Starting phenix.real_space_refine on Thu Mar 14 17:02:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1a_30938/03_2024/7e1a_30938_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1a_30938/03_2024/7e1a_30938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1a_30938/03_2024/7e1a_30938.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1a_30938/03_2024/7e1a_30938.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1a_30938/03_2024/7e1a_30938_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1a_30938/03_2024/7e1a_30938_updated.pdb" } resolution = 3.66 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= 0.006 sd= 0.079 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 55 5.16 5 C 5951 2.51 5 N 1566 2.21 5 O 1712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "U ARG 184": "NH1" <-> "NH2" Residue "U ARG 303": "NH1" <-> "NH2" Residue "U ARG 313": "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 792": "NH1" <-> "NH2" Residue "U ARG 832": "NH1" <-> "NH2" Residue "U ARG 837": "NH1" <-> "NH2" Residue "U ARG 860": "NH1" <-> "NH2" Residue "U ARG 920": "NH1" <-> "NH2" Residue "U ARG 958": "NH1" <-> "NH2" Residue "U ARG 1001": "NH1" <-> "NH2" Residue "U ARG 1019": "NH1" <-> "NH2" Residue "U ARG 1033": "NH1" <-> "NH2" Residue "U ARG 1187": "NH1" <-> "NH2" Residue "U ARG 1221": "NH1" <-> "NH2" Residue "U ARG 1235": "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: 9284 Number of models: 1 Model: "" Number of chains: 1 Chain: "U" Number of atoms: 9284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 9284 Unusual residues: {'TCH': 1} Classifications: {'peptide': 1189, 'undetermined': 1} Link IDs: {'PTRANS': 32, 'TRANS': 1156, None: 1} Not linked: pdbres="THR U1315 " pdbres="TCH U1401 " Chain breaks: 1 Time building chain proxies: 5.19, per 1000 atoms: 0.56 Number of scatterers: 9284 At special positions: 0 Unit cell: (93.28, 94.34, 161.12, 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 55 16.00 O 1712 8.00 N 1566 7.00 C 5951 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.8 seconds 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 3 sheets defined 39.7% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'U' and resid 64 through 76 removed outlier: 3.778A pdb=" N CYS U 68 " --> pdb=" O VAL U 64 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA U 69 " --> pdb=" O GLY U 65 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE U 70 " --> pdb=" O SER U 66 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N HIS U 72 " --> pdb=" O CYS U 68 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ALA U 75 " --> pdb=" O LEU U 71 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN U 76 " --> pdb=" O HIS U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 83 No H-bonds generated for 'chain 'U' and resid 80 through 83' Processing helix chain 'U' and resid 89 through 99 removed outlier: 3.506A pdb=" N TYR U 93 " --> pdb=" O VAL U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 135 through 138 No H-bonds generated for 'chain 'U' and resid 135 through 138' Processing helix chain 'U' and resid 164 through 167 No H-bonds generated for 'chain 'U' and resid 164 through 167' Processing helix chain 'U' and resid 171 through 180 removed outlier: 3.544A pdb=" N PHE U 179 " --> pdb=" O ARG U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 190 No H-bonds generated for 'chain 'U' and resid 187 through 190' Processing helix chain 'U' and resid 195 through 198 No H-bonds generated for 'chain 'U' and resid 195 through 198' Processing helix chain 'U' and resid 228 through 235 removed outlier: 3.805A pdb=" N LEU U 232 " --> pdb=" O ILE U 228 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU U 233 " --> pdb=" O CYS U 229 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY U 234 " --> pdb=" O GLY U 230 " (cutoff:3.500A) Processing helix chain 'U' and resid 246 through 253 Proline residue: U 250 - end of helix Processing helix chain 'U' and resid 257 through 263 removed outlier: 4.042A pdb=" N SER U 262 " --> pdb=" O THR U 258 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL U 263 " --> pdb=" O ILE U 259 " (cutoff:3.500A) Processing helix