Starting phenix.real_space_refine on Thu Mar 14 19:32:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr0_31583/03_2024/6lr0_31583.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr0_31583/03_2024/6lr0_31583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr0_31583/03_2024/6lr0_31583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr0_31583/03_2024/6lr0_31583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr0_31583/03_2024/6lr0_31583.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lr0_31583/03_2024/6lr0_31583.pdb" } resolution = 3.5 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= 0.007 sd= 0.098 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 6129 2.51 5 N 1627 2.21 5 O 1766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "U ARG 44": "NH1" <-> "NH2" Residue "U PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 184": "NH1" <-> "NH2" Residue "U ARG 237": "NH1" <-> "NH2" Residue "U ARG 289": "NH1" <-> "NH2" Residue "U ARG 299": "NH1" <-> "NH2" Residue "U ARG 317": "NH1" <-> "NH2" Residue "U ARG 415": "NH1" <-> "NH2" Residue "U ARG 432": "NH1" <-> "NH2" Residue "U ARG 487": "NH1" <-> "NH2" Residue "U ARG 571": "NH1" <-> "NH2" Residue "U ARG 575": "NH1" <-> "NH2" Residue "U ARG 637": "NH1" <-> "NH2" Residue "U ARG 646": "NH1" <-> "NH2" Residue "U ARG 692": "NH1" <-> "NH2" Residue "U ARG 832": "NH1" <-> "NH2" Residue "U ARG 860": "NH1" <-> "NH2" Residue "U ARG 920": "NH1" <-> "NH2" Residue "U ARG 958": "NH1" <-> "NH2" Residue "U ARG 1019": "NH1" <-> "NH2" Residue "U ARG 1187": "NH1" <-> "NH2" Residue "U ARG 1221": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9576 Number of models: 1 Model: "" Number of chains: 1 Chain: "U" Number of atoms: 9576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 9576 Classifications: {'peptide': 1230} Link IDs: {'PTRANS': 36, 'TRANS': 1193} Chain breaks: 2 Time building chain proxies: 5.50, per 1000 atoms: 0.57 Number of scatterers: 9576 At special positions: 0 Unit cell: (90.1, 160.06, 112.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1766 8.00 N 1627 7.00 C 6129 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: 3.42 Conformation dependent library (CDL) restraints added in 1.9 seconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 4 sheets defined 36.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'U' and resid 46 through 50 Processing helix chain 'U' and resid 79 through 84 Processing helix chain 'U' and resid 88 through 100 removed outlier: 3.716A pdb=" N GLU U 96 " --> pdb=" O ASP U 92 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU U 99 " --> pdb=" O VAL U 95 " (cutoff:3.500A) Processing helix chain 'U' and resid 147 through 155 removed outlier: 4.004A pdb=" N LEU U 153 " --> pdb=" O ALA U 149 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 183 removed outlier: 3.655A pdb=" N PHE U 179 " --> pdb=" O ARG U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 192 removed outlier: 3.734A pdb=" N PHE U 190 " --> pdb=" O ILE U 187 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS U 192 " --> pdb=" O TRP U 189 " (cutoff:3.500A) Processing helix chain 'U' and resid 230 through 238 removed outlier: 3.769A pdb=" N PHE U 236 " --> pdb=" O LEU U 232 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG U 237 " --> pdb=" O LEU U 233 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY U 238 " --> pdb=" O GLY U 234 " (cutoff:3.500A) Processing helix chain 'U' and resid 240 through 245 removed outlier: 3.740A pdb=" N VAL U 244 " --> pdb=" O LYS U 240 " (cutoff:3.500A) Processing helix chain 'U' and resid 248 through 257 removed outlier: 4.183A pdb=" N ILE U 254 " --> pdb=" O PRO U 250 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY U 255 " --> pdb=" O LEU U 251 " (cutoff:3.500A) Processing helix chain 'U' and resid 258 through 263 Processing helix chain 'U' and resid 266 through 275 removed outlier: 3.567A pdb=" N LEU U 271 " --> pdb=" O THR U 267 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS U 272 " --> pdb=" O ASP U 268 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA U 275 " --> pdb=" O LEU U 271 " (cutoff:3.500A) Processing helix chain 'U' and resid 277 through 282 removed outlier: 3.706A pdb=" N ASP U 282 " --> pdb=" O GLY U 278 " (cutoff:3.500A) Processing helix chain 'U' and resid 287 through 294 removed outlier: 3.678A pdb=" N VAL U 291 " --> pdb=" O SER U 287 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA U 293 " --> pdb=" O ARG U 289 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE U 294 " --> pdb=" O THR U 290 " (cutoff:3.500A) Processing helix chain 'U' and resid 308 through 312 removed outlier: 3.684A pdb=" N ALA U 311 " --> pdb=" O LEU U 308 " (cutoff:3.500A) Processing helix chain 'U' and resid 320 through 325 Processing helix chain 'U' and resid 329 through 334 removed outlier: 3.919A pdb=" N PHE U 334 " --> pdb=" O TRP U 330 " (cutoff:3.500A) Processing helix chain 'U' and resid 335 through 344 removed outlier: 3.978A pdb=" N LEU U 339 " --> pdb=" O LEU U 335 " (cutoff:3.500A) Processing helix chain 'U' and resid 363 through 376 removed outlier: 3.621A pdb=" N ILE U 367 " --> pdb=" O PHE U 363 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY U 369 " --> pdb=" O SER U 365 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU U 373 " --> pdb=" O GLY U 369 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY U 374 " --> pdb=" O ALA U 370 " (cutoff:3.500A) Processing helix chain 'U' and resid 377 through 386 removed outlier: 4.929A pdb=" N PHE U 383 " --> pdb=" O CYS U 379 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA U 384 " --> pdb=" O LEU U 380 " (cutoff:3.500A) Processing helix chain 'U' and resid 392 through 397 removed outlier: 3.716A pdb=" N THR U 396 " --> pdb=" O SER U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 462 through 467 Processing helix chain 'U' and resid 490 through 495 Processing helix chain 'U' and resid 525 through 535 removed outlier: 3.749A pdb=" N GLN U 530 " --> pdb=" O GLU U 526 " (cutoff:3.500A) Processing helix chain 'U' and resid 540 through 544 removed outlier: 3.508A pdb=" N LEU U 544 " --> pdb=" O ILE U 541 " (cutoff:3.500A) Processing helix chain 'U' and resid 563 through 575 removed outlier: 3.615A pdb=" N ALA U 570 " --> pdb=" O ARG U 566 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG U 575 " --> pdb=" O ARG U 571 " (cutoff:3.500A) Processing helix chain 'U' and resid 593 through 603 removed outlier: 3.766A pdb=" N VAL U 597 " --> pdb=" O SER U 593 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL U 600 " --> pdb=" O MET U 596 " (cutoff:3.500A) Processing helix chain 'U' and resid 652 through 656 Processing helix chain 'U' and resid 700 through 704 removed outlier: 3.660A pdb=" N SER U 704 " --> pdb=" O SER U 701 " (cutoff:3.500A) Processing helix chain 'U' and resid 742 through 747 Processing helix chain 'U' and resid 748 through 752 Processing helix chain 'U' and resid 775 through 780 removed outlier: 3.556A pdb=" N LEU U 780 " --> pdb=" O PHE U 776 " (cutoff:3.500A) Processing helix chain 'U' and resid 789 through 802 removed outlier: 3.621A pdb=" N ILE U 795 " --> pdb=" O GLN U 791 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN U 796 " --> pdb=" O ARG U 792 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS U 799 " --> pdb=" O ILE U 795 " (cutoff:3.500A) Processing helix chain 'U' and resid 803 through 806 Processing helix chain 'U' and resid 828 through 833 removed outlier: 3.685A pdb=" N LYS U 833 " --> pdb=" O LYS U 829 " (cutoff:3.500A) Processing helix chain 'U' and resid 834 through 836 No H-bonds generated for 'chain 'U' and resid 834 through 836' Processing helix chain 'U' and resid 838 through 842 removed outlier: 3.983A pdb=" N GLN U 842 " --> pdb=" O MET U 839 " (cutoff:3.500A) Processing helix chain 'U' and resid 843 through 847 removed outlier: 4.072A pdb=" N TRP U 846 " --> pdb=" O ASP U 843 " (cutoff:3.500A) Processing helix chain 'U' and resid 875 through 881 Processing helix chain 'U' and resid 885 through 897 removed outlier: 3.825A pdb=" N ALA U 889 " --> pdb=" O ASN U 885 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE U 891 " --> pdb=" O THR U 887 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE U 894 " --> pdb=" O MET U 890 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE U 896 " --> pdb=" O ILE U 892 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER U 897 " --> pdb=" O ALA U 893 " (cutoff:3.500A) Processing helix chain 'U' and resid 904 through 907 Processing helix chain 'U' and resid 908 through 913 Processing helix chain 'U' and resid 925 through 930 removed outlier: 3.774A pdb=" N LYS U 930 " --> pdb=" O ALA U 926 " (cutoff:3.500A) Processing helix chain 'U' and resid 935 through 940 Processing helix chain 'U' and resid 940 through 945 removed outlier: 3.555A pdb=" N SER U 945 " --> pdb=" O ASN U 941 " (cutoff:3.500A) Processing helix chain 'U' and resid 946 through 951 Processing helix chain 'U' and resid 956 through 962 Processing helix chain 'U' and resid 994 through 1007 removed outlier: 3.639A pdb=" N SER U 999 " --> pdb=" O ALA U 995 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR U1000 " --> pdb=" O ASN U 996 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG U1001 " --> pdb=" O SER U 997 " (cutoff:3.500A) Processing helix chain 'U' and resid 1013 through 1015 No H-bonds generated for 'chain 'U' and resid 1013 through 1015' Processing helix chain 'U' and resid 1016 through 1021 removed outlier: 3.614A pdb=" N ILE U1021 " --> pdb=" O VAL U1017 " (cutoff:3.500A) Processing helix chain 'U' and resid 1031 through 1035 removed outlier: 3.917A pdb=" N PHE U1035 " --> pdb=" O GLY U1032 " (cutoff:3.500A) Processing helix chain 'U' and resid 1037 through 1043 removed outlier: 3.558A pdb=" N TYR U1041 " --> pdb=" O TYR U1037 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA U1042 " --> pdb=" O THR U1038 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS U1043 " --> pdb=" O PRO U1039 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 1037 through 1043' Processing helix chain 'U' and resid 1048 through 1053 removed outlier: 3.843A pdb=" N PHE U1052 " --> pdb=" O ALA U1048 " (cutoff:3.500A) Processing helix chain 'U' and resid 1120 through 1125 removed outlier: 3.553A pdb=" N GLN U1124 " --> pdb=" O SER U1120 " (cutoff:3.500A) Processing helix chain 'U' and resid 1148 through 1153 removed outlier: 3.509A pdb=" N LEU U1152 " --> pdb=" O ASN U1148 " (cutoff:3.500A) Processing helix chain 'U' and resid 1171 through 1176 removed outlier: 3.714A pdb=" N LYS