Starting phenix.real_space_refine on Thu Feb 15 18:35:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omv_20132/02_2024/6omv_20132.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omv_20132/02_2024/6omv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omv_20132/02_2024/6omv_20132.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omv_20132/02_2024/6omv_20132.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omv_20132/02_2024/6omv_20132.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6omv_20132/02_2024/6omv_20132.pdb" } 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 Residue "A ARG 217": "NH1" <-> "NH2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "B GLU 5": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B GLU 659": "OE1" <-> "OE2" Residue "B GLU 672": "OE1" <-> "OE2" Residue "B GLU 674": "OE1" <-> "OE2" Residue "B GLU 675": "OE1" <-> "OE2" Residue "B GLU 696": "OE1" <-> "OE2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "B ARG 737": "NH1" <-> "NH2" Residue "B ARG 747": "NH1" <-> "NH2" Residue "B ARG 883": "NH1" <-> "NH2" Residue "B ARG 887": "NH1" <-> "NH2" Residue "B GLU 898": "OE1" <-> "OE2" Residue "B GLU 913": "OE1" <-> "OE2" Residue "B GLU 916": "OE1" <-> "OE2" Residue "B GLU 925": "OE1" <-> "OE2" Residue "B GLU 981": "OE1" <-> "OE2" Residue "B GLU 1097": "OE1" <-> "OE2" Residue "B GLU 1117": "OE1" <-> "OE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C GLU 227": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.79, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 6.15 Conformation dependent library (CDL) restraints added in 2.2 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: 4.91 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: 5.92 Time building geometry restraints manager: 6.55 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: 97.93 - 105.20: 404 105.20 - 112.48: 6650 112.48 - 119.76: 5124 119.76 - 127.04: 6000 127.04 - 134.32: 233 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 2.520 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 120 through 233) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 3.620 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 44.120 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.980 ------------------------------------------------------------------------------- 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= 0.477 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 *********************** 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 fitting. rotamer outliers: 21 poor density : 268 time to evaluate : 1.585 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: 0.3168 time to fit residues: 122.8973 Evaluate side-chains 198 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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: 6.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 163 GLN A 168 ASN A 181 GLN A 231 ASN B 100 ASN B 142 ASN B 145 ASN B 160 ASN B 231 GLN B 263 ASN B 306 ASN ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13480 Z= 0.170 Angle : 0.639 10.840 18411 Z= 0.343 Chirality : 0.043 0.283 2001 Planarity : 0.004 0.063 2148 Dihedral : 16.989 178.005 2333 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.50 % Favored : 92.43 % Rotamer: Outliers : 2.59 % Allowed : 17.16 % Favored : 80.24 % 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: -3.10 (0.20), residues: 1427 helix: -1.37 (0.19), residues: 592 sheet: -1.89 (0.40), residues: 142 loop : -2.74 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 602 HIS 0.004 0.001 HIS B 633 PHE 0.019 0.001 PHE C 196 TYR 0.022 0.002 TYR C 209 ARG 0.004 0.000 ARG B 18 *********************** 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 257 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 223 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.1538 (mtp) cc_final: 0.0886 (mmt) REVERT: A 133 ILE cc_start: 0.9100 (mt) cc_final: 0.8783 (mm) REVERT: A 135 GLU cc_start: 0.8939 (tp30) cc_final: 0.8689 (tp30) REVERT: A 142 GLN cc_start: 0.8807 (tt0) cc_final: 0.8491 (tp-100) REVERT: A 144 TYR cc_start: 0.7630 (t80) cc_final: 0.6841 (t80) REVERT: A 154 LYS cc_start: 0.9469 (mttp) cc_final: 0.9044 (mtmt) REVERT: A 157 ASN cc_start: 0.9026 (m-40) cc_final: 0.8794 (t0) REVERT: A 181 GLN cc_start: 0.8398 (tt0) cc_final: 0.7814 (tp-100) REVERT: A 193 GLN cc_start: 0.8571 (tt0) cc_final: 0.8274 (tm-30) REVERT: A 202 LYS cc_start: 0.8165 (mmtp) cc_final: 0.7684 (ptpp) REVERT: A 230 ARG cc_start: 0.8885 (ttm110) cc_final: 0.8608 (ttm110) REVERT: A 232 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8071 (mt) REVERT: B 178 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8144 (mt-10) REVERT: B 350 ASP cc_start: 0.7313 (m-30) cc_final: 