Starting phenix.real_space_refine on Thu Jul 31 12:11:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6omv_20132/07_2025/6omv_20132.cif Found real_map, /net/cci-nas-00/data/ceres_data/6omv_20132/07_2025/6omv_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6omv_20132/07_2025/6omv_20132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6omv_20132/07_2025/6omv_20132.map" model { file = "/net/cci-nas-00/data/ceres_data/6omv_20132/07_2025/6omv_20132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6omv_20132/07_2025/6omv_20132.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.66, per 1000 atoms: 0.66 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: 3.42 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 4.81 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: 5.60 Time building geometry restraints manager: 4.03 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: 97.220 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: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 37.590 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.850 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.002 TRP B 999 HIS 0.010 0.002 HIS C 233 PHE 0.020 0.003 PHE B 19 TYR 0.039 0.003 TYR A 188 ARG 0.006 0.001 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.18847 ( 496) hydrogen bonds : angle 8.23253 ( 1389) covalent geometry : bond 0.00758 (13480) covalent geometry : angle 1.05348 (18411) *********************** 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 : 1.377 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: 0.2066 (mtp) cc_final: 0.1295 (mmt) REVERT: A 133 ILE cc_start: 0.9188 (mt) cc_final: 0.8798 (mm) REVERT: A 135 GLU cc_start: 0.8961 (tp30) cc_final: 0.8616 (tp30) REVERT: A 137 ASP cc_start: 0.9154 (m-30) cc_final: 0.8902 (m-30) REVERT: A 142 GLN cc_start: 0.8795 (tt0) cc_final: 0.8368 (tp-100) REVERT: A 144 TYR cc_start: 0.7948 (t80) cc_final: 0.7063 (t80) REVERT: A 154 LYS cc_start: 0.9543 (mttp) cc_final: 0.9154 (mtpt) REVERT: A 157 ASN cc_start: 0.9157 (m110) cc_final: 0.8859 (t0) REVERT: A 193 GLN cc_start: 0.8778 (tt0) cc_final: 0.8307 (tm-30) REVERT: A 202 LYS cc_start: 0.8308 (mmtp) cc_final: 0.7858 (ptpp) REVERT: A 232 LEU cc_start: 0.8683 (tt) cc_final: 0.8180 (mt) REVERT: B 167 LYS cc_start: 0.7527 (pttt) cc_final: 0.7319 (pttt) REVERT: B 308 LEU cc_start: 0.9037 (mm) cc_final: 0.8829 (mp) REVERT: B 558 MET cc_start: 0.7671 (mpp) cc_final: 0.7426 (mpp) REVERT: B 815 GLU cc_start: 0.8788 (tp30) cc_final: 0.8428 (tp30) REVERT: B 840 TYR cc_start: 0.8986 (t80) cc_final: 0.8667 (t80) REVERT: B 927 LEU cc_start: 0.8558 (mt) cc_final: 0.8117 (tt) REVERT: B 940 LYS cc_start: 0.9209 (tttt) cc_final: 0.8778 (tttp) REVERT: B 941 GLN cc_start: 0.8569 (tp40) cc_final: 0.8294 (tp40) REVERT: B 944 GLN cc_start: 0.8401 (mt0) cc_final: 0.8020 (mt0) REVERT: B 945 LYS cc_start: 0.9029 (tptm) cc_final: 0.8725 (ttpt) REVERT: B 1003 LYS cc_start: 0.9350 (mttt) cc_final: 0.9025 (mttm) REVERT: B 1128 MET cc_start: 0.8921 (tpt) cc_final: 0.8672 (tpp) REVERT: B 1167 TYR cc_start: 0.8382 (m-80) cc_final: 0.7989 (m-80) REVERT: C 142 GLN cc_start: 0.9200 (mt0) cc_final: 0.8979 (tm-30) REVERT: C 154 LYS cc_start: 0.8757 (mttm) cc_final: 0.8492 (ttmm) REVERT: C 165 LEU cc_start: 0.9300 (tp) cc_final: 0.9099 (tp) REVERT: C 187 ARG cc_start: 0.7833 (tpp80) cc_final: 0.6979 (tpp80) REVERT: C 192 ASP cc_start: 0.9072 (OUTLIER) cc_final: 0.8516 (p0) REVERT: C 217 ARG cc_start: 0.6125 (tpt170) cc_final: 0.5806 (tpt170) REVERT: C 219 GLU cc_start: 0.8753 (mp0) cc_final: 0.8386 (mp0) REVERT: C 230 ARG cc_start: 0.7564 (mtt-85) cc_final: 0.7318 (mtt-85) outliers start: 21 outliers final: 4 residues processed: 283 average time/residue: 0.3237 time to fit residues: 126.3423 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 : 1.363 ------------------------------------------------------------------------------- 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 123 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 C 233 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.107251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.083120 restraints weight = 44692.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.082502 restraints weight = 24764.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.084574 restraints weight = 17875.408| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13480 Z= 0.147 Angle : 0.661 11.600 18411 Z= 0.356 Chirality : 0.043 0.281 2001 Planarity : 0.004 0.063 2148 Dihedral : 17.011 178.093 2333 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.50 % Favored : 92.43 % Rotamer: Outliers : 2.67 % Allowed : 16.40 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.20), residues: 1427 helix: -1.46 (0.19), residues: 607 sheet: -1.89 (0.40), residues: 142 loop : -2.77 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 602 HIS 0.005 0.001 HIS B 633 PHE 0.016 0.001 PHE C 196 TYR 0.023 0.002 TYR C 209 ARG 0.004 0.001 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.04351 ( 496) hydrogen bonds : angle 5.61304 ( 1389) covalent geometry : bond 0.00304 (13480) covalent geometry : angle 0.66071 (18411) *********************** 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 255 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 1.624 