U1175 " --> pdb=" O MET U1171 " (cutoff:3.500A) Processing helix chain 'U' and resid 1185 through 1191 removed outlier: 4.306A pdb=" N ILE U1189 " --> pdb=" O MET U1185 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA U1190 " --> pdb=" O GLU U1186 " (cutoff:3.500A) Processing helix chain 'U' and resid 1200 through 1204 removed outlier: 3.822A pdb=" N LEU U1204 " --> pdb=" O VAL U1201 " (cutoff:3.500A) Processing helix chain 'U' and resid 1220 through 1223 Processing helix chain 'U' and resid 1224 through 1233 removed outlier: 3.830A pdb=" N ALA U1228 " --> pdb=" O LYS U1224 " (cutoff:3.500A) Processing helix chain 'U' and resid 1250 through 1264 removed outlier: 3.537A pdb=" N VAL U1257 " --> pdb=" O SER U1253 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL U1259 " --> pdb=" O LYS U1255 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA U1260 " --> pdb=" O THR U1256 " (cutoff:3.500A) Processing helix chain 'U' and resid 1308 through 1314 removed outlier: 3.519A pdb=" N LYS U1312 " --> pdb=" O GLY U1308 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU U1313 " --> pdb=" O ALA U1309 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'U' and resid 438 through 445 removed outlier: 6.806A pdb=" N ASN U 439 " --> pdb=" O THR U 426 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR U 426 " --> pdb=" O ASN U 439 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU U 441 " --> pdb=" O ASN U 424 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN U 424 " --> pdb=" O LEU U 441 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE U 420 " --> pdb=" O ILE U 445 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'U' and resid 450 through 451 removed outlier: 6.175A pdb=" N THR U 451 " --> pdb=" O SER U 612 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU U 580 " --> pdb=" O ILE U 611 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL U 613 " --> pdb=" O LEU U 580 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU U 582 " --> pdb=" O VAL U 613 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'U' and resid 1079 through 1080 Processing sheet with id=AA4, first strand: chain 'U' and resid 1156 through 1159 removed outlier: 6.714A pdb=" N GLY U1157 " --> pdb=" O LEU U1241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 158 hydrogen bonds defined for protein. 420 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2048 1.33 - 1.45: 2223 1.45 - 1.57: 5402 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 9761 Sorted by residual: bond pdb=" C GLN U 76 " pdb=" N PRO U 77 " ideal model delta sigma weight residual 1.333 1.378 -0.045 7.80e-03 1.64e+04 3.37e+01 bond pdb=" CG1 ILE U 171 " pdb=" CD1 ILE U 171 " ideal model delta sigma weight residual 1.513 1.363 0.150 3.90e-02 6.57e+02 1.49e+01 bond pdb=" CB VAL U1024 " pdb=" CG2 VAL U1024 " ideal model delta sigma weight residual 1.521 1.421 0.100 3.30e-02 9.18e+02 9.18e+00 bond pdb=" CG ARG U 175 " pdb=" CD ARG U 175 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.22e+00 bond pdb=" CB ILE U 160 " pdb=" CG2 ILE U 160 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.66e+00 ... (remaining 9756 not shown) Histogram of bond angle deviations from ideal: 97.33 - 104.71: 145 104.71 - 112.08: 4357 112.08 - 119.46: 3782 119.46 - 126.83: 4806 126.83 - 134.20: 109 Bond angle restraints: 13199 Sorted by residual: angle pdb=" N ILE U1170 " pdb=" CA ILE U1170 " pdb=" C ILE U1170 " ideal model delta sigma weight residual 112.83 104.69 8.14 9.90e-01 1.02e+00 6.75e+01 angle pdb=" N ILE U 213 " pdb=" CA ILE U 213 " pdb=" C ILE U 213 " ideal model delta sigma weight residual 113.71 107.32 6.39 9.50e-01 1.11e+00 4.53e+01 angle pdb=" N LEU U 67 " pdb=" CA LEU U 67 " pdb=" C LEU U 67 " ideal model delta sigma weight residual 113.38 105.94 7.44 1.23e+00 6.61e-01 3.66e+01 angle pdb=" C ASN U 946 " pdb=" N ILE U 947 " pdb=" CA ILE U 947 " ideal model delta sigma weight residual 120.53 127.26 -6.73 1.41e+00 5.03e-01 2.28e+01 angle pdb=" N GLY U 924 " pdb=" CA GLY U 924 " pdb=" C GLY U 924 " ideal model delta sigma weight residual 115.46 107.75 7.71 1.63e+00 3.76e-01 2.24e+01 ... (remaining 13194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 5279 16.28 - 32.56: 428 32.56 - 48.84: 99 48.84 - 65.12: 10 65.12 - 81.40: 7 Dihedral angle restraints: 5823 sinusoidal: 2288 harmonic: 3535 Sorted by residual: dihedral pdb=" CA LEU U 712 " pdb=" C LEU U 712 " pdb=" N ALA U 713 " pdb=" CA ALA U 713 " ideal model delta harmonic sigma weight residual 180.00 135.33 44.67 0 5.00e+00 4.00e-02 7.98e+01 dihedral pdb=" CA TYR U1037 " pdb=" C TYR U1037 " pdb=" N THR U1038 " pdb=" CA THR U1038 " ideal model delta harmonic sigma weight residual -180.00 -142.24 -37.76 0 5.00e+00 4.00e-02 5.70e+01 dihedral pdb=" CA ILE U1271 " pdb=" C ILE U1271 " pdb=" N VAL U1272 " pdb=" CA VAL U1272 " ideal model delta harmonic sigma weight residual -180.00 -146.00 -34.00 0 5.00e+00 4.00e-02 4.62e+01 ... (remaining 5820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1305 0.093 - 0.187: 177 0.187 - 0.280: 16 0.280 - 0.374: 3 0.374 - 0.467: 1 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CB ILE U 785 " pdb=" CA ILE U 785 " pdb=" CG1 ILE U 785 " pdb=" CG2 ILE U 785 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CB VAL U 808 " pdb=" CA