0.7060 (p0) REVERT: B 601 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7624 (pptt) REVERT: B 605 TYR cc_start: 0.8146 (m-80) cc_final: 0.7815 (m-80) REVERT: B 746 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8076 (ptm) REVERT: B 815 GLU cc_start: 0.8709 (tp30) cc_final: 0.8351 (tp30) REVERT: B 840 TYR cc_start: 0.8929 (t80) cc_final: 0.8424 (t80) REVERT: B 895 ASN cc_start: 0.7840 (m110) cc_final: 0.7600 (m-40) REVERT: B 927 LEU cc_start: 0.8443 (mt) cc_final: 0.7892 (tt) REVERT: B 940 LYS cc_start: 0.8904 (tttt) cc_final: 0.8176 (ptmm) REVERT: B 941 GLN cc_start: 0.8531 (tp40) cc_final: 0.8033 (tp40) REVERT: B 944 GLN cc_start: 0.8363 (mt0) cc_final: 0.7981 (mt0) REVERT: B 949 MET cc_start: 0.7944 (ttm) cc_final: 0.7630 (ttm) REVERT: B 1003 LYS cc_start: 0.9323 (mttt) cc_final: 0.9028 (mttm) REVERT: B 1216 LYS cc_start: 0.9004 (ttmm) cc_final: 0.8303 (tppt) REVERT: C 133 ILE cc_start: 0.8721 (mm) cc_final: 0.8387 (tp) REVERT: C 137 ASP cc_start: 0.9218 (m-30) cc_final: 0.8952 (m-30) REVERT: C 148 LYS cc_start: 0.8968 (ttmm) cc_final: 0.8447 (mtmm) REVERT: C 209 TYR cc_start: 0.8156 (m-80) cc_final: 0.7874 (m-80) REVERT: C 222 ARG cc_start: 0.9105 (tpp-160) cc_final: 0.8819 (tpp80) outliers start: 34 outliers final: 17 residues processed: 241 average time/residue: 0.2775 time to fit residues: 94.7826 Evaluate side-chains 216 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 541 ASP Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 746 MET Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1207 ASP 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 73 optimal weight: 0.0470 chunk 41 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 143 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 131 optimal weight: 0.0570 chunk 45 optimal weight: 20.0000 chunk 106 optimal weight: 0.8980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN B 759 HIS B 808 ASN B1100 ASN B1108 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2700 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= 0.161 Angle : 0.598 9.917 18411 Z= 0.317 Chirality : 0.042 0.183 2001 Planarity : 0.003 0.053 2148 Dihedral : 16.632 177.483 2327 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.64 % Favored : 92.29 % Rotamer: Outliers : 3.51 % Allowed : 18.92 % Favored : 77.57 % 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: -2.36 (0.21), residues: 1427 helix: -0.61 (0.20), residues: 594 sheet: -1.55 (0.43), residues: 132 loop : -2.47 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 602 HIS 0.004 0.001 HIS B 633 PHE 0.012 0.001 PHE C 196 TYR 0.020 0.001 TYR B 510 ARG 0.003 0.000 ARG B 385 *********************** 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 277 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 231 time to evaluate : 1.490 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: 0.1924 (mtp) cc_final: 0.1588 (mmt) REVERT: A 134 LYS cc_start: 0.9171 (mttm) cc_final: 0.8830 (ttmt) REVERT: A 142 GLN cc_start: 0.8858 (tt0) cc_final: 0.8571 (tp-100) REVERT: A 144 TYR cc_start: 0.7738 (t80) cc_final: 0.6777 (t80) REVERT: A 154 LYS cc_start: 0.9485 (mttp) cc_final: 0.9048 (mtmt) REVERT: A 157 ASN cc_start: 0.9047 (m-40) cc_final: 0.8802 (t0) REVERT: A 181 GLN cc_start: 0.8485 (tt0) cc_final: 0.8274 (tt0) REVERT: A 193 GLN cc_start: 0.8500 (tt0) cc_final: 0.8295 (tm-30) REVERT: A 202 LYS cc_start: 0.7981 (mmtp) cc_final: 0.7395 (ptpp) REVERT: A 219 GLU cc_start: 0.8569 (pp20) cc_final: 0.7838 (pp20) REVERT: A 221 GLU cc_start: 0.8875 (tt0) cc_final: 0.8520 (tp30) REVERT: A 232 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8023 (mt) REVERT: B 110 LYS cc_start: 0.8620 (pttm) cc_final: 0.8176 (pttm) REVERT: B 510 TYR cc_start: 0.7584 (t80) cc_final: 0.6502 (t80) REVERT: B 513 GLN cc_start: 0.6062 (OUTLIER) cc_final: 0.4327 (pp30) REVERT: B 601 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7475 (pptt) REVERT: B 605 TYR cc_start: 0.8122 (m-80) cc_final: 0.7829 (m-80) REVERT: B 614 LYS cc_start: 0.9685 (mmmt) cc_final: 0.9421 (pttp) REVERT: B 659 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7657 (mp0) REVERT: B 815 GLU cc_start: 0.8725 (tp30) cc_final: 0.8399 (tp30) REVERT: B 840 TYR cc_start: 0.8901 (t80) cc_final: 0.8345 (t80) REVERT: B 919 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8241 (t0) REVERT: B 927 LEU cc_start: 0.8459 (mt) cc_final: 0.7845 (tt) REVERT: B 940 LYS cc_start: 0.8805 (tttt) cc_final: 0.8146 (ptmm) REVERT: B 944 GLN cc_start: 0.8392 (mt0) cc_final: 0.8162 (mt0) REVERT: B 949 MET cc_start: 0.8051 (ttm) cc_final: 0.7701 (ttp) REVERT: B 1003 LYS cc_start: 0.9302 (mttt) cc_final: 0.8953 (mttm) REVERT: B 1108 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7788 (mp10) REVERT: B 1131 MET cc_start: 