chain 'U' and resid 268 through 271 No H-bonds generated for 'chain 'U' and resid 268 through 271' Processing helix chain 'U' and resid 277 through 284 removed outlier: 4.035A pdb=" N ASP U 282 " --> pdb=" O GLY U 278 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL U 284 " --> pdb=" O VAL U 280 " (cutoff:3.500A) Processing helix chain 'U' and resid 288 through 294 removed outlier: 3.609A pdb=" N PHE U 294 " --> pdb=" O THR U 290 " (cutoff:3.500A) Processing helix chain 'U' and resid 302 through 312 removed outlier: 3.748A pdb=" N LYS U 306 " --> pdb=" O GLU U 302 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN U 307 " --> pdb=" O ARG U 303 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU U 308 " --> pdb=" O TYR U 304 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL U 309 " --> pdb=" O GLU U 305 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N PHE U 310 " --> pdb=" O LYS U 306 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ALA U 311 " --> pdb=" O ASN U 307 " (cutoff:3.500A) Processing helix chain 'U' and resid 316 through 323 removed outlier: 3.669A pdb=" N VAL U 321 " --> pdb=" O ARG U 317 " (cutoff:3.500A) Processing helix chain 'U' and resid 332 through 350 removed outlier: 3.655A pdb=" N TYR U 343 " --> pdb=" O LEU U 339 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU U 347 " --> pdb=" O TYR U 343 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU U 349 " --> pdb=" O SER U 345 " (cutoff:3.500A) Processing helix chain 'U' and resid 367 through 374 removed outlier: 4.175A pdb=" N ASN U 372 " --> pdb=" O VAL U 368 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU U 373 " --> pdb=" O GLY U 369 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY U 374 " --> pdb=" O ALA U 370 " (cutoff:3.500A) Processing helix chain 'U' and resid 381 through 388 removed outlier: 4.130A pdb=" N GLY U 386 " --> pdb=" O ALA U 382 " (cutoff:3.500A) Processing helix chain 'U' and resid 393 through 396 No H-bonds generated for 'chain 'U' and resid 393 through 396' Processing helix chain 'U' and resid 463 through 466 No H-bonds generated for 'chain 'U' and resid 463 through 466' Processing helix chain 'U' and resid 491 through 497 removed outlier: 4.568A pdb=" N ASP U 496 " --> pdb=" O GLN U 492 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN U 497 " --> pdb=" O TRP U 493 " (cutoff:3.500A) Processing helix chain 'U' and resid 512 through 518 removed outlier: 3.635A pdb=" N ILE U 516 " --> pdb=" O ILE U 512 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG U 517 " --> pdb=" O ALA U 513 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR U 518 " --> pdb=" O GLU U 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 512 through 518' Processing helix chain 'U' and resid 525 through 534 removed outlier: 4.588A pdb=" N GLN U 530 " --> pdb=" O GLU U 526 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA U 531 " --> pdb=" O ASP U 527 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA U 532 " --> pdb=" O ILE U 528 " (cutoff:3.500A) Processing helix chain 'U' and resid 539 through 542 No H-bonds generated for 'chain 'U' and resid 539 through 542' Processing helix chain 'U' and resid 551 through 553 No H-bonds generated for 'chain 'U' and resid 551 through 553' Processing helix chain 'U' and resid 561 through 573 removed outlier: 4.503A pdb=" N GLN U 565 " --> pdb=" O GLY U 561 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG U 566 " --> pdb=" O GLY U 562 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL U 567 " --> pdb=" O GLN U 563 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA U 570 " --> pdb=" O ARG U 566 " (cutoff:3.500A) Processing helix chain 'U' and resid 591 through 601 removed outlier: 3.980A pdb=" N ALA U 595 " --> pdb=" O ASN U 591 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET U 596 " --> pdb=" O GLU U 592 " (cutoff:3.500A) Processing helix chain 'U' and resid 651 through 657 removed outlier: 3.518A pdb=" N THR U 655 " --> pdb=" O PHE U 651 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU U 656 " --> pdb=" O THR U 652 " (cutoff:3.500A) Processing helix chain 'U' and resid 742 through 747 Processing