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: 0.2077 (mtp) cc_final: 0.1294 (mmt) REVERT: A 133 ILE cc_start: 0.9198 (mt) cc_final: 0.8832 (mm) REVERT: A 154 LYS cc_start: 0.9411 (mttp) cc_final: 0.9009 (mtmt) REVERT: A 181 GLN cc_start: 0.8302 (tt0) cc_final: 0.7915 (tp-100) REVERT: A 202 LYS cc_start: 0.8237 (mmtp) cc_final: 0.7777 (ptpp) REVERT: A 227 GLU cc_start: 0.9091 (mp0) cc_final: 0.8778 (mp0) REVERT: A 230 ARG cc_start: 0.8846 (ttm110) cc_final: 0.8517 (ttm110) REVERT: A 232 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8046 (mt) REVERT: B 28 GLN cc_start: 0.8970 (tp40) cc_final: 0.8753 (tm-30) REVERT: B 495 ASP cc_start: 0.6778 (p0) cc_final: 0.6475 (p0) REVERT: B 603 MET cc_start: 0.9349 (mpp) cc_final: 0.9117 (pmm) REVERT: B 614 LYS cc_start: 0.9689 (mmmt) cc_final: 0.9362 (mmmm) REVERT: B 706 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8257 (p0) REVERT: B 746 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7950 (ptm) REVERT: B 815 GLU cc_start: 0.8422 (tp30) cc_final: 0.8163 (tp30) REVERT: B 840 TYR cc_start: 0.8914 (t80) cc_final: 0.8667 (t80) REVERT: B 895 ASN cc_start: 0.7904 (m110) cc_final: 0.7656 (m-40) REVERT: B 927 LEU cc_start: 0.8334 (mt) cc_final: 0.7801 (tt) REVERT: B 940 LYS cc_start: 0.8920 (tttt) cc_final: 0.8288 (ptmm) REVERT: B 941 GLN cc_start: 0.8507 (tp40) cc_final: 0.8040 (tp40) REVERT: B 944 GLN cc_start: 0.8248 (mt0) cc_final: 0.8003 (mt0) REVERT: B 949 MET cc_start: 0.7879 (ttm) cc_final: 0.7624 (ttm) REVERT: B 1003 LYS cc_start: 0.9221 (mttt) cc_final: 0.8955 (mttm) REVERT: B 1216 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8565 (tppt) REVERT: C 133 ILE cc_start: 0.8761 (mm) cc_final: 0.8443 (tp) REVERT: C 137 ASP cc_start: 0.9262 (m-30) cc_final: 0.9033 (m-30) REVERT: C 186 MET cc_start: 0.7571 (tpp) cc_final: 0.7311 (ttt) REVERT: C 209 TYR cc_start: 0.8111 (m-80) cc_final: 0.7818 (m-80) REVERT: C 222 ARG cc_start: 0.9111 (tpp-160) cc_final: 0.8808 (tpp80) outliers start: 35 outliers final: 17 residues processed: 240 average time/residue: 0.2971 time to fit residues: 103.1610 Evaluate side-chains 210 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 706 ASN Chi-restraints excluded: chain B residue 746 MET Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 877 ASP 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 223 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 72 optimal weight: 0.0000 chunk 104 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 102 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 HIS B1108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.105908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.082396 restraints weight = 45730.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.081389 restraints weight = 25366.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.083720 restraints weight = 18662.181| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13480 Z= 0.182 Angle : 0.650 10.194 18411 Z= 0.351 Chirality : 0.043 0.183 2001 Planarity : 0.004 0.052 2148 Dihedral : 16.826 178.140 2325 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.20 % Favored : 91.73 % Rotamer: Outliers : 3.89 % Allowed : 18.15 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.21), residues: 1427 helix: -0.71 (0.20), residues: 599 sheet: -1.61 (0.41), residues: 143 loop : -2.56 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 602 HIS 0.005 0.001 HIS B 633 PHE 0.014 0.001 PHE B 946 TYR 0.021 0.002 TYR B 510 ARG 0.003 0.000 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 496) hydrogen bonds : angle 5.33070 ( 1389) covalent geometry : bond 0.00386 (13480) covalent geometry : angle 0.64981 (18411) *********************** 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 257 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 206 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.2353 (mtp) cc_final: 0.1662 (mmt) REVERT: A 134 LYS cc_start: 0.9174 (mttm) cc_final: 0.8882 (ttmt) REVERT: A 144 TYR cc_start: 0.7883 (t80) cc_final: 0.6965 (t80) REVERT: A 154 LYS cc_start: 0.9458 (mttp) cc_final: 0.9094 (mtpt) REVERT: A 184 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.6055 (mt-10) REVERT: A 202 LYS cc_start: 0.8291 (mmtp) cc_final: 0.7789 (ptpp) REVERT: A 232 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8056 (mt) REVERT: B 110 LYS cc_start: 0.8563 (pttm) cc_final: 0.8061 (pttm) REVERT: B 450 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7728 (t70) REVERT: B 510 TYR cc_start: 0.7489 (t80) cc_final: 0.6389 (t80) REVERT: B 513 GLN cc_start: 0.6013 (OUTLIER) cc_final: 0.4219 (pp30) REVERT: B 614 LYS cc_start: 0.9673 (mmmt) cc_final: 0.9420 (pttp) REVERT: B 815 GLU cc_start: 0.8476 (tp30) cc_final: 0.8220 (tp30) REVERT: B 840 TYR cc_start: 0.8910 (t80) cc_final: 0.8653 (t80) REVERT: B 895 ASN cc_start: 0.7876 (m110) cc_final: 0.7659 (m-40) REVERT: B 919 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8061 (t0) REVERT: B 927 LEU cc_start: 0.8380 (mt) cc_final: 0.7803 (tt) REVERT: B 940 LYS cc_start: 0.8965 (tttt) cc_final: 0.8401 (ptmm) REVERT: B 941 GLN cc_start: 0.8429 (tp40) cc_final: 0.7823 (tp40) REVERT: B 949 MET cc_start: 0.8009 (ttm) cc_final: 0.7721 (ttm) REVERT: B 1003 LYS cc_start: 0.9238 (mttt) cc_final: 0.9005 (mttm) REVERT: B 1108 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7863 (mp10) REVERT: B 1131 MET cc_start: 0.9131 (tpp) cc_final: 0.8897 (mmm) REVERT: B 1216 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8588 (tppt) REVERT: C 133 ILE cc_start: 0.8915 (mm) cc_final: 0.8596 (tp) REVERT: C 137 ASP cc_start: 0.9276 (m-30) cc_final: 0.9049 (m-30) REVERT: C 148 LYS cc_start: 0.9122 (ttmm) cc_final: 0.8525 (mtmm) REVERT: C 209 TYR cc_start: 0.8337 (m-80) cc_final: 0.8027 (m-80) REVERT: C 222 ARG cc_start: 0.9106 (tpp-160) cc_final: 0.8828 (tpp80) REVERT: C 230 ARG cc_start: 0.7433 (mtt-85) cc_final: 0.6550 (mtt-85) outliers start: 51 outliers final: 26 residues processed: 233 average time/residue: 0.2769 time to fit residues: 92.1244 Evaluate side-chains 217 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 450 ASP 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 919 ASP 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 223 VAL Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 100 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 ASN B1108 GLN ** B1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 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 = 0.3897 r_free = 0.3897 target = 0.105552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.076028 restraints weight = 44903.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.078638 restraints weight = 19962.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.080126 restraints weight = 12637.142| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13480 Z= 0.148 Angle : 0.638 9.723 18411 Z= 0.337 Chirality : 0.043 0.199 2001 Planarity : 0.004 0.046 2148 Dihedral : 16.714 177.373 2325 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.06 % Favored : 91.87 % Rotamer: Outliers : 3.20 % Allowed : 20.90 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.22), residues: 1427 helix: -0.30 (0.21), residues: 600 sheet: -1.45 (0.44), residues: 132 loop : -2.36 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 602 HIS 0.005 0.001 HIS B 633 PHE 0.015 0.001 PHE B 173 TYR 0.016 0.001 TYR B1102 ARG 0.007 0.000 ARG A 230 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 496) hydrogen bonds : angle 5.08951 ( 1389) covalent geometry : bond 0.00315 (13480) covalent geometry : angle 0.63777 (18411) *********************** 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 251 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 1.433 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: 0.2022 (mtp) cc_final: 0.1668 (mmt) REVERT: A 134 LYS cc_start: 0.9052 (mttm) cc_final: 0.8747 (ttmt) REVERT: A 144 TYR cc_start: 0.7696 (t80) cc_final: 0.6874 (t80) REVERT: A 154 LYS cc_start: 0.9529 (mttp) cc_final: 0.9036 (mtmt) REVERT: A 184 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6249 (mt-10) REVERT: A 186 MET cc_start: 0.7129 (mmm) cc_final: 0.6683 (mmm) REVERT: A 202 LYS cc_start: 0.8178 (mmtp) cc_final: 0.7474 (ptpp) REVERT: A 227 GLU cc_start: 0.9231 (mp0) cc_final: 0.8552 (mp0) REVERT: A 230 ARG cc_start: 0.9034 (ttm110) cc_final: 0.8492 (mtt90) REVERT: A 232 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8004 (mt) REVERT: B 110 LYS cc_start: 0.8650 (pttm) cc_final: 0.8264 (pttm) REVERT: B 116 LYS cc_start: 0.9051 (mmtp) cc_final: 0.8191 (pttm) REVERT: B 219 PHE cc_start: 0.7934 (m-80) cc_final: 0.7731 (m-80) REVERT: B 510 TYR cc_start: 0.7583 (t80) cc_final: 0.6590 (t80) REVERT: B 513 GLN cc_start: 0.6192 (OUTLIER) cc_final: 0.4481 (pp30) REVERT: B 614 LYS cc_start: 0.9690 (mmmt) cc_final: 0.9316 (mmmm) REVERT: B 659 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7689 (mp0) REVERT: B 815 GLU cc_start: 0.8826 (tp30) cc_final: 0.8495 (tp30) REVERT: B 840 TYR cc_start: 0.8941 (t80) cc_final: 0.8428 (t80) REVERT: B 853 GLN cc_start: 0.8485 (pm20) cc_final: 0.8283 (pm20) REVERT: B 919 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8157 (t0) REVERT: B 927 LEU cc_start: 0.8345 (mt) cc_final: 0.7767 (tt) REVERT: B 941 GLN cc_start: 0.8430 (tp40) cc_final: 0.8078 (tp40) REVERT: B 949 MET cc_start: 0.7989 (ttm) cc_final: 0.7655 (ttm) REVERT: B 957 MET cc_start: 0.8436 (tpp) cc_final: 0.8111 (tpp) REVERT: B 1003 LYS cc_start: 0.9294 (mttt) cc_final: 0.8977 (mttm) REVERT: B 1068 TYR cc_start: 0.9379 (t80) cc_final: 0.9027 (t80) REVERT: B 1131 MET cc_start: 0.9277 (tpp) cc_final: 0.9013 (mmm) REVERT: B 1216 LYS cc_start: 0.9038 (ttmm) cc_final: 0.8395 (tppt) REVERT: C 133 ILE cc_start: 0.8869 (mm) cc_final: 0.8551 (tp) REVERT: C 137 ASP cc_start: 0.9206 (m-30) cc_final: 0.8807 (m-30) REVERT: C 148 LYS cc_start: 0.8998 (ttmm) cc_final: 0.8465 (mtmm) REVERT: C 186 MET cc_start: 0.7557 (tpp) cc_final: 0.7308 (ttt) REVERT: C 192 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8517 (m-30) REVERT: C 209 TYR cc_start: 0.8263 (m-80) cc_final: 0.7952 (m-80) REVERT: C 222 ARG cc_start: 0.9128 (tpp-160) cc_final: 0.8889 (tpp80) outliers start: 42 outliers final: 25 residues processed: 234 average time/residue: 0.2658 time to fit residues: 89.4454 Evaluate side-chains 218 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 184 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 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 919 ASP 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 192 ASP Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 109 optimal weight: 0.0970 chunk 18 optimal weight: 0.7980 chunk 145 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 112 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.106111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.076587 restraints weight = 45205.