0.9330 (tpp) cc_final: 0.8992 (mmm) REVERT: B 1216 LYS cc_start: 0.9038 (ttmm) cc_final: 0.8349 (tppt) REVERT: B 1219 LEU cc_start: 0.9613 (mt) cc_final: 0.9407 (mt) REVERT: C 133 ILE cc_start: 0.8848 (mm) cc_final: 0.8526 (tp) REVERT: C 137 ASP cc_start: 0.9257 (m-30) cc_final: 0.8939 (m-30) REVERT: C 148 LYS cc_start: 0.9028 (ttmm) cc_final: 0.8480 (mtmm) REVERT: C 163 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7959 (mm-40) REVERT: C 209 TYR cc_start: 0.8371 (m-80) cc_final: 0.8042 (m-80) REVERT: C 222 ARG cc_start: 0.9142 (tpp-160) cc_final: 0.8877 (tpp80) REVERT: C 230 ARG cc_start: 0.7237 (mtt-85) cc_final: 0.6634 (ptp-170) outliers start: 46 outliers final: 23 residues processed: 254 average time/residue: 0.2773 time to fit residues: 99.9221 Evaluate side-chains 233 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 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 1108 GLN Chi-restraints excluded: chain B residue 1207 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.0000 chunk 99 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN B 112 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 ASN B1108 GLN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3085 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= 0.157 Angle : 0.610 10.058 18411 Z= 0.318 Chirality : 0.042 0.201 2001 Planarity : 0.003 0.045 2148 Dihedral : 16.491 177.405 2327 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.29 % Favored : 92.64 % Rotamer: Outliers : 3.28 % Allowed : 20.90 % Favored : 75.82 % 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: -2.05 (0.22), residues: 1427 helix: -0.26 (0.21), residues: 602 sheet: -1.61 (0.41), residues: 142 loop : -2.35 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 602 HIS 0.004 0.001 HIS B 633 PHE 0.015 0.001 PHE B 490 TYR 0.020 0.001 TYR B 995 ARG 0.013 0.000 ARG A 230 *********************** 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 259 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 216 time to evaluate : 1.340 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: 0.1988 (mtp) cc_final: 0.1569 (mmt) REVERT: A 134 LYS cc_start: 0.9116 (mttm) cc_final: 0.8850 (ttmt) REVERT: A 142 GLN cc_start: 0.8972 (tt0) cc_final: 0.8508 (tp-100) REVERT: A 144 TYR cc_start: 0.7690 (t80) cc_final: 0.6747 (t80) REVERT: A 154 LYS cc_start: 0.9523 (mttp) cc_final: 0.8773 (mtmt) REVERT: A 157 ASN cc_start: 0.9066 (m-40) cc_final: 0.8836 (t0) REVERT: A 186 MET cc_start: 0.7380 (mmm) cc_final: 0.6733 (mmm) REVERT: A 193 GLN cc_start: 0.8442 (tt0) cc_final: 0.8234 (tm-30) REVERT: A 202 LYS cc_start: 0.8073 (mmtp) cc_final: 0.7607 (mtmm) REVERT: A 230 ARG cc_start: 0.8906 (ttm110) cc_final: 0.8170 (mtt-85) REVERT: B 110 LYS cc_start: 0.8639 (pttm) cc_final: 0.8310 (pttm) REVERT: B 116 LYS cc_start: 0.9098 (mmtp) cc_final: 0.8204 (pttm) REVERT: B 311 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7345 (p0) REVERT: B 510 TYR cc_start: 0.7551 (t80) cc_final: 0.6516 (t80) REVERT: B 513 GLN cc_start: 0.6244 (OUTLIER) cc_final: 0.4489 (pp30) REVERT: B 531 MET cc_start: 0.9003 (mmm) cc_final: 0.8298 (tpp) REVERT: B 557 ILE cc_start: 0.8218 (mm) cc_final: 0.7980 (mm) REVERT: B 601 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7329 (pptt) REVERT: B 605 TYR cc_start: 0.8087 (m-80) cc_final: 0.7853 (m-80) REVERT: B 614 LYS cc_start: 0.9678 (mmmt) cc_final: 0.9317 (mmmm) REVERT: B 659 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7629 (mp0) REVERT: B 815 GLU cc_start: 0.8736 (tp30) cc_final: 0.8375 (tp30) REVERT: B 840 TYR cc_start: 0.8926 (t80) cc_final: 0.8527 (t80) REVERT: B 895 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7555 (t0) REVERT: B 919 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8284 (t0) REVERT: B 927 LEU cc_start: 0.8411 (mt) cc_final: 0.7794 (tt) REVERT: B 940 LYS cc_start: 0.8841 (tttt) cc_final: 0.8100 (ptmm) REVERT: B 949 MET cc_start: 0.8043 (ttm) cc_final: 0.7726 (ttp) REVERT: B 957 MET cc_start: 0.8371 (tpp) cc_final: 0.8093 (tpp) REVERT: B 1003 LYS cc_start: 0.9298 (mttt) cc_final: 0.8974 (mttm) REVERT: B 1068 TYR cc_start: 0.9299 (t80) cc_final: 0.8810 (t80) REVERT: B 1131 MET cc_start: 0.9371 (tpp) cc_final: 0.9022 (mmm) REVERT: B 1216 LYS cc_start: 0.9065 (ttmm) cc_final: 0.8406 (tppt) REVERT: C 133 ILE cc_start: 0.8874 (mm) cc_final: 0.8447 (tp) REVERT: C 137 ASP cc_start: 0.9276 (m-30) cc_final: 0.8756 (m-30) REVERT: C 148 LYS cc_start: 0.9008 (ttmm) cc_final: 0.8488 (mtmm) REVERT: C 163 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8127 (mm-40) REVERT: C 209 TYR cc_start: 0.8391 (m-80) cc_final: 0.8041 (m-80) REVERT: C 222 ARG cc_start: 0.9135 (tpp-160) cc_final: 0.8869 (tpp80) outliers start: 43 outliers final: 28 residues processed: 239 average