VAL U 808 " pdb=" CG1 VAL U 808 " pdb=" CG2 VAL U 808 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB VAL U 360 " pdb=" CA VAL U 360 " pdb=" CG1 VAL U 360 " pdb=" CG2 VAL U 360 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 1499 not shown) Planarity restraints: 1689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS U 969 " 0.060 5.00e-02 4.00e+02 8.99e-02 1.29e+01 pdb=" N PRO U 970 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO U 970 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO U 970 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE U 383 " -0.023 2.00e-02 2.50e+03 2.06e-02 7.44e+00 pdb=" CG PHE U 383 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE U 383 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE U 383 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE U 383 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE U 383 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE U 383 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER U 249 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO U 250 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO U 250 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO U 250 " -0.037 5.00e-02 4.00e+02 ... (remaining 1686 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2970 2.81 - 3.33: 8225 3.33 - 3.86: 14900 3.86 - 4.38: 17263 4.38 - 4.90: 29290 Nonbonded interactions: 72648 Sorted by model distance: nonbonded pdb=" O GLN U 546 " pdb=" OG1 THR U 550 " model vdw 2.291 2.440 nonbonded pdb=" OG1 THR U 227 " pdb=" O GLY U 369 " model vdw 2.295 2.440 nonbonded pdb=" O SER U1027 " pdb=" OG SER U1027 " model vdw 2.308 2.440 nonbonded pdb=" O GLN U1196 " pdb=" NH2 ARG U1226 " model vdw 2.316 2.520 nonbonded pdb=" O THR U 155 " pdb=" OG1 THR U 155 " model vdw 2.330 2.440 ... (remaining 72643 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.450 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: 2.680 Check model and map are aligned: 0.170 Set scattering table: 0.090 Process input model: 26.910 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 : 0.011 0.150 9761 Z= 0.698 Angle : 1.380 14.085 13199 Z= 0.753 Chirality : 0.066 0.467 1502 Planarity : 0.007 0.090 1689 Dihedral : 13.072 81.405 3551 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.03 % Favored : 88.89 % Rotamer: Outliers : 0.88 % Allowed : 9.26 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -6.35 (0.16), residues: 1224 helix: -4.96 (0.08), residues: 637 sheet: -3.98 (0.66), residues: 36 loop : -3.12 (0.23), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP U 846 HIS 0.007 0.002 HIS U 717 PHE 0.046 0.004 PHE U 383 TYR 0.027 0.003 TYR U 145 ARG 0.010 0.001 ARG U 317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 208 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 76 GLN cc_start: 0.8450 (tp40) cc_final: 0.8100 (tp-100) REVERT: U 97 LEU cc_start: 0.8465 (tp) cc_final: 0.8217 (tt) REVERT: U 228 ILE cc_start: 0.9055 (tp) cc_final: 0.8829 (mt) REVERT: U 922 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6947 (tp) outliers start: 9 outliers final: 2 residues processed: 214 average time/residue: 0.2428 time to fit residues: 69.6644 Evaluate side-chains 125 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1026 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 170 GLN U 207 ASN U 466 GLN U 492 GLN ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 536 ASN U 546 GLN U 576 ASN U 605 GLN U 640 HIS U 697 GLN U 708 HIS U 778 GLN U 791 GLN U 842 GLN ** U 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1097 ASN ** U1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9761 Z= 0.222 Angle : 0.715 8.540 13199 Z= 0.369 Chirality : 0.044 0.240 1502 Planarity : 0.004 0.051 1689 Dihedral : 7.404 58.913 1333 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.33 % Favored : 91.58 % Rotamer: Outliers : 3.51 % Allowed : 14.04 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.49 (0.19), residues: 1224 helix: -4.34 (0.12), residues: 631 sheet: -3.26 (0.70), residues: 36 loop : -2.63 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U1071 HIS 0.005 0.001 HIS U 640 PHE 0.025 0.002 PHE U 383 TYR 0.012 0.001 TYR U1208 ARG 0.006 0.000 ARG U 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 288 MET cc_start: 0.8161 (tpt) cc_final: 0.7834 (tpt) REVERT: U 317 ARG cc_start: 0.8206 (ttp-110) cc_final: 0.7993 (mtm180) REVERT: U 373 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8952 (tp) REVERT: U 398 ASP cc_start: 0.7366 (t0) cc_final: 0.7046 (t70) REVERT: U 443 MET cc_start: 0.8150 (ppp) cc_final: 0.7294 (ptt) REVERT: U 696 ARG cc_start: 0.7654 (mtp85) cc_final: 0.7400 (mtp85) REVERT: U 743 ARG cc_start: 0.6795 (tpt-90) cc_final: 0.6251 (ttp-170) REVERT: U 834 PHE cc_start: 0.8359 (t80) cc_final: 0.8070 (t80) REVERT: U 891 ILE cc_start: 0.8623 (mm) cc_final: 0.8233 (mt) outliers start: 36 outliers final: 14 residues processed: 174 average time/residue: 0.1969 time to fit residues: 49.1190 Evaluate side-chains 132 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 522 ASP Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 582 LEU Chi-restraints excluded: chain U residue 643 LEU Chi-restraints excluded: chain U residue 769 THR Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 