helix chain 'U' and resid 749 through 751 No H-bonds generated for 'chain 'U' and resid 749 through 751' Processing helix chain 'U' and resid 757 through 763 removed outlier: 3.730A pdb=" N GLY U 761 " --> pdb=" O VAL U 757 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA U 762 " --> pdb=" O GLY U 758 " (cutoff:3.500A) Processing helix chain 'U' and resid 769 through 779 removed outlier: 3.692A pdb=" N PHE U 774 " --> pdb=" O PRO U 770 " (cutoff:3.500A) Processing helix chain 'U' and resid 788 through 822 removed outlier: 3.956A pdb=" N ARG U 792 " --> pdb=" O LYS U 788 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN U 796 " --> pdb=" O ARG U 792 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU U 800 " --> pdb=" O ASN U 796 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU U 801 " --> pdb=" O GLY U 797 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE U 802 " --> pdb=" O VAL U 798 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL U 803 " --> pdb=" O CYS U 799 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA U 804 " --> pdb=" O LEU U 800 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER U 809 " --> pdb=" O MET U 805 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU U 810 " --> pdb=" O GLY U 806 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE U 811 " --> pdb=" O CYS U 807 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN U 813 " --> pdb=" O SER U 809 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU U 815 " --> pdb=" O PHE U 811 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN U 816 " --> pdb=" O THR U 812 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY U 817 " --> pdb=" O GLN U 813 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA U 819 " --> pdb=" O LEU U 815 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE U 820 " --> pdb=" O GLN U 816 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA U 821 " --> pdb=" O GLY U 817 " (cutoff:3.500A) Processing helix chain 'U' and resid 830 through 838 Processing helix chain 'U' and resid 844 through 846 No H-bonds generated for 'chain 'U' and resid 844 through 846' Processing helix chain 'U' and resid 856 through 863 removed outlier: 4.971A pdb=" N LEU U 861 " --> pdb=" O LEU U 857 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA U 862 " --> pdb=" O THR U 858 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR U 863 " --> pdb=" O THR U 859 " (cutoff:3.500A) Processing helix chain 'U' and resid 873 through 876 No H-bonds generated for 'chain 'U' and resid 873 through 876' Processing helix chain 'U' and resid 881 through 887 removed outlier: 4.628A pdb=" N VAL U 886 " --> pdb=" O SER U 882 " (cutoff:3.500A) Processing helix chain 'U' and resid 889 through 895 Processing helix chain 'U' and resid 901 through 912 removed outlier: 3.612A pdb=" N LEU U 905 " --> pdb=" O SER U 901 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE U 907 " --> pdb=" O VAL U 903 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE U 908 " --> pdb=" O ILE U 904 " (cutoff:3.500A) Proline residue: U 909 - end of helix removed outlier: 3.529A pdb=" N ALA U 912 " --> pdb=" O PHE U 908 " (cutoff:3.500A) Processing helix chain 'U' and resid 919 through 922 No H-bonds generated for 'chain 'U' and resid 919 through 922' Processing helix chain 'U' and resid 930 through 933 No H-bonds generated for 'chain 'U' and resid 930 through 933' Processing helix chain 'U' and resid 936 through 939 No H-bonds generated for 'chain 'U' and resid 936 through 939' Processing helix chain 'U' and resid 947 through 950 No H-bonds generated for 'chain 'U' and resid 947 through 950' Processing helix chain 'U' and resid 957 through 967 removed outlier: 4.539A pdb=" N LEU U 963 " --> pdb=" O PHE U 959 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU U 964 " --> pdb=" O ILE U 960 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR U 965 " --> pdb=" O GLU U 961 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU U 966 " --> pdb=" O ALA U 962 " (cutoff:3.500A) Processing helix chain 'U' and resid 995 through 1009 removed outlier: 3.659A pdb=" N SER U 999 " --> pdb=" O ALA U 995 