time/residue: 0.2602 time to fit residues: 88.8352 Evaluate side-chains 234 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 201 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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 166 ASP Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 311 ASN 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 603 MET Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1207 ASP 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 117 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 181 GLN ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 ASN B 613 GLN ** B 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN B 895 ASN B 928 ASN C 163 GLN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3123 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= 0.376 Angle : 0.728 9.300 18411 Z= 0.388 Chirality : 0.046 0.183 2001 Planarity : 0.004 0.047 2148 Dihedral : 16.778 177.975 2327 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.39 % Favored : 90.54 % Rotamer: Outliers : 4.35 % Allowed : 21.82 % Favored : 73.84 % 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: -1.98 (0.22), residues: 1427 helix: -0.20 (0.21), residues: 602 sheet: -1.62 (0.40), residues: 167 loop : -2.31 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 602 HIS 0.008 0.002 HIS B 759 PHE 0.025 0.002 PHE B 946 TYR 0.029 0.002 TYR B 562 ARG 0.006 0.001 ARG B 182 *********************** 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 250 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 193 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.1361 (mtp) cc_final: 0.0692 (mmt) REVERT: A 134 LYS cc_start: 0.9164 (mttm) cc_final: 0.8851 (ttpp) REVERT: A 142 GLN cc_start: 0.9093 (tt0) cc_final: 0.8642 (tp-100) REVERT: A 154 LYS cc_start: 0.9526 (mttp) cc_final: 0.9015 (mtmt) REVERT: A 157 ASN cc_start: 0.9211 (m-40) cc_final: 0.8902 (t0) REVERT: A 184 GLU cc_start: 0.6552 (mt-10) cc_final: 0.6318 (mt-10) REVERT: A 193 GLN cc_start: 0.8649 (tt0) cc_final: 0.8267 (tm-30) REVERT: A 202 LYS cc_start: 0.8545 (mmtp) cc_final: 0.8297 (mtmm) REVERT: B 116 LYS cc_start: 0.9136 (mmtp) cc_final: 0.8305 (pttm) REVERT: B 386 ARG cc_start: -0.1011 (OUTLIER) cc_final: -0.1378 (ptt180) REVERT: B 510 TYR cc_start: 0.7530 (t80) cc_final: 0.6575 (t80) REVERT: B 513 GLN cc_start: 0.6585 (OUTLIER) cc_final: 0.4447 (pp30) REVERT: B 516 TYR cc_start: 0.5341 (OUTLIER) cc_final: 0.4632 (p90) REVERT: B 614 LYS cc_start: 0.9688 (mmmt) cc_final: 0.9304 (mmmm) REVERT: B 659 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7658 (mp0) REVERT: B 665 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7622 (t0) REVERT: B 753 LYS cc_start: 0.9389 (mmmt) cc_final: 0.9181 (mmmt) REVERT: B 815 GLU cc_start: 0.8851 (tp30) cc_final: 0.8541 (tp30) REVERT: B 895 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.7828 (t0) REVERT: B 927 LEU cc_start: 0.8565 (mt) cc_final: 0.8225 (tt) REVERT: B 1003 LYS cc_start: 0.9365 (mttt) cc_final: 0.9039 (mttm) REVERT: B 1054 ARG cc_start: 0.9106 (ttm170) cc_final: 0.8565 (mtt-85) REVERT: B 1131 MET cc_start: 0.9390 (tpp) cc_final: 0.9043 (mmm) REVERT: B 1216 LYS cc_start: 0.8953 (ttmm) cc_final: 0.8288 (tppt) REVERT: C 133 ILE cc_start: 0.8888 (mm) cc_final: 0.8508 (tp) REVERT: C 137 ASP cc_start: 0.9259 (m-30) cc_final: 0.8805 (m-30) REVERT: C 148 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8531 (mtmm) REVERT: C 163 GLN cc_start: 0.8562 (mm110) cc_final: 0.8321 (mm-40) REVERT: C 209 TYR cc_start: 0.8137 (m-80) cc_final: 0.7806 (m-80) outliers start: 57 outliers final: 42 residues processed: 230 average time/residue: 0.2767 time to fit residues: 90.8800 Evaluate side-chains 226 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 179 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 32 ASP 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 268 GLN Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 575 ASN Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 656 ASN Chi-restraints excluded: chain B residue 665 ASP 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 882 GLU Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1207 ASP Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 223 VAL 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 47 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 0.0040 chunk 141 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 74 optimal weight: 0.0170 overall best weight: 1.0036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 181 GLN ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 ASN C 208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3370 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= 0.168 Angle : 0.618 9.118 18411 Z= 0.323 