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.079200 restraints weight = 20332.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.080819 restraints weight = 12933.547| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3229 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= 0.130 Angle : 0.619 8.893 18411 Z= 0.325 Chirality : 0.043 0.206 2001 Planarity : 0.003 0.044 2148 Dihedral : 16.562 177.129 2325 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 3.36 % Allowed : 22.50 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.22), residues: 1427 helix: -0.14 (0.21), residues: 602 sheet: -1.51 (0.42), residues: 136 loop : -2.24 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 602 HIS 0.005 0.001 HIS B 633 PHE 0.011 0.001 PHE B 490 TYR 0.016 0.001 TYR B 516 ARG 0.003 0.000 ARG B1189 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 496) hydrogen bonds : angle 4.89334 ( 1389) covalent geometry : bond 0.00280 (13480) covalent geometry : angle 0.61934 (18411) *********************** 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 256 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 1.542 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: 0.2117 (mtp) cc_final: 0.1691 (mmt) REVERT: A 134 LYS cc_start: 0.9115 (mttm) cc_final: 0.8826 (ttmt) REVERT: A 144 TYR cc_start: 0.7725 (t80) cc_final: 0.6959 (t80) REVERT: A 154 LYS cc_start: 0.9532 (mttp) cc_final: 0.8869 (mtmt) REVERT: A 181 GLN cc_start: 0.8453 (tt0) cc_final: 0.8180 (tt0) REVERT: A 184 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6148 (mt-10) REVERT: A 186 MET cc_start: 0.7209 (mmm) cc_final: 0.6677 (mmm) REVERT: A 193 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7481 (tm-30) REVERT: A 202 LYS cc_start: 0.8321 (mmtp) cc_final: 0.7741 (mtmm) REVERT: A 206 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8081 (ttp80) REVERT: B 116 LYS cc_start: 0.9071 (mmtp) cc_final: 0.8242 (pttm) REVERT: B 167 LYS cc_start: 0.7477 (pttt) cc_final: 0.7239 (pttt) REVERT: B 182 ARG cc_start: 0.8767 (mtp180) cc_final: 0.8466 (mtm180) REVERT: B 219 PHE cc_start: 0.7968 (m-80) cc_final: 0.7660 (m-80) REVERT: B 247 GLU cc_start: 0.3922 (OUTLIER) cc_final: 0.3284 (mp0) REVERT: B 386 ARG cc_start: -0.1121 (OUTLIER) cc_final: -0.1477 (ptt180) REVERT: B 510 TYR cc_start: 0.7479 (t80) cc_final: 0.6482 (t80) REVERT: B 513 GLN cc_start: 0.6309 (OUTLIER) cc_final: 0.4823 (pp30) REVERT: B 614 LYS cc_start: 0.9698 (mmmt) cc_final: 0.9315 (mmmm) REVERT: B 659 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7698 (mp0) REVERT: B 815 GLU cc_start: 0.8870 (tp30) cc_final: 0.8487 (tp30) REVERT: B 840 TYR cc_start: 0.8937 (t80) cc_final: 0.8383 (t80) REVERT: B 895 ASN cc_start: 0.7746 (OUTLIER) cc_final: 0.7394 (t0) REVERT: B 919 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8228 (t0) REVERT: B 941 GLN cc_start: 0.8506 (tp40) cc_final: 0.8189 (tp40) REVERT: B 957 MET cc_start: 0.8306 (tpp) cc_final: 0.8028 (tpp) REVERT: B 1003 LYS cc_start: 0.9285 (mttt) cc_final: 0.8969 (mttm) REVERT: B 1131 MET cc_start: 0.9242 (tpp) cc_final: 0.9019 (mmm) REVERT: B 1216 LYS cc_start: 0.9034 (ttmm) cc_final: 0.8430 (tppt) REVERT: C 133 ILE cc_start: 0.8904 (mm) cc_final: 0.8537 (tp) REVERT: C 137 ASP cc_start: 0.9205 (m-30) cc_final: 0.8766 (m-30) REVERT: C 148 LYS cc_start: 0.9094 (ttmm) cc_final: 0.8542 (mtmm) REVERT: C 163 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8144 (mm-40) REVERT: C 209 TYR cc_start: 0.8335 (m-80) cc_final: 0.8007 (m-80) outliers start: 44 outliers final: 27 residues processed: 239 average time/residue: 0.2779 time to fit residues: 95.9712 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 : 1.608 ------------------------------------------------------------------------------- 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 166 ASP 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 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 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 30 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN B 399 GLN ** B 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.101681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.078118 restraints weight = 46507.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.079869 restraints weight = 27354.