853 SER Chi-restraints excluded: chain U residue 900 LEU Chi-restraints excluded: chain U residue 961 GLU Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1159 VAL Chi-restraints excluded: chain U residue 1160 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 120 optimal weight: 30.0000 chunk 99 optimal weight: 0.0870 chunk 110 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 546 GLN ** U 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 875 GLN ** U 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1124 GLN U1258 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9761 Z= 0.284 Angle : 0.713 10.040 13199 Z= 0.358 Chirality : 0.044 0.161 1502 Planarity : 0.004 0.046 1689 Dihedral : 6.713 59.907 1329 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 4.58 % Allowed : 15.11 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.08 (0.20), residues: 1224 helix: -3.95 (0.14), residues: 655 sheet: -2.59 (0.66), residues: 43 loop : -2.42 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 342 HIS 0.003 0.001 HIS U 717 PHE 0.020 0.002 PHE U1151 TYR 0.012 0.001 TYR U 178 ARG 0.005 0.000 ARG U 957 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 128 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 59 ILE cc_start: 0.8832 (tp) cc_final: 0.8536 (tt) REVERT: U 171 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7761 (mt) REVERT: U 182 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8628 (tt) REVERT: U 251 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8463 (tt) REVERT: U 373 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8980 (tp) REVERT: U 398 ASP cc_start: 0.7241 (t0) cc_final: 0.7007 (t70) REVERT: U 443 MET cc_start: 0.8160 (ppp) cc_final: 0.7408 (ptt) REVERT: U 696 ARG cc_start: 0.7544 (mtp85) cc_final: 0.7265 (mtp85) REVERT: U 743 ARG cc_start: 0.6736 (tpt-90) cc_final: 0.6238 (ttp-170) REVERT: U 834 PHE cc_start: 0.8475 (t80) cc_final: 0.8147 (t80) REVERT: U 891 ILE cc_start: 0.8560 (mm) cc_final: 0.8164 (mt) REVERT: U 1226 ARG cc_start: 0.7062 (ptm160) cc_final: 0.6695 (ptm160) outliers start: 47 outliers final: 22 residues processed: 166 average time/residue: 0.1946 time to fit residues: 47.0741 Evaluate side-chains 140 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 153 LEU Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 171 ILE Chi-restraints excluded: chain U residue 182 ILE Chi-restraints excluded: chain U residue 251 LEU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 522 ASP Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 582 LEU Chi-restraints excluded: chain U residue 617 LEU Chi-restraints excluded: chain U residue 643 LEU Chi-restraints excluded: chain U residue 744 ILE Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 769 THR Chi-restraints excluded: chain U residue 777 SER Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 946 ASN Chi-restraints excluded: chain U residue 961 GLU Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1027 SER Chi-restraints excluded: chain U residue 1087 TYR Chi-restraints excluded: chain U residue 1159 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U1258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9761 Z= 0.235 Angle : 0.670 9.945 13199 Z= 0.333 Chirality : 0.043 0.158 1502 Planarity : 0.003 0.039 1689 Dihedral : 6.320 58.517 1329 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.39 % Allowed : 16.86 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.79 (0.21), residues: 1224 helix: -3.73 (0.15), residues: 659 sheet: -2.04 (0.74), residues: 43 loop : -2.29 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 314 HIS 0.003 0.001 HIS U 717 PHE 0.015 0.001 PHE U 383 TYR 0.012 0.001 TYR U 178 ARG 0.003 0.000 ARG U1128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 116 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 59 ILE cc_start: 0.8871 (tp) cc_final: 0.8516 (tt) REVERT: U 60 TRP cc_start: 0.7155 (t-100) cc_final: 0.6896 (m100) REVERT: U 251 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8366 (tt) REVERT: U 373 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8981 (tp) REVERT: U 743 ARG cc_start: 0.6834 (tpt-90) cc_final: 0.6255 (ttp-170) REVERT: U 799 CYS cc_start: 0.7313 (OUTLIER) cc_final: 0.7095 (m) REVERT: U 891 ILE cc_start: 0.8542 (mm) cc_final: 0.8151 (mt) REVERT: U 955 LYS cc_start: 0.6787 (mmmt) cc_final: 0.6357 (mmmt) REVERT: U 1162 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7718 (pp20) REVERT: U 1289 MET cc_start: 0.4255 (mtt) cc_final: 0.3624 (mtt) outliers start: 45 outliers final: 26 residues processed: 152 average time/residue: 0.1903 time to fit residues: 42.6545 Evaluate side-chains 135 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain U residue 228 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 251 LEU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 355 THR Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 522 ASP Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 582 LEU Chi-restraints excluded: chain U residue 617 LEU Chi-restraints excluded: chain U residue 643 LEU Chi-restraints excluded: chain U residue 744 ILE Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 769 THR Chi-restraints excluded: chain U residue 777 SER Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 