Chirality : 0.042 0.192 2001 Planarity : 0.003 0.049 2148 Dihedral : 16.521 176.620 2327 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.28 % Allowed : 23.87 % Favored : 72.85 % 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: -1.71 (0.22), residues: 1427 helix: 0.09 (0.21), residues: 605 sheet: -1.57 (0.42), residues: 142 loop : -2.22 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 649 HIS 0.005 0.001 HIS B 633 PHE 0.012 0.001 PHE B 521 TYR 0.022 0.001 TYR B 562 ARG 0.007 0.000 ARG A 230 *********************** 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 244 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 201 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.1122 (mtp) cc_final: 0.0541 (mmt) REVERT: A 134 LYS cc_start: 0.9125 (mttm) cc_final: 0.8811 (ttpp) REVERT: A 142 GLN cc_start: 0.9062 (tt0) cc_final: 0.8697 (tp-100) REVERT: A 144 TYR cc_start: 0.7750 (t80) cc_final: 0.6967 (t80) REVERT: A 154 LYS cc_start: 0.9524 (mttp) cc_final: 0.9002 (mtmt) REVERT: A 157 ASN cc_start: 0.9110 (m-40) cc_final: 0.8867 (t0) REVERT: A 186 MET cc_start: 0.7433 (mmm) cc_final: 0.6978 (mmm) REVERT: A 193 GLN cc_start: 0.8643 (tt0) cc_final: 0.8406 (tm-30) REVERT: A 202 LYS cc_start: 0.8297 (mmtp) cc_final: 0.7932 (mtmm) REVERT: A 224 MET cc_start: 0.8473 (ttm) cc_final: 0.8216 (ttm) REVERT: A 228 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8656 (pt0) REVERT: B 116 LYS cc_start: 0.9060 (mmtp) cc_final: 0.8279 (pttm) REVERT: B 247 GLU cc_start: 0.3875 (OUTLIER) cc_final: 0.3283 (mp0) REVERT: B 311 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7047 (p0) REVERT: B 386 ARG cc_start: -0.1074 (OUTLIER) cc_final: -0.1368 (ptt180) REVERT: B 510 TYR cc_start: 0.7466 (t80) cc_final: 0.6579 (t80) REVERT: B 513 GLN cc_start: 0.6264 (OUTLIER) cc_final: 0.4507 (pp30) REVERT: B 614 LYS cc_start: 0.9688 (mmmt) cc_final: 0.9296 (mmmm) REVERT: B 659 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7683 (mp0) REVERT: B 815 GLU cc_start: 0.8780 (tp30) cc_final: 0.8419 (tp30) REVERT: B 840 TYR cc_start: 0.8978 (t80) cc_final: 0.8258 (t80) REVERT: B 895 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7654 (t0) REVERT: B 919 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8036 (t0) REVERT: B 1003 LYS cc_start: 0.9296 (mttt) cc_final: 0.8994 (mttm) REVERT: B 1131 MET cc_start: 0.9353 (tpp) cc_final: 0.9033 (mmm) REVERT: B 1216 LYS cc_start: 0.8959 (ttmm) cc_final: 0.8325 (tppt) REVERT: C 133 ILE cc_start: 0.8880 (mm) cc_final: 0.8501 (tp) REVERT: C 137 ASP cc_start: 0.9243 (m-30) cc_final: 0.8749 (m-30) REVERT: C 148 LYS cc_start: 0.9031 (ttmm) cc_final: 0.8527 (mtmm) REVERT: C 163 GLN cc_start: 0.8571 (mm110) cc_final: 0.8318 (mm-40) REVERT: C 209 TYR cc_start: 0.8374 (m-80) cc_final: 0.8057 (m-80) REVERT: C 222 ARG cc_start: 0.9105 (tpp-160) cc_final: 0.8849 (tpp80) outliers start: 43 outliers final: 32 residues processed: 227 average time/residue: 0.2675 time to fit residues: 87.5513 Evaluate side-chains 226 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 188 time to evaluate : 1.444 ------------------------------------------------------------------------------- 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 177 LEU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 656 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 882 GLU Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1207 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 140 optimal weight: 0.0980 chunk 88 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 ASN C 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3561 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= 0.165 Angle : 0.613 10.373 18411 Z= 0.318 Chirality : 0.041 0.177 2001 Planarity : 0.003 0.046 2148 Dihedral : 16.408 177.325 2327 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.97 % Allowed : 24.18 % Favored : 72.85 % 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: -1.49 (0.22), residues: 1427 helix: 0.27 (0.22), residues: 598 sheet: -1.47 (0.43), residues: 142 loop : -2.07 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 602 HIS 0.004 0.001 HIS B 633 PHE 0.018 0.001 PHE B 173 TYR 0.017 0.001 TYR B 562 ARG 0.013 0.000 ARG A 230 *********************** 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 235 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 196 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.0904 (mtp) cc_final: 0.0346 (mmt) REVERT: A 134 LYS cc_start: 0.9169 (mttm) cc_final: 0.8826 (ttpp) REVERT: A 142 GLN cc_start: 0.9085 (tt0) cc_final: 0.8707 (tp-100) REVERT: A 144 TYR cc_start: 0.7636 (t80) cc_final: 0.7034 (t80) REVERT: A 154 LYS cc_start: 0.9514 (mttp) cc_final: 0.9062 (mtmt) REVERT: A 157 ASN cc_start: 0.9091 (m-40) cc_final: 