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.079050 restraints weight = 21092.859| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13480 Z= 0.266 Angle : 0.717 9.922 18411 Z= 0.381 Chirality : 0.046 0.181 2001 Planarity : 0.004 0.051 2148 Dihedral : 16.751 177.821 2325 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.02 % Favored : 89.91 % Rotamer: Outliers : 3.66 % Allowed : 22.81 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.22), residues: 1427 helix: -0.14 (0.21), residues: 599 sheet: -1.78 (0.37), residues: 177 loop : -2.35 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 178 HIS 0.006 0.002 HIS B 909 PHE 0.021 0.002 PHE B 946 TYR 0.027 0.002 TYR B 562 ARG 0.005 0.001 ARG A 230 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 496) hydrogen bonds : angle 5.19986 ( 1389) covalent geometry : bond 0.00569 (13480) covalent geometry : angle 0.71677 (18411) *********************** 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 239 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 1.399 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: 0.2090 (OUTLIER) cc_final: 0.1348 (mmt) REVERT: A 144 TYR cc_start: 0.7920 (t80) cc_final: 0.7443 (t80) REVERT: A 154 LYS cc_start: 0.9451 (mttp) cc_final: 0.9107 (mtpt) REVERT: A 184 GLU cc_start: 0.6199 (OUTLIER) cc_final: 0.5686 (mt-10) REVERT: A 186 MET cc_start: 0.7851 (mmm) cc_final: 0.7055 (mmm) REVERT: A 202 LYS cc_start: 0.8467 (mmtp) cc_final: 0.7917 (mtmm) REVERT: B 219 PHE cc_start: 0.7974 (m-80) cc_final: 0.7555 (m-10) REVERT: B 247 GLU cc_start: 0.3967 (OUTLIER) cc_final: 0.3073 (mp0) REVERT: B 386 ARG cc_start: -0.0173 (OUTLIER) cc_final: -0.0985 (ptt180) REVERT: B 510 TYR cc_start: 0.7391 (t80) cc_final: 0.6453 (t80) REVERT: B 513 GLN cc_start: 0.6358 (OUTLIER) cc_final: 0.6032 (tp-100) REVERT: B 514 LYS cc_start: 0.8614 (tptp) cc_final: 0.8321 (tptp) REVERT: B 614 LYS cc_start: 0.9689 (mmmt) cc_final: 0.9254 (mmmm) REVERT: B 659 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7703 (mp0) REVERT: B 815 GLU cc_start: 0.8565 (tp30) cc_final: 0.8304 (tp30) REVERT: B 919 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8079 (t0) REVERT: B 941 GLN cc_start: 0.8553 (tp40) cc_final: 0.8119 (tp40) REVERT: B 1003 LYS cc_start: 0.9234 (mttt) cc_final: 0.8991 (mttm) REVERT: B 1216 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8345 (tppt) REVERT: C 133 ILE cc_start: 0.8984 (mm) cc_final: 0.8551 (tp) REVERT: C 137 ASP cc_start: 0.9248 (m-30) cc_final: 0.8826 (m-30) REVERT: C 148 LYS cc_start: 0.9125 (ttmm) cc_final: 0.8572 (mtmm) REVERT: C 163 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7801 (mm-40) REVERT: C 187 ARG cc_start: 0.7694 (tpp80) cc_final: 0.7432 (tpp80) REVERT: C 209 TYR cc_start: 0.8251 (m-80) cc_final: 0.7983 (m-80) outliers start: 48 outliers final: 34 residues processed: 221 average time/residue: 0.2785 time to fit residues: 89.7058 Evaluate side-chains 220 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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 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 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 311 ASN 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 636 ILE 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 996 ILE 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 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 Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 127 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 chunk 15 optimal weight: 0.4980 chunk 116 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN B 803 ASN B 808 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.106097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.076623 restraints weight = 44872.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.079300 restraints weight = 19700.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.080942 restraints weight = 12324.829| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13480 Z= 0.121 Angle : 0.637 12.088 18411 Z= 0.328 Chirality : 0.043 0.201 2001 Planarity : 0.003 0.042 2148 Dihedral : 16.501 175.912 2325 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.90 % Allowed : 23.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.22), residues: 1427 helix: 0.06 (0.21), residues: 600 sheet: -1.66 (0.41), residues: 142 loop : -2.12 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 602 HIS 0.005 0.001 HIS B 633 PHE 0.014 0.001 PHE C 196 TYR 0.023 0.001 TYR B 562 ARG 0.004 0.000 ARG B1189 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 496) hydrogen bonds : angle 4.83899 ( 1389) covalent geometry : bond 0.00254 (13480) covalent geometry : angle 0.63656 (18411) *********************** 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 240 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.1406 (mtp) cc_final: 0.0839 (mmt) REVERT: A 134 LYS cc_start: 0.9109 (mttm) cc_final: 0.8710 (ttpp) REVERT: A 144 TYR cc_start: 0.7792 (t80) cc_final: 0.7140 (t80) REVERT: A 154 LYS cc_start: 0.9484 (mttp) cc_final: 0.9118 (mtpt) REVERT: A 181 GLN cc_start: 0.8418 (tt0) cc_final: 0.8127 (tt0) REVERT: A 184 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.5688 (mt-10) REVERT: A 186 MET cc_start: 0.7357 (mmm) cc_final: 0.6881 (mmm) REVERT: A 196 PHE cc_start: 0.8608 (m-80) cc_final: 0.8398 (m-80) REVERT: A 202 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7566 (mtmm) REVERT: A 206 ARG cc_start: 0.8369 (ttp80) cc_final: 0.8111 (ttp80) REVERT: A 221 GLU cc_start: 0.8941 (pt0) cc_final: 0.8224 (pm20) REVERT: B 7 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: B 110 LYS cc_start: 0.8677 (pttm) cc_final: 0.8302 (pttm) REVERT: B 116 LYS cc_start: 0.9049 (mmtp) cc_final: 0.8231 (pttm) REVERT: B 247 GLU cc_start: 0.3641 (OUTLIER) cc_final: 0.2996 (mp0) REVERT: B 386 ARG cc_start: -0.0959 (OUTLIER) cc_final: -0.1294 (ptt180) REVERT: B 510 TYR cc_start: 0.7338 (t80) cc_final: 0.6331 (t80) REVERT: B 513 GLN cc_start: 0.6452 (OUTLIER) cc_final: 0.6052 (tp-100) REVERT: B 603 MET cc_start: 0.9448 (pmm) cc_final: 0.9247 (pmm) REVERT: B 614 LYS cc_start: 0.9682 (mmmt) cc_final: 0.9292 (mmmm) REVERT: B 659 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7697 (mp0) REVERT: B 755 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: B 815 GLU cc_start: 0.8868 (tp30) cc_final: 0.8463 (tp30) REVERT: B 840 TYR cc_start: 0.8949 (t80) cc_final: 0.8255 (t80) REVERT: B 895 ASN cc_start: 0.7692 (OUTLIER) cc_final: 0.7390 (t0) REVERT: B 941 GLN cc_start: 0.8623 (tp40) cc_final: 0.8147 (tp40) REVERT: B 1003 LYS cc_start: 0.9251 (mttt) cc_final: 0.8855 (mttm) REVERT: B 1131 MET cc_start: 0.9081 (mmm) cc_final: 0.8809 (mmm) REVERT: B 1216 LYS cc_start: 0.9032 (ttmm) cc_final: 0.8363 (tppt) REVERT: C 133 ILE cc_start: 0.8901 (mm) cc_final: 0.8524 (tp) REVERT: C 137 ASP cc_start: 0.9199 (m-30) cc_final: 0.8777 (m-30) REVERT: C 148 LYS cc_start: 0.9161 (ttmm) cc_final: 0.8674 (mtmm) REVERT: C 163 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8110 (mm-40) REVERT: C 187 ARG cc_start: 0.7738 (tpp80) cc_final: 0.7320 (tpp80) REVERT: C 209 TYR cc_start: 0.8467 (m-80) cc_final: 0.8113 (m-80) outliers start: 38 outliers final: 26 residues processed: 227 average time/residue: 0.2650 time to fit residues: 87.1989 Evaluate side-chains 226 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 7 PHE 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 618 ASN Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1053 SER Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 90 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 chunk 133 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN B 76 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 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 = 0.3916 r_free = 0.3916 target = 0.106477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.076961 restraints weight = 45183.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.079606 restraints weight = 20568.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.081177 restraints weight = 13059.660| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13480 Z= 0.123 Angle : 0.648 11.702 18411 Z= 0.330 Chirality : 0.042 0.186 2001 Planarity : 0.004 0.056 2148 Dihedral : 16.409 176.788 2325 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.82 % Allowed : 23.80 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.22), residues: 1427 helix: 0.25 (0.22), residues: 594 sheet: -1.60 (0.42), residues: 142 loop : -1.97 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 602 HIS 0.005 0.001 HIS B 633 PHE 0.012 0.001 PHE B 521 TYR 0.019 0.001 TYR B 562 ARG 0.009 0.000 ARG A 230 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 496) hydrogen bonds : angle 4.72382 ( 1389) covalent geometry : bond 0.00262 (13480) covalent geometry : angle 0.64772 (18411) *********************** 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 243 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.1425 (mtp) cc_final: 0.1018 (mmt) REVERT: A 144 TYR cc_start: 0.7757 (t80) cc_final: 0.7239 (t80) REVERT: A 154 LYS cc_start: 0.9488 (mttp) cc_final: 0.9129 (mtpt) REVERT: A 181 GLN cc_start: 0.8448 (tt0) cc_final: 0.8156 (tt0) REVERT: A 184 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.5930 (mt-10) REVERT: A 186 MET cc_start: 0.7549 (mmm) cc_final: 0.6862 (mmm) REVERT: A 196 PHE cc_start: 0.8558 (m-80) cc_final: 0.8318 (m-80) REVERT: A 202 LYS cc_start: 0.8176 (mmtp) cc_final: 0.7624 (mtmm) REVERT: A 221 GLU cc_start: 0.8865 (pt0) cc_final: 0.8191 (pm20) REVERT: A 228 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8571 (mt-10) REVERT: B 110 LYS cc_start: 0.8694 (pttm) cc_final: 0.8315 (pttm) REVERT: B 116 LYS cc_start: 0.9051 (mmtp) cc_final: 0.8267 (pttm) REVERT: B 247 GLU cc_start: 0.3720 (OUTLIER) cc_final: 0.3160 (mp0) REVERT: B 386 ARG cc_start: -0.1343 (OUTLIER) cc_final: -0.1588 (ptt180) REVERT: B 436 PHE cc_start: 0.5027 (m-80) cc_final: 0.4806 (m-80) REVERT: B 458 ASP cc_start: 0.9213 (m-30) cc_final: 0.8767 (p0) REVERT: B 510 TYR cc_start: 0.7356 (t80) cc_final: 0.6322 (t80) REVERT: B 614 LYS cc_start: 0.9680 (mmmt) cc_final: 0.9289 (mmmm) REVERT: B 659 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7632 (mp0) REVERT: B 755 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8291 (mp0) REVERT: B 815 GLU cc_start: 0.8895 (tp30) cc_final: 0.8514 (tp30) REVERT: B 840 TYR cc_start: 0.8976 (t80) cc_final: 0.8233 (t80) REVERT: B 895 ASN cc_start: 0.7688 (OUTLIER) cc_final: 0.7461 (t0) REVERT: B 941 GLN cc_start: 0.8661 (tp40) cc_final: 0.8208 (tp40) REVERT: B 1003 LYS cc_start: 0.9249 (mttt) cc_final: 0.8840 (mttm) REVERT: B 1131 MET cc_start: 0.9038 (mmm) cc_final: 0.8727 (mmm) REVERT: B 1216 LYS cc_start: 0.9031 (ttmm) cc_final: 0.8379 (tppt) REVERT: C 133 ILE cc_start: 0.8914 (mm) cc_final: 0.8517 (tp) REVERT: C 137 ASP cc_start: 0.9167 (m-30) cc_final: 0.8650 (m-30) REVERT: C 148 LYS cc_start: 0.9152 (ttmm) cc_final: 0.8688 (mtmm) REVERT: C 163 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8181 (mm-40) REVERT: C 186 MET cc_start: 0.7513 (tpp) cc_final: 0.7294 (ttt) REVERT: C 187 ARG cc_start: 0.7710 (tpp80) cc_final: 0.7394 (tpp80) REVERT: C 209 TYR cc_start: 0.8474 (m-80) cc_final: 0.8143 (m-80) outliers start: 37 outliers final: 25 residues processed: 230 average time/residue: 0.2670 time to fit residues: 88.0174 Evaluate side-chains 225 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 184 GLU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 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 954 LEU Chi-restraints excluded: chain B residue 996 ILE 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 1211 ILE Chi-restraints excluded: chain C residue 123 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 31 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 168 ASN B 112 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN C 193 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.105046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.075273 restraints weight = 45291.