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR U1000 " --> pdb=" O ASN U 996 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR U1002 " --> pdb=" O ALA U 998 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER U1008 " --> pdb=" O GLY U1004 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN U1009 " --> pdb=" O TYR U1005 " (cutoff:3.500A) Processing helix chain 'U' and resid 1014 through 1021 removed outlier: 3.736A pdb=" N PHE U1018 " --> pdb=" O SER U1015 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG U1019 " --> pdb=" O TYR U1016 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL U1020 " --> pdb=" O VAL U1017 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE U1021 " --> pdb=" O PHE U1018 " (cutoff:3.500A) Processing helix chain 'U' and resid 1026 through 1035 removed outlier: 3.622A pdb=" N ALA U1030 " --> pdb=" O LEU U1026 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU U1031 " --> pdb=" O SER U1027 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA U1034 " --> pdb=" O ALA U1030 " (cutoff:3.500A) Processing helix chain 'U' and resid 1041 through 1055 removed outlier: 4.102A pdb=" N LYS U1045 " --> pdb=" O ALA U1042 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ILE U1046 " --> pdb=" O LYS U1043 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA U1048 " --> pdb=" O LYS U1045 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA U1049 " --> pdb=" O ILE U1046 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG U1050 " --> pdb=" O SER U1047 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE U1052 " --> pdb=" O ALA U1049 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN U1053 " --> pdb=" O ARG U1050 " (cutoff:3.500A) Processing helix chain 'U' and resid 1121 through 1124 No H-bonds generated for 'chain 'U' and resid 1121 through 1124' Processing helix chain 'U' and resid 1144 through 1146 No H-bonds generated for 'chain 'U' and resid 1144 through 1146' Processing helix chain 'U' and resid 1149 through 1152 No H-bonds generated for 'chain 'U' and resid 1149 through 1152' Processing helix chain 'U' and resid 1170 through 1177 removed outlier: 3.564A pdb=" N ILE U1174 " --> pdb=" O ILE U1170 " (cutoff:3.500A) Processing helix chain 'U' and resid 1186 through 1194 removed outlier: 4.083A pdb=" N ALA U1190 " --> pdb=" O GLU U1186 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA U1192 " --> pdb=" O VAL U1188 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS U1193 " --> pdb=" O ILE U1189 " (cutoff:3.500A) Processing helix chain 'U' and resid 1200 through 1203 No H-bonds generated for 'chain 'U' and resid 1200 through 1203' Processing helix chain 'U' and resid 1221 through 1234 removed outlier: 4.231A pdb=" N ARG U1226 " --> pdb=" O GLY U1222 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE U1227 " --> pdb=" O GLU U1223 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA U1228 " --> pdb=" O LYS U1224 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA U1230 " --> pdb=" O ARG U1226 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA U1232 " --> pdb=" O ALA U1228 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL U1234 " --> pdb=" O ALA U1230 " (cutoff:3.500A) Processing helix chain 'U' and resid 1253 through 1263 removed outlier: 3.559A pdb=" N GLN U1258 " --> pdb=" O GLU U1254 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL U1259 " --> pdb=" O LYS U1255 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA U1260 " --> pdb=" O THR U1256 " (cutoff:3.500A) Processing helix chain 'U' and resid 1300 through 1302 No H-bonds generated for 'chain 'U' and resid 1300 through 1302' Processing helix chain 'U' and resid 1309 through 1313 Processing sheet with id= A, first strand: chain 'U' and resid 420 through 422 Processing sheet with id= B, first strand: chain 'U' and resid 498 through 501 removed outlier: 6.406A pdb=" N ILE U 579 " --> pdb=" O GLY U 499 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL U 501 " --> pdb=" O ILE U 579 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU U 581 " --> pdb=" O VAL U 501 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N THR U 609 " --> pdb=" O LEU U 580 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N LEU U 582 " --> pdb=" O THR U 609 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE U 611 " --> pdb=" O LEU U 582 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'U' and resid 1156 through 1159 removed outlier: 6.338A pdb=" N ILE U1239 " --> pdb=" O GLY U1157 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N VAL U1159 " --> pdb=" O ILE U1239 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU U1241 " --> pdb=" O VAL U1159 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 127 hydrogen bonds defined for protein. 