedral : 16.426 177.021 2325 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.13 % Allowed : 23.26 % Favored : 73.61 % 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: -1.56 (0.22), residues: 1427 helix: 0.19 (0.22), residues: 599 sheet: -1.45 (0.42), residues: 143 loop : -2.09 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 102 TYR 0.032 0.002 TYR B1185 PHE 0.015 0.001 PHE B 521 TRP 0.011 0.001 TRP A 178 HIS 0.004 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00324 (13480) covalent geometry : angle 0.65288 (18411) hydrogen bonds : bond 0.03483 ( 496) hydrogen bonds : angle 4.76734 ( 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 237 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 0.498 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: 0.2366 (OUTLIER) cc_final: 0.2012 (mmt) REVERT: A 142 GLN cc_start: 0.8991 (tt0) cc_final: 0.8592 (tp-100) REVERT: A 144 TYR cc_start: 0.7714 (t80) cc_final: 0.6973 (t80) REVERT: A 154 LYS cc_start: 0.9474 (mttp) cc_final: 0.9049 (mtmt) REVERT: A 181 GLN cc_start: 0.8400 (tt0) cc_final: 0.8144 (tt0) REVERT: A 186 MET cc_start: 0.7646 (mmm) cc_final: 0.6897 (mmm) REVERT: A 202 LYS cc_start: 0.8211 (mmtp) cc_final: 0.7764 (mtmm) REVERT: A 230 ARG cc_start: 0.9128 (ttm110) cc_final: 0.8669 (ptp-110) REVERT: B 116 LYS cc_start: 0.8931 (mmtp) cc_final: 0.8252 (pttm) REVERT: B 219 PHE cc_start: 0.7959 (m-80) cc_final: 0.7607 (m-80) REVERT: B 247 GLU cc_start: 0.3868 (OUTLIER) cc_final: 0.3168 (mp0) REVERT: B 386 ARG cc_start: -0.0839 (OUTLIER) cc_final: -0.1262 (ptt180) REVERT: B 458 ASP cc_start: 0.9219 (m-30) cc_final: 0.8734 (p0) REVERT: B 510 TYR cc_start: 0.7515 (t80) cc_final: 0.6455 (t80) REVERT: B 513 GLN cc_start: 0.6539 (OUTLIER) cc_final: 0.6003 (tp-100) REVERT: B 614 LYS cc_start: 0.9673 (mmmt) cc_final: 0.9314 (mmmm) REVERT: B 659 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7623 (mp0) REVERT: B 815 GLU cc_start: 0.8836 (tp30) cc_final: 0.8463 (tp30) REVERT: B 840 TYR cc_start: 0.8982 (t80) cc_final: 0.8444 (t80) REVERT: B 895 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7567 (t0) REVERT: B 919 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8315 (t0) REVERT: B 941 GLN cc_start: 0.8480 (tp40) cc_final: 0.8083 (tp40) REVERT: B 949 MET cc_start: 0.7922 (ttm) cc_final: 0.7602 (ttm) REVERT: B 1003 LYS cc_start: 0.9254 (mttt) cc_final: 0.8978 (mttm) REVERT: B 1054 ARG cc_start: 0.8942 (ttm170) cc_final: 0.8447 (mmt-90) REVERT: B 1131 MET cc_start: 0.9008 (mmm) cc_final: 0.8575 (mmm) REVERT: B 1134 MET cc_start: 0.8847 (tpt) cc_final: 0.8641 (tpt) REVERT: B 1216 LYS cc_start: 0.8971 (ttmm) cc_final: 0.8422 (tppt) REVERT: C 133 ILE cc_start: 0.8870 (mm) cc_final: 0.8369 (tp) REVERT: C 137 ASP cc_start: 0.9234 (m-30) cc_final: 0.8551 (m-30) REVERT: C 138 LEU cc_start: 0.9078 (tp) cc_final: 0.8874 (tp) REVERT: C 163 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8160 (mm-40) REVERT: C 192 ASP cc_start: 0.8449 (m-30) cc_final: 0.8062 (m-30) REVERT: C 209 TYR cc_start: 0.8384 (m-80) cc_final: 0.8033 (m-80) outliers start: 41 outliers final: 30 residues processed: 222 average time/residue: 0.1195 time to fit residues: 38.2717 Evaluate side-chains 221 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 177 LEU 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 132 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 513 GLN 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 620 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 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 927 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 1108 GLN Chi-restraints excluded: chain B residue 1189 ARG Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 107 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 ASN B1108 GLN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.104995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.081566 restraints weight = 44862.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.080026 restraints weight = 25428.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.080771 restraints weight = 19173.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.081108 restraints weight = 14489.