0.8768 (t0) REVERT: A 186 MET cc_start: 0.7431 (mmm) cc_final: 0.6944 (mmm) REVERT: A 193 GLN cc_start: 0.8602 (tt0) cc_final: 0.8382 (tm-30) REVERT: A 202 LYS cc_start: 0.8289 (mmtp) cc_final: 0.7869 (mtmm) REVERT: A 224 MET cc_start: 0.8492 (ttm) cc_final: 0.8181 (ttm) REVERT: A 228 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8622 (pt0) REVERT: B 110 LYS cc_start: 0.8677 (pttm) cc_final: 0.8321 (pttm) REVERT: B 116 LYS cc_start: 0.9043 (mmtp) cc_final: 0.8294 (pttm) REVERT: B 311 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7210 (p0) REVERT: B 386 ARG cc_start: -0.1065 (OUTLIER) cc_final: -0.1352 (ptt180) REVERT: B 458 ASP cc_start: 0.9157 (m-30) cc_final: 0.8718 (p0) REVERT: B 510 TYR cc_start: 0.7428 (t80) cc_final: 0.6302 (t80) REVERT: B 513 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.5844 (tp-100) REVERT: B 614 LYS cc_start: 0.9678 (mmmt) cc_final: 0.9288 (mmmm) REVERT: B 815 GLU cc_start: 0.8780 (tp30) cc_final: 0.8412 (tp30) REVERT: B 840 TYR cc_start: 0.8997 (t80) cc_final: 0.8263 (t80) REVERT: B 895 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7852 (t0) REVERT: B 919 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8149 (t0) REVERT: B 927 LEU cc_start: 0.8125 (tp) cc_final: 0.7851 (tp) REVERT: B 1003 LYS cc_start: 0.9281 (mttt) cc_final: 0.8977 (mttm) REVERT: B 1131 MET cc_start: 0.9406 (tpp) cc_final: 0.9033 (mmm) REVERT: B 1216 LYS cc_start: 0.8999 (ttmm) cc_final: 0.8446 (tppt) REVERT: C 133 ILE cc_start: 0.8876 (mm) cc_final: 0.8471 (tp) REVERT: C 137 ASP cc_start: 0.9228 (m-30) cc_final: 0.8728 (m-30) REVERT: C 148 LYS cc_start: 0.9056 (ttmm) cc_final: 0.8512 (mtmm) REVERT: C 163 GLN cc_start: 0.8576 (mm110) cc_final: 0.8327 (mm-40) REVERT: C 209 TYR cc_start: 0.8428 (m-80) cc_final: 0.8100 (m-80) outliers start: 39 outliers final: 28 residues processed: 221 average time/residue: 0.2723 time to fit residues: 87.2000 Evaluate side-chains 221 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 188 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 656 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 882 GLU Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1207 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 89 optimal weight: 0.4980 chunk 95 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 110 optimal weight: 0.4980 chunk 128 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 168 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13480 Z= 0.170 Angle : 0.628 13.957 18411 Z= 0.322 Chirality : 0.041 0.167 2001 Planarity : 0.003 0.056 2148 Dihedral : 16.346 177.119 2327 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 3.13 % Allowed : 25.32 % Favored : 71.55 % 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: -1.33 (0.23), residues: 1427 helix: 0.54 (0.22), residues: 587 sheet: -1.55 (0.40), residues: 163 loop : -2.04 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 602 HIS 0.004 0.001 HIS B 633 PHE 0.022 0.001 PHE C 196 TYR 0.016 0.001 TYR B 516 ARG 0.010 0.000 ARG A 230 *********************** 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 235 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 194 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.0788 (mtp) cc_final: 0.0285 (mmt) REVERT: A 134 LYS cc_start: 0.9163 (mttm) cc_final: 0.8840 (ttpp) REVERT: A 142 GLN cc_start: 0.9093 (tt0) cc_final: 0.8584 (tp-100) REVERT: A 144 TYR cc_start: 0.7662 (t80) cc_final: 0.7274 (t80) REVERT: A 154 LYS cc_start: 0.9532 (mttp) cc_final: 0.9110 (mtmt) REVERT: A 157 ASN cc_start: 0.9078 (m-40) cc_final: 0.8778 (t0) REVERT: A 186 MET cc_start: 0.7464 (mmm) cc_final: 0.6964 (mmm) REVERT: A 193 GLN cc_start: 0.8557 (tt0) cc_final: 0.8342 (tm-30) REVERT: A 202 LYS cc_start: 0.8251 (mmtp) cc_final: 0.7969 (mtmm) REVERT: A 224 MET cc_start: 0.8489 (ttm) cc_final: 0.8182 (ttm) REVERT: A 228 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8624 (pt0) REVERT: B 110 LYS cc_start: 0.8702 (pttm) cc_final: 0.8328 (pttm) REVERT: B 116 LYS cc_start: 0.8992 (mmtp) cc_final: 0.8308 (pttm) REVERT: B 247 GLU cc_start: 0.3818 (OUTLIER) cc_final: 0.3196 (mp0) REVERT: B 311 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7228 (p0) REVERT: B 386 ARG cc_start: -0.1419 (OUTLIER) cc_final: -0.1628 (ptt180) REVERT: B 510 TYR cc_start: 0.7405 (t80) cc_final: 0.6224 (t80) REVERT: B 513 GLN cc_start: 0.6431 (OUTLIER) cc_final: 0.5887 (tp-100) REVERT: B 614 LYS cc_start: 0.9673 (mmmt) cc_final: 0.9275 (mmmm) REVERT: B 724 PHE cc_start: 0.9004 (t80) cc_final: 0.8802 (t80) REVERT: B 815 GLU cc_start: 0.8787 (tp30) cc_final: 0.8414 (tp30) REVERT: B 895 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7873 (t0) REVERT: B 919 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8274 (t0) REVERT: B 927 LEU cc_start: 0.8128 (tp) cc_final: 0.7817 (tp) REVERT: B 1003 LYS cc_start: 0.9279 (mttt) cc_final: 0.8974 (mttm) REVERT: B 1131 MET cc_start: 0.9431 (tpp) cc_final: 0.9021 (mmm) REVERT: B 1216 LYS cc_start: 0.8989 (ttmm) cc_final: 0.8391 (tppt) REVERT: C 133 ILE cc_start: 0.8873 (mm) cc_final: 0.8442 (tp) REVERT: C 137 ASP cc_start: 0.9213 (m-30) cc_final: 0.8664 (m-30) REVERT: C 148 LYS cc_start: 0.9104 (ttmm) cc_final: 0.8615 (mtmm) REVERT: C 163 GLN cc_start: 0.8552 (mm110) cc_final: 0.8311 (mm-40) REVERT: C 209 TYR cc_start: 0.8460 (m-80) cc_final: 0.8145 (m-80) outliers start: 41 outliers final: 33 residues processed: 220 average time/residue: 0.2666 time to fit residues: 84.5759 Evaluate side-chains 225 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 186 time to evaluate : 1.514 ------------------------------------------------------------------------------- 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 166 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 32 ASP 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 268 GLN Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 656 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 882 GLU Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 905 SER Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1207 ASP 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 131 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 0.0770 chunk 102 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 168 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN B 895 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13480 Z= 0.146 Angle : 0.631 15.888 18411 Z= 0.320 Chirality : 0.041 0.241 2001 Planarity : 0.003 0.043 2148 Dihedral : 16.217 176.812 2327 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.28 % Allowed : 25.25 % Favored : 71.47 % 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: -1.22 (0.23), residues: 1427 helix: 0.64 (0.22), residues: 588 sheet: -1.54 (0.40), residues: 163 loop : -1.98 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 602 HIS 0.003 0.001 HIS B 633 PHE 0.020 0.001 PHE B 173 TYR 0.015 0.001 TYR B 516 ARG 0.009 0.000 ARG A 230 *********************** 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 247 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 204 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.1023 (mtp) cc_final: 0.0318 (mmt) REVERT: A 134 LYS cc_start: 0.9173 (mttm) cc_final: 0.8778 (ttpp) REVERT: A 142 GLN cc_start: 0.9033 (tt0) cc_final: 0.8587 (tp-100) REVERT: A 144 TYR cc_start: 0.7747 (t80) cc_final: 0.7236 (t80) REVERT: A 154 LYS cc_start: 0.9531 (mttp) cc_final: 0.9154 (mtpt) REVERT: A 157 ASN cc_start: 0.9104 (m-40) cc_final: 0.8867 (t0) REVERT: A 186 MET cc_start: 0.7296 (mmm) cc_final: 0.6864 (mmm) REVERT: A 202 LYS cc_start: 0.8100 (mmtp) cc_final: 0.7864 (mtmm) REVERT: A 224 MET cc_start: 0.8452 (ttm) cc_final: 0.8168 (ttm) REVERT: B 110 LYS cc_start: 0.8725 (pttm) cc_final: 0.8440 (pttm) REVERT: B 116 LYS cc_start: 0.8929 (mmtp) cc_final: 0.8277 (pttm) REVERT: B 182 ARG cc_start: 0.8794 (mtp180) cc_final: 0.8473 (mtt180) REVERT: B 247 GLU cc_start: 0.3718 (OUTLIER) cc_final: 0.3142 (mp0) REVERT: B 311 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7369 (p0) REVERT: B 510 TYR cc_start: 0.7396 (t80) cc_final: 0.6231 (t80) REVERT: B 513 GLN cc_start: 0.6471 (OUTLIER) cc_final: 0.5967 (tp-100) REVERT: B 614 LYS cc_start: 0.9655 (mmmt) cc_final: 0.9254 (mmmm) REVERT: B 815 GLU cc_start: 0.8775 (tp30) cc_final: 0.8397 (tp30) REVERT: B 895 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7696 (t0) REVERT: B 919 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8332 (t0) REVERT: B 927 LEU cc_start: 0.7996 (tp) cc_final: 0.7685 (tp) REVERT: B 1003 LYS cc_start: 0.9256 (mttt) cc_final: 0.8960 (mttm) REVERT: B 1131 MET cc_start: 0.9444 (tpp) cc_final: 0.8992 (mmm) REVERT: B 1216 LYS cc_start: 0.9013 (ttmm) cc_final: 0.8397 (tppt) REVERT: C 133 ILE cc_start: 0.8916 (mm) cc_final: 0.8482 (tp) REVERT: C 137 ASP cc_start: 0.9195 (m-30) cc_final: 0.8672 (m-30) REVERT: C 148 LYS cc_start: 0.9154 (ttmm) cc_final: 0.8677 (mtmm) REVERT: C 163 GLN cc_start: 0.8505 (mm110) cc_final: 0.8252 (mm-40) REVERT: C 209 TYR cc_start: 0.8529 (m-80) cc_final: 0.8234 (m-80) outliers start: 43 outliers final: 30 residues processed: 229 average time/residue: 0.2855 time to fit residues: 93.0838 Evaluate side-chains 226 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 191 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 656 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 882 GLU Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 905 SER Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1207 