357 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: 2.31 Time building geometry restraints manager: 3.59 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: 2349 1.33 - 1.45: 1944 1.45 - 1.57: 5082 1.57 - 1.69: 1 1.69 - 1.81: 89 Bond restraints: 9465 Sorted by residual: bond pdb=" C ALA U 214 " pdb=" N ASP U 215 " ideal model delta sigma weight residual 1.335 1.269 0.065 1.42e-02 4.96e+03 2.12e+01 bond pdb=" O3S TCH U1401 " pdb=" S26 TCH U1401 " ideal model delta sigma weight residual 1.475 1.549 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CG1 ILE U 171 " pdb=" CD1 ILE U 171 " ideal model delta sigma weight residual 1.513 1.376 0.137 3.90e-02 6.57e+02 1.23e+01 bond pdb=" CG1 ILE U 245 " pdb=" CD1 ILE U 245 " ideal model delta sigma weight residual 1.513 1.382 0.131 3.90e-02 6.57e+02 1.13e+01 bond pdb=" CB VAL U1024 " pdb=" CG2 VAL U1024 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.62e+00 ... (remaining 9460 not shown) Histogram of bond angle deviations from ideal: 96.30 - 106.24: 222 106.24 - 116.17: 5873 116.17 - 126.11: 6594 126.11 - 136.04: 116 136.04 - 145.98: 1 Bond angle restraints: 12806 Sorted by residual: angle pdb=" N VAL U 152 " pdb=" CA VAL U 152 " pdb=" C VAL U 152 " ideal model delta sigma weight residual 113.20 104.66 8.54 9.60e-01 1.09e+00 7.91e+01 angle pdb=" C HIS U1013 " pdb=" N PHE U1014 " pdb=" CA PHE U1014 " ideal model delta sigma weight residual 120.82 131.96 -11.14 1.50e+00 4.44e-01 5.52e+01 angle pdb=" N ILE U 158 " pdb=" CA ILE U 158 " pdb=" C ILE U 158 " ideal model delta sigma weight residual 113.53 106.72 6.81 9.80e-01 1.04e+00 4.83e+01 angle pdb=" N ILE U 221 " pdb=" CA ILE U 221 " pdb=" C ILE U 221 " ideal model delta sigma weight residual 111.91 105.90 6.01 8.90e-01 1.26e+00 4.56e+01 angle pdb=" N VAL U1017 " pdb=" CA VAL U1017 " pdb=" C VAL U1017 " ideal model delta sigma weight residual 112.96 106.66 6.30 1.00e+00 1.00e+00 3.97e+01 ... (remaining 12801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 5084 15.42 - 30.84: 471 30.84 - 46.25: 112 46.25 - 61.67: 4 61.67 - 77.09: 15 Dihedral angle restraints: 5686 sinusoidal: 2275 harmonic: 3411 Sorted by residual: dihedral pdb=" CA PRO U1039 " pdb=" C PRO U1039 " pdb=" N SER U1040 " pdb=" CA SER U1040 " ideal model delta harmonic sigma weight residual -180.00 -148.85 -31.15 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA ARG U 181 " pdb=" C ARG U 181 " pdb=" N ILE U 182 " pdb=" CA ILE U 182 " ideal model delta harmonic sigma weight residual 180.00 149.73 30.27 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA ILE U 362 " pdb=" C ILE U 362 " pdb=" N PHE U 363 " pdb=" CA PHE U 363 " ideal model delta harmonic sigma weight residual 180.00 150.24 29.76 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 5683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 989 0.063 - 0.126: 380 0.126 - 0.189: 66 0.189 - 0.251: 20 0.251 - 0.314: 7 Chirality restraints: 1462 Sorted by residual: chirality pdb=" CB VAL U 764 " pdb=" CA VAL U 764 " pdb=" CG1 VAL U 764 " pdb=" CG2 VAL U 764 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CB ILE U 221 " pdb=" CA ILE U 221 " pdb=" CG1 ILE U 221 " pdb=" CG2 ILE U 221 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB VAL U 248 " pdb=" CA VAL U 248 " pdb=" CG1 VAL U 248 " pdb=" CG2 VAL U 248 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1459 not shown) Planarity restraints: 1631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C23 TCH U1401 " 0.142 2.00e-02 2.50e+03 1.65e-01 3.39e+02 pdb=" C24 TCH U1401 " -0.054 2.00e-02 2.50e+03 