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.081253 restraints weight = 13373.681| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3725 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= 0.163 Angle : 0.660 11.616 18411 Z= 0.342 Chirality : 0.043 0.181 2001 Planarity : 0.004 0.052 2148 Dihedral : 16.416 176.812 2325 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.13 % Allowed : 23.19 % Favored : 73.68 % 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: -1.50 (0.23), residues: 1427 helix: 0.24 (0.22), residues: 598 sheet: -1.53 (0.42), residues: 145 loop : -2.03 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 102 TYR 0.027 0.002 TYR B1185 PHE 0.024 0.001 PHE C 196 TRP 0.010 0.001 TRP B 602 HIS 0.004 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00352 (13480) covalent geometry : angle 0.66001 (18411) hydrogen bonds : bond 0.03522 ( 496) hydrogen bonds : angle 4.78920 ( 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 230 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.2422 (OUTLIER) cc_final: 0.2112 (mmt) REVERT: A 142 GLN cc_start: 0.9010 (tt0) cc_final: 0.8652 (tp-100) REVERT: A 144 TYR cc_start: 0.7861 (t80) cc_final: 0.7120 (t80) REVERT: A 154 LYS cc_start: 0.9472 (mttp) cc_final: 0.9082 (mtmt) REVERT: A 181 GLN cc_start: 0.8368 (tt0) cc_final: 0.8132 (tt0) REVERT: A 186 MET cc_start: 0.7847 (mmm) cc_final: 0.7041 (mmm) REVERT: A 193 GLN cc_start: 0.8553 (tt0) cc_final: 0.8345 (tm-30) REVERT: A 196 PHE cc_start: 0.8617 (m-80) cc_final: 0.8388 (m-80) REVERT: A 202 LYS cc_start: 0.8200 (mmtp) cc_final: 0.7769 (mtmm) REVERT: A 228 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8700 (mt-10) REVERT: A 230 ARG cc_start: 0.9167 (ttm110) cc_final: 0.8730 (ptp-110) REVERT: B 116 LYS cc_start: 0.8958 (mmtp) cc_final: 0.8285 (pttm) REVERT: B 247 GLU cc_start: 0.3785 (OUTLIER) cc_final: 0.3063 (mp0) REVERT: B 386 ARG cc_start: -0.0707 (OUTLIER) cc_final: -0.1139 (ptt180) REVERT: B 458 ASP cc_start: 0.9190 (m-30) cc_final: 0.8746 (p0) REVERT: B 510 TYR cc_start: 0.7535 (t80) cc_final: 0.6706 (t80) REVERT: B 513 GLN cc_start: 0.6529 (OUTLIER) cc_final: 0.4729 (pp30) REVERT: B 614 LYS cc_start: 0.9679 (mmmt) cc_final: 0.9314 (mmmm) REVERT: B 659 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7641 (mp0) REVERT: B 815 GLU cc_start: 0.8842 (tp30) cc_final: 0.8480 (tp30) REVERT: B 840 TYR cc_start: 0.8992 (t80) cc_final: 0.8391 (t80) REVERT: B 895 ASN cc_start: 0.8146 (OUTLIER) cc_final: 0.7698 (t0) REVERT: B 919 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8310 (t0) REVERT: B 941 GLN cc_start: 0.8519 (tp40) cc_final: 0.8190 (tp40) REVERT: B 949 MET cc_start: 0.7936 (ttm) cc_final: 0.7636 (ttm) REVERT: B 986 MET cc_start: 0.8576 (mpp) cc_final: 0.7995 (mpp) REVERT: B 1003 LYS cc_start: 0.9250 (mttt) cc_final: 0.8891 (mttm) REVERT: B 1054 ARG cc_start: 0.8979 (ttm170) cc_final: 0.8491 (mmt-90) REVERT: B 1131 MET cc_start: 0.9022 (mmm) cc_final: 0.8569 (mmm) REVERT: B 1216 LYS cc_start: 0.8969 (ttmm) cc_final: 0.8395 (tppt) REVERT: C 137 ASP cc_start: 0.9250 (m-30) cc_final: 0.8861 (m-30) REVERT: C 163 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8194 (mm-40) REVERT: C 209 TYR cc_start: 0.8407 (m-80) cc_final: 0.8046 (m-80) outliers start: 41 outliers final: 28 residues processed: 218 average time/residue: 0.1206 time to fit residues: 38.1020 Evaluate side-chains 220 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 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 513 GLN 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 620 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 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 927 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 1189 ARG Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 72 optimal weight: 0.0980 chunk 17 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** 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 = 0.3890 r_free = 0.3890 target = 0.105741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.076643 restraints weight = 44711.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.079250 restraints weight = 20362.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.080847 restraints weight = 12905.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.081632 restraints weight = 10043.