853 SER Chi-restraints excluded: chain U residue 961 GLU Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1027 SER Chi-restraints excluded: chain U residue 1087 TYR Chi-restraints excluded: chain U residue 1159 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U1124 GLN U1258 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9761 Z= 0.228 Angle : 0.652 9.499 13199 Z= 0.322 Chirality : 0.043 0.148 1502 Planarity : 0.003 0.037 1689 Dihedral : 6.073 57.995 1329 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.39 % Allowed : 16.96 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.63 (0.21), residues: 1224 helix: -3.58 (0.15), residues: 671 sheet: -1.84 (0.74), residues: 43 loop : -2.20 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 314 HIS 0.002 0.001 HIS U 717 PHE 0.018 0.002 PHE U1129 TYR 0.012 0.001 TYR U 178 ARG 0.003 0.000 ARG U 957 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 115 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 60 TRP cc_start: 0.7083 (t-100) cc_final: 0.6854 (m100) REVERT: U 251 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8324 (tt) REVERT: U 373 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8955 (tp) REVERT: U 505 PRO cc_start: 0.8469 (Cg_exo) cc_final: 0.8246 (Cg_endo) REVERT: U 743 ARG cc_start: 0.6831 (tpt-90) cc_final: 0.6264 (ttp-170) REVERT: U 891 ILE cc_start: 0.8500 (mm) cc_final: 0.8109 (mt) REVERT: U 1289 MET cc_start: 0.4366 (mtt) cc_final: 0.3614 (mtt) outliers start: 45 outliers final: 26 residues processed: 148 average time/residue: 0.1876 time to fit residues: 40.8793 Evaluate side-chains 134 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 251 LEU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 355 THR Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 582 LEU Chi-restraints excluded: chain U residue 611 ILE Chi-restraints excluded: chain U residue 617 LEU Chi-restraints excluded: chain U residue 643 LEU Chi-restraints excluded: chain U residue 744 ILE Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 769 THR Chi-restraints excluded: chain U residue 777 SER Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 961 GLU Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1027 SER Chi-restraints excluded: chain U residue 1087 TYR Chi-restraints excluded: chain U residue 1156 ILE Chi-restraints excluded: chain U residue 1159 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 55 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.0030 chunk 62 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 466 GLN ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 765 ASN U1258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9761 Z= 0.197 Angle : 0.633 8.629 13199 Z= 0.311 Chirality : 0.043 0.160 1502 Planarity : 0.003 0.035 1689 Dihedral : 5.821 58.403 1329 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.58 % Allowed : 17.74 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.42 (0.21), residues: 1224 helix: -3.39 (0.16), residues: 669 sheet: -1.74 (0.74), residues: 43 loop : -2.14 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U1071 HIS 0.002 0.000 HIS U1300 PHE 0.017 0.001 PHE U 427 TYR 0.011 0.001 TYR U 178 ARG 0.003 0.000 ARG U1128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 117 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 251 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8316 (tt) REVERT: U 373 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8966 (tp) REVERT: U 395 GLU cc_start: 0.6657 (tp30) cc_final: 0.6425 (tp30) REVERT: U 505 PRO cc_start: 0.8432 (Cg_exo) cc_final: 0.8218 (Cg_endo) REVERT: U 743 ARG cc_start: 0.6830 (tpt-90) cc_final: 0.6383 (ttp-170) REVERT: U 828 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8553 (m) REVERT: U 891 ILE cc_start: 0.8489 (mm) cc_final: 0.8119 (mt) REVERT: U 1289 MET cc_start: 0.4529 (mtt) cc_final: 0.3836 (mtt) outliers start: 47 outliers final: 30 residues processed: 154 average time/residue: 0.1893 time to fit residues: 42.3173 Evaluate side-chains 142 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 109 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 187 ILE Chi-restraints excluded: chain U residue 228 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 251 LEU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 355 THR Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 522 ASP Chi-restraints excluded: chain U residue 527 ASP Chi-restraints excluded: chain U residue 617 LEU Chi-restraints excluded: chain U residue 643 LEU Chi-restraints excluded: chain U residue 744 ILE Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 769 THR Chi-restraints excluded: chain U residue 777 SER Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 828 THR Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 853 SER Chi-restraints excluded: chain U residue 961 GLU Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1087 TYR Chi-restraints excluded: chain U residue 1156 ILE Chi-restraints excluded: chain U residue 1159 VAL Chi-restraints excluded: chain U residue 1160 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 73 optimal weight: 0.0060 chunk 47 optimal weight: 10.0000 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9761 Z= 0.173 Angle : 0.622 11.569 13199 Z= 0.304 Chirality : 