pdb=" C25 TCH U1401 " 0.198 2.00e-02 2.50e+03 pdb=" N24 TCH U1401 " -0.270 2.00e-02 2.50e+03 pdb=" O24 TCH U1401 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS U 969 " 0.051 5.00e-02 4.00e+02 7.57e-02 9.16e+00 pdb=" N PRO U 970 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO U 970 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO U 970 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN U 76 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO U 77 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO U 77 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO U 77 " 0.042 5.00e-02 4.00e+02 ... (remaining 1628 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2071 2.77 - 3.30: 8590 3.30 - 3.83: 14597 3.83 - 4.37: 17075 4.37 - 4.90: 28378 Nonbonded interactions: 70711 Sorted by model distance: nonbonded pdb=" OD1 ASP U 864 " pdb=" OG SER U1047 " model vdw 2.233 2.440 nonbonded pdb=" O SER U 809 " pdb=" OG SER U 809 " model vdw 2.238 2.440 nonbonded pdb=" OH TYR U 145 " pdb=" O2S TCH U1401 " model vdw 2.256 2.440 nonbonded pdb=" OG1 THR U 355 " pdb=" OG1 THR U 358 " model vdw 2.260 2.440 nonbonded pdb=" O THR U 155 " pdb=" OG1 THR U 155 " model vdw 2.262 2.440 ... (remaining 70706 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: 0.470 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: 2.650 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 27.360 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.012 0.137 9465 Z= 0.796 Angle : 1.391 25.169 12806 Z= 0.775 Chirality : 0.069 0.314 1462 Planarity : 0.009 0.165 1631 Dihedral : 13.322 77.090 3496 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.65 % Favored : 88.27 % Rotamer: Outliers : 0.81 % Allowed : 8.91 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -6.43 (0.15), residues: 1185 helix: -4.74 (0.08), residues: 637 sheet: -4.05 (0.64), residues: 37 loop : -3.46 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP U 314 HIS 0.022 0.003 HIS U 72 PHE 0.031 0.004 PHE U 363 TYR 0.034 0.004 TYR U 178 ARG 0.009 0.001 ARG U 832 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 209 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: U 123 MET cc_start: 0.3728 (mtp) cc_final: 0.2894 (ttm) REVERT: U 183 MET cc_start: 0.8632 (mmm) cc_final: 0.8096 (mmm) REVERT: U 205 ASP cc_start: 0.8685 (t0) cc_final: 0.8440 (t0) REVERT: U 217 MET cc_start: 0.8143 (tpp) cc_final: 0.7781 (tpt) REVERT: U 252 ILE cc_start: 0.7727 (tt) cc_final: 0.6928 (mt) REVERT: U 442 ASN cc_start: 0.8085 (m-40) cc_final: 0.7852 (m-40) REVERT: U 453 LEU cc_start: 0.7903 (tm) cc_final: 0.7688 (tt) REVERT: U 478 MET cc_start: 0.7594 (ppp) cc_final: 0.6893 (ppp) REVERT: U 492 GLN cc_start: 0.8508 (mm110) cc_final: 0.7674 (tm-30) REVERT: U 600 VAL cc_start: 0.8954 (t) cc_final: 0.8745 (t) REVERT: U 863 THR cc_start: 0.8222 (m) cc_final: 0.7954 (t) REVERT: U 891 ILE cc_start: 0.8531 (mm) cc_final: 0.8174 (mt) REVERT: U 921 MET cc_start: 0.7516 (tmt) cc_final: 0.6862 (tmt) REVERT: U 1111 PHE cc_start: 0.8693 (m-10) cc_final: 0.8158 (m-10) REVERT: U 1299 THR cc_start: 0.4668 (OUTLIER) cc_final: 0.4310 (m) outliers start: 8 outliers final: 1 residues processed: 216 average time/residue: 0.2548 time to fit residues: 72.0224 Evaluate side-chains 123 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 1299 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.0060 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 492 GLN U 503 GLN U 515 ASN U 598 GLN U 605 GLN U 640 HIS U 842 GLN U 931 GLN U1134 GLN U1196 GLN ** U1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9465 Z= 0.178 Angle : 0.688 18.848 12806 Z= 0.349 Chirality : 0.042 0.160 1462 Planarity : 0.005 0.043 1631 Dihedral : 8.121 86.776 1359 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.14 % Allowed : 13.56 % Favored : 83.30 % 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: -5.61 (0.18), residues: 1185 helix: -4.05 (0.12), residues: 636 sheet: -3.76 (0.75), residues: 40 loop : -3.08 (0.23), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 752 HIS 0.004 0.001 HIS U1013 PHE 0.013 0.001 PHE U 811 TYR 0.012 0.001 TYR U 274 ARG 0.004 0.000 ARG U 928 