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.082167 restraints weight = 8834.950| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3850 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= 0.146 Angle : 0.666 10.892 18411 Z= 0.341 Chirality : 0.043 0.183 2001 Planarity : 0.004 0.058 2148 Dihedral : 16.376 176.490 2325 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.05 % Allowed : 23.80 % 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: -1.39 (0.23), residues: 1427 helix: 0.35 (0.22), residues: 591 sheet: -1.53 (0.42), residues: 145 loop : -1.96 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 187 TYR 0.027 0.001 TYR B1185 PHE 0.016 0.001 PHE C 196 TRP 0.009 0.001 TRP B 602 HIS 0.004 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00318 (13480) covalent geometry : angle 0.66553 (18411) hydrogen bonds : bond 0.03450 ( 496) hydrogen bonds : angle 4.76305 ( 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 233 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 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: A 120 MET cc_start: 0.2449 (OUTLIER) cc_final: 0.2188 (mmt) REVERT: A 142 GLN cc_start: 0.9071 (tt0) cc_final: 0.8680 (tp-100) REVERT: A 144 TYR cc_start: 0.7823 (t80) cc_final: 0.7192 (t80) REVERT: A 154 LYS cc_start: 0.9473 (mttp) cc_final: 0.9028 (mtpt) REVERT: A 181 GLN cc_start: 0.8447 (tt0) cc_final: 0.8161 (tt0) REVERT: A 193 GLN cc_start: 0.8566 (tt0) cc_final: 0.8292 (tm-30) REVERT: A 196 PHE cc_start: 0.8666 (m-80) cc_final: 0.8411 (m-80) REVERT: A 202 LYS cc_start: 0.8175 (mmtp) cc_final: 0.7754 (mtmm) REVERT: A 228 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8673 (mt-10) REVERT: A 230 ARG cc_start: 0.9167 (ttm110) cc_final: 0.8793 (ptp-110) REVERT: B 116 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8275 (pttm) REVERT: B 247 GLU cc_start: 0.3793 (OUTLIER) cc_final: 0.3062 (mp0) REVERT: B 386 ARG cc_start: -0.0934 (OUTLIER) cc_final: -0.1288 (ptt180) REVERT: B 458 ASP cc_start: 0.9150 (m-30) cc_final: 0.8708 (p0) REVERT: B 510 TYR cc_start: 0.7507 (t80) cc_final: 0.6476 (t80) REVERT: B 513 GLN cc_start: 0.6537 (OUTLIER) cc_final: 0.6083 (tp-100) REVERT: B 614 LYS cc_start: 0.9685 (mmmt) cc_final: 0.9268 (mmmm) REVERT: B 659 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7534 (mp0) REVERT: B 815 GLU cc_start: 0.8838 (tp30) cc_final: 0.8462 (tp30) REVERT: B 840 TYR cc_start: 0.9008 (t80) cc_final: 0.8267 (t80) REVERT: B 895 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7752 (t0) REVERT: B 919 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8286 (t0) REVERT: B 941 GLN cc_start: 0.8569 (tp40) cc_final: 0.8175 (tp40) REVERT: B 949 MET cc_start: 0.7972 (ttm) cc_final: 0.7682 (ttm) REVERT: B 1003 LYS cc_start: 0.9255 (mttt) cc_final: 0.8854 (mttm) REVERT: B 1013 LEU cc_start: 0.8561 (tp) cc_final: 0.8350 (tp) REVERT: B 1131 MET cc_start: 0.9062 (mmm) cc_final: 0.8640 (mmm) REVERT: B 1216 LYS cc_start: 0.9003 (ttmm) cc_final: 0.8398 (tppt) REVERT: C 129 ARG cc_start: 0.8138 (ptt180) cc_final: 0.7583 (ptp-170) REVERT: C 137 ASP cc_start: 0.9203 (m-30) cc_final: 0.8735 (m-30) REVERT: C 148 LYS cc_start: 0.9114 (ttmm) cc_final: 0.8651 (mtmm) REVERT: C 163 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8168 (mm-40) REVERT: C 209 TYR cc_start: 0.8422 (m-80) cc_final: 0.8076 (m-80) outliers start: 40 outliers final: 29 residues processed: 222 average time/residue: 0.1266 time to fit residues: 40.3879 Evaluate side-chains 224 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 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 513 GLN 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 620 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 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1053 SER Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1189 ARG Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 182 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 0.0170 chunk 108 optimal weight: 0.0370 chunk 23 optimal weight: 0.7980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 ASN C 191 ASN C 193 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.108043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.078801 restraints weight = 45233.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.081468 restraints weight = 20528.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.083130 restraints weight = 13031.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.083949 restraints weight = 10069.