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.077909 restraints weight = 20490.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.079475 restraints weight = 12941.755| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13480 Z= 0.174 Angle : 0.694 15.556 18411 Z= 0.353 Chirality : 0.043 0.183 2001 Planarity : 0.004 0.039 2148 Dihedral : 16.452 176.988 2325 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.75 % Allowed : 24.18 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.23), residues: 1427 helix: 0.31 (0.22), residues: 595 sheet: -1.63 (0.41), residues: 147 loop : -1.95 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 178 HIS 0.006 0.001 HIS C 190 PHE 0.014 0.001 PHE B 521 TYR 0.020 0.002 TYR B 516 ARG 0.006 0.000 ARG A 230 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 496) hydrogen bonds : angle 4.84124 ( 1389) covalent geometry : bond 0.00375 (13480) covalent geometry : angle 0.69384 (18411) *********************** 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 234 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.1359 (OUTLIER) cc_final: 0.0793 (mmt) REVERT: A 134 LYS cc_start: 0.9187 (mttm) cc_final: 0.8706 (ttpp) REVERT: A 144 TYR cc_start: 0.7815 (t80) cc_final: 0.7343 (t80) REVERT: A 154 LYS cc_start: 0.9493 (mttp) cc_final: 0.9144 (mtpt) REVERT: A 181 GLN cc_start: 0.8424 (tt0) cc_final: 0.8142 (tt0) REVERT: A 184 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.6012 (mt-10) REVERT: A 186 MET cc_start: 0.7682 (mmm) cc_final: 0.6959 (mmm) REVERT: A 196 PHE cc_start: 0.8609 (m-80) cc_final: 0.8336 (m-80) REVERT: A 202 LYS cc_start: 0.8162 (mmtp) cc_final: 0.7695 (mtmm) REVERT: A 221 GLU cc_start: 0.8838 (pt0) cc_final: 0.8189 (pm20) REVERT: A 228 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8678 (mt-10) REVERT: A 230 ARG cc_start: 0.9276 (ttm110) cc_final: 0.9001 (ptp-110) REVERT: B 7 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: B 116 LYS cc_start: 0.9055 (mmtp) cc_final: 0.8292 (pttm) REVERT: B 247 GLU cc_start: 0.3757 (OUTLIER) cc_final: 0.3116 (mp0) REVERT: B 386 ARG cc_start: -0.1300 (OUTLIER) cc_final: -0.1565 (ptt180) REVERT: B 458 ASP cc_start: 0.9208 (m-30) cc_final: 0.8764 (p0) REVERT: B 514 LYS cc_start: 0.8895 (tptp) cc_final: 0.8509 (tptp) REVERT: B 531 MET cc_start: 0.9022 (mmm) cc_final: 0.7716 (tmm) REVERT: B 614 LYS cc_start: 0.9680 (mmmt) cc_final: 0.9271 (mmmm) REVERT: B 659 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7462 (mp0) REVERT: B 755 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: B 815 GLU cc_start: 0.8877 (tp30) cc_final: 0.8504 (tp30) REVERT: B 840 TYR cc_start: 0.9061 (t80) cc_final: 0.8281 (t80) REVERT: B 895 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7421 (t0) REVERT: B 919 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8225 (t0) REVERT: B 941 GLN cc_start: 0.8651 (tp40) cc_final: 0.8257 (tp40) REVERT: B 1003 LYS cc_start: 0.9284 (mttt) cc_final: 0.8902 (mttm) REVERT: B 1054 ARG cc_start: 0.9002 (ttm170) cc_final: 0.8510 (mmt-90) REVERT: B 1131 MET cc_start: 0.8954 (mmm) cc_final: 0.8602 (mmm) REVERT: B 1216 LYS cc_start: 0.8998 (ttmm) cc_final: 0.8402 (tppt) REVERT: C 133 ILE cc_start: 0.8898 (mm) cc_final: 0.8488 (tp) REVERT: C 137 ASP cc_start: 0.9203 (m-30) cc_final: 0.8680 (m-30) REVERT: C 148 LYS cc_start: 0.9165 (ttmm) cc_final: 0.8679 (mtmm) REVERT: C 163 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8100 (mm-40) REVERT: C 187 ARG cc_start: 0.7716 (tpp80) cc_final: 0.7301 (tpp80) REVERT: C 209 TYR cc_start: 0.8389 (m-80) cc_final: 0.8035 (m-80) outliers start: 36 outliers final: 27 residues processed: 224 average time/residue: 0.2970 time to fit residues: 94.3236 Evaluate side-chains 226 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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 174 GLU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 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 954 LEU Chi-restraints excluded: chain B residue 996 ILE 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 1211 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 191 ASN 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 103 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 109 optimal weight: 0.0570 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.105975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.076564 restraints weight = 44698.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.079093 restraints weight = 20851.