0.043 0.172 1502 Planarity : 0.003 0.035 1689 Dihedral : 5.598 58.387 1329 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.19 % Allowed : 18.52 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.25 (0.21), residues: 1224 helix: -3.24 (0.16), residues: 682 sheet: -1.53 (0.77), residues: 43 loop : -2.04 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP U1071 HIS 0.001 0.000 HIS U1300 PHE 0.019 0.001 PHE U 427 TYR 0.010 0.001 TYR U 178 ARG 0.003 0.000 ARG U 957 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 114 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 67 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8392 (tt) REVERT: U 217 MET cc_start: 0.8112 (tpp) cc_final: 0.7592 (tpt) REVERT: U 251 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8295 (tt) REVERT: U 373 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8939 (tp) REVERT: U 743 ARG cc_start: 0.6833 (tpt-90) cc_final: 0.6431 (ttp-170) REVERT: U 828 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8548 (m) REVERT: U 891 ILE cc_start: 0.8429 (mm) cc_final: 0.8073 (mt) REVERT: U 1271 ILE cc_start: 0.9057 (mt) cc_final: 0.8843 (mm) outliers start: 43 outliers final: 28 residues processed: 146 average time/residue: 0.1831 time to fit residues: 39.2139 Evaluate side-chains 141 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 187 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 251 LEU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 522 ASP Chi-restraints excluded: chain U residue 527 ASP Chi-restraints excluded: chain U residue 611 ILE Chi-restraints excluded: chain U residue 643 LEU Chi-restraints excluded: chain U residue 744 ILE Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 769 THR Chi-restraints excluded: chain U residue 777 SER Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 828 THR Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 853 SER Chi-restraints excluded: chain U residue 936 VAL Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1027 SER Chi-restraints excluded: chain U residue 1087 TYR Chi-restraints excluded: chain U residue 1156 ILE Chi-restraints excluded: chain U residue 1160 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 442 ASN ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9761 Z= 0.154 Angle : 0.616 11.766 13199 Z= 0.300 Chirality : 0.042 0.147 1502 Planarity : 0.003 0.035 1689 Dihedral : 5.427 59.199 1329 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.51 % Allowed : 19.30 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.12 (0.22), residues: 1224 helix: -3.08 (0.16), residues: 691 sheet: -1.32 (0.79), residues: 43 loop : -2.05 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP U1071 HIS 0.001 0.000 HIS U1300 PHE 0.019 0.001 PHE U 427 TYR 0.008 0.001 TYR U 178 ARG 0.004 0.000 ARG U 520 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 114 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 67 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8428 (tt) REVERT: U 217 MET cc_start: 0.8153 (tpp) cc_final: 0.7635 (tpt) REVERT: U 251 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8250 (tt) REVERT: U 493 TRP cc_start: 0.8066 (t-100) cc_final: 0.7838 (t-100) REVERT: U 505 PRO cc_start: 0.8334 (Cg_exo) cc_final: 0.8063 (Cg_endo) REVERT: U 696 ARG cc_start: 0.7653 (mtp85) cc_final: 0.7438 (mtp85) REVERT: U 743 ARG cc_start: 0.6810 (tpt-90) cc_final: 0.6406 (ttp-170) REVERT: U 828 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8543 (m) REVERT: U 891 ILE cc_start: 0.8373 (mm) cc_final: 0.8047 (mt) REVERT: U 1087 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.6767 (t80) outliers start: 36 outliers final: 24 residues processed: 139 average time/residue: 0.1849 time to fit residues: 38.0058 Evaluate side-chains 135 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 107 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain U residue 187 ILE Chi-restraints excluded: chain U residue 228 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 251 LEU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 424 ASN Chi-restraints excluded: chain U residue 522 ASP Chi-restraints excluded: chain U residue 527 ASP Chi-restraints excluded: chain U residue 611 ILE Chi-restraints excluded: chain U residue 744 ILE Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 777 SER Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 828 THR Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 853 SER Chi-restraints excluded: chain U residue 936 VAL Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1087 TYR Chi-restraints excluded: chain U residue 1156 ILE Chi-restraints excluded: chain U residue 1159 VAL Chi-restraints excluded: chain U residue 1160 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 113 optimal weight: 0.0770 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 172 GLN U 375 ASN ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9761 Z= 0.271 Angle : 0.664 10.436 13199 Z= 0.324 Chirality : 0.045 0.161 1502 Planarity : 0.003 0.035 1689 Dihedral : 5.705 58.213 1329 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.70 % Allowed : 19.69 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.98 (0.22), residues: 1224 helix: -3.04 (0.17), residues: 678 sheet: -1.16 (0.79), residues: 43 loop : -1.94 