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.084564 restraints weight = 8821.849| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4125 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= 0.119 Angle : 0.670 11.389 18411 Z= 0.338 Chirality : 0.042 0.188 2001 Planarity : 0.003 0.051 2148 Dihedral : 16.267 175.744 2325 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.36 % Allowed : 24.41 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.23), residues: 1427 helix: 0.40 (0.22), residues: 591 sheet: -1.42 (0.42), residues: 144 loop : -1.86 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 203 TYR 0.029 0.001 TYR B1185 PHE 0.014 0.001 PHE C 196 TRP 0.006 0.001 TRP B 602 HIS 0.005 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00256 (13480) covalent geometry : angle 0.66966 (18411) hydrogen bonds : bond 0.03396 ( 496) hydrogen bonds : angle 4.63956 ( 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 227 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLN cc_start: 0.9136 (tt0) cc_final: 0.8706 (tp-100) REVERT: A 144 TYR cc_start: 0.7660 (t80) cc_final: 0.7007 (t80) REVERT: A 154 LYS cc_start: 0.9497 (mttp) cc_final: 0.9133 (mtpt) REVERT: A 181 GLN cc_start: 0.8463 (tt0) cc_final: 0.8171 (tt0) REVERT: A 193 GLN cc_start: 0.8560 (tt0) cc_final: 0.8220 (tm-30) REVERT: A 205 LEU cc_start: 0.8923 (tp) cc_final: 0.8651 (tp) REVERT: A 228 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8661 (mt-10) REVERT: A 230 ARG cc_start: 0.9165 (ttm110) cc_final: 0.8842 (ptp-110) REVERT: B 110 LYS cc_start: 0.8713 (pttm) cc_final: 0.8435 (pttm) REVERT: B 116 LYS cc_start: 0.8876 (mmtp) cc_final: 0.8254 (pttm) REVERT: B 247 GLU cc_start: 0.3807 (OUTLIER) cc_final: 0.3184 (mp0) REVERT: B 386 ARG cc_start: -0.0988 (OUTLIER) cc_final: -0.1332 (ptt180) REVERT: B 510 TYR cc_start: 0.7416 (t80) cc_final: 0.6295 (t80) REVERT: B 513 GLN cc_start: 0.6518 (OUTLIER) cc_final: 0.6089 (tp-100) REVERT: B 614 LYS cc_start: 0.9667 (mmmt) cc_final: 0.9259 (mmmm) REVERT: B 815 GLU cc_start: 0.8929 (tp30) cc_final: 0.8519 (tp30) REVERT: B 840 TYR cc_start: 0.8960 (t80) cc_final: 0.8171 (t80) REVERT: B 895 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7566 (t0) REVERT: B 941 GLN cc_start: 0.8573 (tp40) cc_final: 0.8237 (tp40) REVERT: B 1003 LYS cc_start: 0.9207 (mttt) cc_final: 0.8780 (mttm) REVERT: B 1013 LEU cc_start: 0.8452 (tp) cc_final: 0.8209 (tp) REVERT: B 1131 MET cc_start: 0.9106 (mmm) cc_final: 0.8648 (mmm) REVERT: B 1216 LYS cc_start: 0.9048 (ttmm) cc_final: 0.8390 (tppt) REVERT: C 137 ASP cc_start: 0.9234 (m-30) cc_final: 0.8792 (m-30) REVERT: C 163 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8282 (mm-40) REVERT: C 209 TYR cc_start: 0.8478 (m-80) cc_final: 0.8167 (m-80) outliers start: 31 outliers final: 26 residues processed: 218 average time/residue: 0.1172 time to fit residues: 37.0901 Evaluate side-chains 219 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 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 513 GLN Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 620 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 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1189 ARG Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 182 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 Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 42 optimal weight: 7.9990 chunk 29 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 chunk 102 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 ASN C 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.107864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.084708 restraints weight = 44867.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.083562 restraints weight = 25355.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.086169 restraints weight = 18294.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.085760 restraints weight = 11886.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.086636 restraints weight = 11554.155| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13480 Z= 0.134 Angle : 0.692 18.746 18411 Z= 0.350 Chirality : 0.042 0.195 2001 Planarity : 0.004 0.053 2148 Dihedral : 16.233 176.483 2325 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.52 % Allowed : 24.94 % 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: -1.25 (0.23), residues: 1427 helix: 0.46 (0.22), residues: 589 sheet: -1.41 (0.42), residues: 144 loop : -1.87 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 203 TYR 0.029 0.001 TYR B 995 PHE 0.019 0.001 PHE B 173 TRP 0.007 0.001 TRP A 178 HIS 0.004 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00296 (13480) covalent geometry : angle 0.69211 (18411) hydrogen bonds : bond 0.03392 ( 496) hydrogen bonds : angle 4.69315 ( 1389) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2614.89 seconds wall clock time: 45 minutes 52.41 seconds (2752.41 seconds total)