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.080643 restraints weight = 13438.347| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3950 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= 0.146 Angle : 0.703 18.042 18411 Z= 0.353 Chirality : 0.043 0.253 2001 Planarity : 0.004 0.051 2148 Dihedral : 16.410 176.374 2325 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.90 % Allowed : 24.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.23), residues: 1427 helix: 0.35 (0.22), residues: 592 sheet: -1.63 (0.42), residues: 144 loop : -1.95 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 178 HIS 0.011 0.001 HIS C 190 PHE 0.021 0.001 PHE B 173 TYR 0.022 0.002 TYR B 510 ARG 0.006 0.000 ARG A 230 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 496) hydrogen bonds : angle 4.79464 ( 1389) covalent geometry : bond 0.00319 (13480) covalent geometry : angle 0.70334 (18411) ********************** 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 236 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 1.542 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: 0.1273 (OUTLIER) cc_final: 0.0726 (mmt) REVERT: A 144 TYR cc_start: 0.7768 (t80) cc_final: 0.7386 (t80) REVERT: A 145 ASN cc_start: 0.9284 (t0) cc_final: 0.8523 (m110) REVERT: A 154 LYS cc_start: 0.9487 (mttp) cc_final: 0.9132 (mtpt) REVERT: A 181 GLN cc_start: 0.8464 (tt0) cc_final: 0.8180 (tt0) REVERT: A 184 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5962 (mt-10) REVERT: A 186 MET cc_start: 0.7597 (mmm) cc_final: 0.6897 (mmm) REVERT: A 196 PHE cc_start: 0.8570 (m-80) cc_final: 0.8303 (m-80) REVERT: A 202 LYS cc_start: 0.8202 (mmtp) cc_final: 0.7658 (mtmm) REVERT: A 220 ILE cc_start: 0.8718 (mp) cc_final: 0.8412 (mm) REVERT: A 228 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8666 (mt-10) REVERT: B 7 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.8270 (m-80) REVERT: B 110 LYS cc_start: 0.8720 (pttm) cc_final: 0.8340 (pttm) REVERT: B 116 LYS cc_start: 0.9023 (mmtp) cc_final: 0.8264 (pttm) REVERT: B 219 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7986 (m-80) REVERT: B 247 GLU cc_start: 0.3796 (OUTLIER) cc_final: 0.3169 (mp0) REVERT: B 386 ARG cc_start: -0.1312 (OUTLIER) cc_final: -0.1551 (ptt180) REVERT: B 458 ASP cc_start: 0.9095 (m-30) cc_final: 0.8645 (p0) REVERT: B 514 LYS cc_start: 0.8864 (tptp) cc_final: 0.8446 (tptp) REVERT: B 614 LYS cc_start: 0.9678 (mmmt) cc_final: 0.9272 (mmmm) REVERT: B 659 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7524 (mp0) REVERT: B 755 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8246 (mp0) REVERT: B 815 GLU cc_start: 0.8897 (tp30) cc_final: 0.8476 (tp30) REVERT: B 895 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7404 (t0) REVERT: B 919 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8236 (t0) REVERT: B 941 GLN cc_start: 0.8679 (tp40) cc_final: 0.8264 (tp40) REVERT: B 1003 LYS cc_start: 0.9267 (mttt) cc_final: 0.8859 (mttm) REVERT: B 1131 MET cc_start: 0.9027 (mmm) cc_final: 0.8653 (mmm) REVERT: B 1216 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8387 (tppt) REVERT: C 133 ILE cc_start: 0.8901 (mm) cc_final: 0.8490 (tp) REVERT: C 137 ASP cc_start: 0.9187 (m-30) cc_final: 0.8659 (m-30) REVERT: C 148 LYS cc_start: 0.9133 (ttmm) cc_final: 0.8651 (mtmm) REVERT: C 163 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8114 (mm-40) REVERT: C 187 ARG cc_start: 0.7731 (tpp80) cc_final: 0.7361 (tpp80) REVERT: C 191 ASN cc_start: 0.8104 (p0) cc_final: 0.7785 (p0) REVERT: C 209 TYR cc_start: 0.8482 (m-80) cc_final: 0.8143 (m-80) outliers start: 38 outliers final: 25 residues processed: 228 average time/residue: 0.2729 time to fit residues: 88.6833 Evaluate side-chains 227 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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 184 GLU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 219 PHE 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 555 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 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 954 LEU Chi-restraints excluded: chain B residue 996 ILE 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 1211 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN C 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.105459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.075713 restraints weight = 45374.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.078310 restraints weight = 20568.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.079885 restraints weight = 13045.099| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13480 Z= 0.164 Angle : 0.725 18.739 18411 Z= 0.361 Chirality : 0.044 0.248 2001 Planarity : 0.004 0.047 2148 Dihedral : 16.417 176.757 2325 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.90 % Allowed : 25.25 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.23), residues: 1427 helix: 0.29 (0.22), residues: 593 sheet: -1.73 (0.41), residues: 149 loop : -1.92 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 178 HIS 0.004 0.001 HIS B 909 PHE 0.011 0.001 PHE B 474 TYR 0.031 0.002 TYR B1185 ARG 0.012 0.001 ARG B1189 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 496) hydrogen bonds : angle 4.86506 ( 1389) covalent geometry : bond 0.00359 (13480) covalent geometry : angle 0.72484 (18411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5602.16 seconds wall clock time: 99 minutes 52.97 seconds (5992.97 seconds total)