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 846 HIS 0.002 0.001 HIS U 72 PHE 0.018 0.002 PHE U1074 TYR 0.015 0.001 TYR U 178 ARG 0.005 0.000 ARG U 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 107 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 251 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8295 (tt) REVERT: U 505 PRO cc_start: 0.8313 (Cg_exo) cc_final: 0.8058 (Cg_endo) REVERT: U 743 ARG cc_start: 0.6831 (tpt-90) cc_final: 0.6433 (ttp-170) REVERT: U 828 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8587 (m) REVERT: U 891 ILE cc_start: 0.8477 (mm) cc_final: 0.8100 (mt) REVERT: U 1087 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.6918 (t80) outliers start: 38 outliers final: 30 residues processed: 135 average time/residue: 0.1932 time to fit residues: 39.3660 Evaluate side-chains 136 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 103 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain U residue 228 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 247 SER Chi-restraints excluded: chain U residue 251 LEU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 424 ASN Chi-restraints excluded: chain U residue 490 ASN Chi-restraints excluded: chain U residue 522 ASP Chi-restraints excluded: chain U residue 527 ASP Chi-restraints excluded: chain U residue 611 ILE Chi-restraints excluded: chain U residue 744 ILE Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 777 SER Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 828 THR Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 853 SER Chi-restraints excluded: chain U residue 936 VAL Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1027 SER Chi-restraints excluded: chain U residue 1087 TYR Chi-restraints excluded: chain U residue 1156 ILE Chi-restraints excluded: chain U residue 1159 VAL Chi-restraints excluded: chain U residue 1160 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 122 optimal weight: 20.0000 chunk 112 optimal weight: 0.0170 chunk 97 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9761 Z= 0.191 Angle : 0.641 12.806 13199 Z= 0.310 Chirality : 0.043 0.141 1502 Planarity : 0.003 0.035 1689 Dihedral : 5.493 59.230 1329 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.02 % Allowed : 20.18 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.94 (0.22), residues: 1224 helix: -2.98 (0.17), residues: 691 sheet: -0.97 (0.77), residues: 43 loop : -1.93 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP U1071 HIS 0.002 0.000 HIS U 608 PHE 0.020 0.001 PHE U 427 TYR 0.013 0.001 TYR U 772 ARG 0.003 0.000 ARG U1128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 251 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8253 (tt) REVERT: U 505 PRO cc_start: 0.8302 (Cg_exo) cc_final: 0.8080 (Cg_endo) REVERT: U 743 ARG cc_start: 0.6820 (tpt-90) cc_final: 0.6425 (ttp-170) REVERT: U 828 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8564 (m) REVERT: U 891 ILE cc_start: 0.8413 (mm) cc_final: 0.8058 (mt) REVERT: U 1087 TYR cc_start: 0.7412 (OUTLIER) cc_final: 0.6907 (t80) outliers start: 31 outliers final: 26 residues processed: 132 average time/residue: 0.1827 time to fit residues: 35.8097 Evaluate side-chains 135 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain U residue 228 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 251 LEU Chi-restraints excluded: chain U residue 280 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 424 ASN Chi-restraints excluded: chain U residue 522 ASP Chi-restraints excluded: chain U residue 527 ASP Chi-restraints excluded: chain U residue 611 ILE Chi-restraints excluded: chain U residue 744 ILE Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 777 SER Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 828 THR Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 853 SER Chi-restraints excluded: chain U residue 936 VAL Chi-restraints excluded: chain U residue 967 LEU Chi-restraints excluded: chain U residue 1027 SER Chi-restraints excluded: chain U residue 1087 TYR Chi-restraints excluded: chain U residue 1156 ILE Chi-restraints excluded: chain U residue 1160 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.0370 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U1258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.217111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.179074 restraints weight = 10839.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.171379 restraints weight = 16758.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.163094 restraints weight = 16183.778| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9761 Z= 0.161 Angle : 0.626 12.338 13199 Z= 0.304 Chirality : 0.042 0.139 1502 Planarity : 0.003 0.035 1689 Dihedral : 5.292 59.993 1329 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.73 % Allowed : 20.96 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.73 (0.22), residues: 1224 helix: -2.82 (0.17), residues: 688 sheet: -0.82 (0.79), residues: 43 loop : -1.84 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP U 163 HIS 0.001 0.000 HIS U 615 PHE 0.049 0.001 PHE U1151 TYR 0.011 0.001 TYR U 772 ARG 0.003 0.000 ARG U1128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1964.39 seconds wall clock time: 36 minutes 4.45 seconds (2164.45 seconds total)