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 0.3980 chunk 84 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 0.0370 chunk 92 optimal weight: 0.0470 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 168 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13480 Z= 0.147 Angle : 0.649 17.541 18411 Z= 0.326 Chirality : 0.041 0.254 2001 Planarity : 0.003 0.051 2148 Dihedral : 16.121 176.523 2327 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.67 % Allowed : 26.32 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.18 (0.23), residues: 1427 helix: 0.59 (0.22), residues: 589 sheet: -1.40 (0.43), residues: 142 loop : -1.91 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 602 HIS 0.003 0.001 HIS B 633 PHE 0.015 0.001 PHE B 728 TYR 0.022 0.001 TYR B1185 ARG 0.005 0.000 ARG A 230 ********************** 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 241 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 206 time to evaluate : 1.479 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: 0.1715 (mtp) cc_final: 0.1149 (mmt) REVERT: A 134 LYS cc_start: 0.9135 (mttm) cc_final: 0.8806 (ttpp) REVERT: A 142 GLN cc_start: 0.9062 (tt0) cc_final: 0.8582 (tp-100) REVERT: A 144 TYR cc_start: 0.7860 (t80) cc_final: 0.7272 (t80) REVERT: A 154 LYS cc_start: 0.9517 (mttp) cc_final: 0.9104 (mtpt) REVERT: A 186 MET cc_start: 0.7110 (mmm) cc_final: 0.6882 (mmm) REVERT: A 196 PHE cc_start: 0.8489 (m-80) cc_final: 0.8268 (m-80) REVERT: A 220 ILE cc_start: 0.8873 (mp) cc_final: 0.8602 (mm) REVERT: B 110 LYS cc_start: 0.8726 (pttm) cc_final: 0.8444 (pttm) REVERT: B 116 LYS cc_start: 0.8888 (mmtp) cc_final: 0.8276 (pttm) REVERT: B 182 ARG cc_start: 0.8780 (mtp180) cc_final: 0.8430 (mtt180) REVERT: B 247 GLU cc_start: 0.3937 (OUTLIER) cc_final: 0.3306 (mp0) REVERT: B 311 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7386 (p0) REVERT: B 510 TYR cc_start: 0.7487 (t80) cc_final: 0.6281 (t80) REVERT: B 513 GLN cc_start: 0.6137 (OUTLIER) cc_final: 0.5899 (tp-100) REVERT: B 531 MET cc_start: 0.8994 (mmm) cc_final: 0.7131 (tmm) REVERT: B 614 LYS cc_start: 0.9650 (mmmt) cc_final: 0.9251 (mmmm) REVERT: B 815 GLU cc_start: 0.8780 (tp30) cc_final: 0.8394 (tp30) REVERT: B 895 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7709 (t0) REVERT: B 1003 LYS cc_start: 0.9244 (mttt) cc_final: 0.8942 (mttm) REVERT: B 1131 MET cc_start: 0.9467 (tpp) cc_final: 0.8964 (mmm) REVERT: B 1216 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8432 (tppt) REVERT: C 133 ILE cc_start: 0.8907 (mm) cc_final: 0.8420 (tp) REVERT: C 137 ASP cc_start: 0.9219 (m-30) cc_final: 0.8587 (m-30) REVERT: C 163 GLN cc_start: 0.8479 (mm110) cc_final: 0.8225 (mm-40) REVERT: C 209 TYR cc_start: 0.8496 (m-80) cc_final: 0.8238 (m-80) outliers start: 35 outliers final: 28 residues processed: 228 average time/residue: 0.2692 time to fit residues: 88.7414 Evaluate side-chains 227 residues out of total 1311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 226 LEU 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 268 GLN Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 656 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 882 GLU Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 905 SER Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain B residue 1130 LEU Chi-restraints excluded: chain B residue 1207 ASP 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 233 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.0670 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.0170 chunk 101 optimal weight: 0.8980 overall best weight: 0.3294 ------------------------------------------------------------------------------- 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 895 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.110335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.081523 restraints weight = 45467.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.084121 restraints weight = 21175.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.085722 restraints weight = 13599.556| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13480 Z= 0.147 Angle : 0.666 17.215 18411 Z= 0.334 Chirality : 0.042 0.268 2001 Planarity : 0.004 0.049 2148 Dihedral : 16.069 176.305 2325 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.75 % Allowed : 26.85 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.19 (0.23), residues: 1427 helix: 0.51 (0.22), residues: 588 sheet: -1.33 (0.44), residues: 142 loop : -1.86 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 999 HIS 0.003 0.001 HIS B 633 PHE 0.023 0.001 PHE C 196 TYR 0.029 0.001 TYR B 995 ARG 0.005 0.000 ARG A 230 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2930.20 seconds wall clock time: 54 minutes 18.50 seconds (3258.50 seconds total)