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 0.842 Fit side-chains REVERT: U 177 PHE cc_start: 0.8120 (t80) cc_final: 0.7685 (t80) REVERT: U 217 MET cc_start: 0.7911 (tpp) cc_final: 0.7635 (tpt) REVERT: U 290 THR cc_start: 0.8781 (p) cc_final: 0.8576 (t) REVERT: U 297 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7388 (tt0) REVERT: U 335 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6927 (mt) REVERT: U 380 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8251 (tt) REVERT: U 413 LEU cc_start: 0.8861 (tt) cc_final: 0.8404 (mp) REVERT: U 414 ASP cc_start: 0.7662 (p0) cc_final: 0.7352 (p0) REVERT: U 453 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7671 (tt) REVERT: U 492 GLN cc_start: 0.8381 (mm-40) cc_final: 0.7608 (tm-30) REVERT: U 502 GLU cc_start: 0.8299 (mp0) cc_final: 0.7979 (mp0) REVERT: U 643 LEU cc_start: 0.6440 (tp) cc_final: 0.6218 (tp) REVERT: U 755 MET cc_start: 0.7054 (mtm) cc_final: 0.6827 (mtm) REVERT: U 823 SER cc_start: 0.8827 (t) cc_final: 0.8597 (t) REVERT: U 891 ILE cc_start: 0.8124 (mm) cc_final: 0.7891 (mt) REVERT: U 1146 LYS cc_start: 0.8561 (mmtt) cc_final: 0.8139 (mmtm) REVERT: U 1202 MET cc_start: 0.5061 (mmm) cc_final: 0.4163 (mtm) REVERT: U 1224 LYS cc_start: 0.8456 (mtmm) cc_final: 0.8090 (mtmm) REVERT: U 1271 ILE cc_start: 0.9133 (mm) cc_final: 0.8929 (mm) REVERT: U 1299 THR cc_start: 0.4346 (OUTLIER) cc_final: 0.4062 (m) REVERT: U 1304 MET cc_start: 0.7274 (mpt) cc_final: 0.6874 (mpp) outliers start: 31 outliers final: 8 residues processed: 174 average time/residue: 0.2058 time to fit residues: 50.1307 Evaluate side-chains 132 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 297 GLU Chi-restraints excluded: chain U residue 335 LEU Chi-restraints excluded: chain U residue 380 LEU Chi-restraints excluded: chain U residue 453 LEU Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 567 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 1014 PHE Chi-restraints excluded: chain U residue 1072 ASP Chi-restraints excluded: chain U residue 1199 ASP Chi-restraints excluded: chain U residue 1299 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 116 optimal weight: 30.0000 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 442 ASN U1258 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9465 Z= 0.282 Angle : 0.695 19.193 12806 Z= 0.345 Chirality : 0.043 0.148 1462 Planarity : 0.004 0.070 1631 Dihedral : 7.604 76.368 1358 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.54 % Allowed : 15.49 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.17 (0.19), residues: 1185 helix: -3.59 (0.14), residues: 653 sheet: -2.79 (1.13), residues: 25 loop : -3.08 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 314 HIS 0.005 0.001 HIS U1142 PHE 0.013 0.001 PHE U1014 TYR 0.012 0.002 TYR U 178 ARG 0.003 0.000 ARG U1221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: U 154 ILE cc_start: 0.8351 (tp) cc_final: 0.8010 (tp) REVERT: U 177 PHE cc_start: 0.8176 (t80) cc_final: 0.7824 (t80) REVERT: U 183 MET cc_start: 0.8798 (mmm) cc_final: 0.8445 (mmm) REVERT: U 217 MET cc_start: 0.8129 (tpp) cc_final: 0.7737 (tpt) REVERT: U 252 ILE cc_start: 0.7514 (tt) cc_final: 0.7144 (tt) REVERT: U 335 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6979 (mt) REVERT: U 359 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8713 (tt) REVERT: U 373 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8480 (tt) REVERT: U 380 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8317 (tt) REVERT: U 413 LEU cc_start: 0.8810 (tt) cc_final: 0.8419 (mp) REVERT: U 443 MET cc_start: 0.8383 (ppp) cc_final: 0.8142 (ppp) REVERT: U 453 LEU cc_start: 0.7834 (tm) cc_final: 0.7550 (tt) REVERT: U 629 PHE cc_start: 0.7100 (p90) cc_final: 0.6555 (p90) REVERT: U 656 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7094 (mt) REVERT: U 891 ILE cc_start: 0.8264 (mm) cc_final: 0.7995 (mt) REVERT: U 1111 PHE cc_start: 0.8521 (m-10) cc_final: 0.7834 (m-10) REVERT: U 1146 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8283 (mmtt) REVERT: U 1202 MET cc_start: 0.5097 (mmm) cc_final: 0.3949 (mtm) REVERT: U 1224 LYS cc_start: 0.8552 (mtmm) cc_final: 0.8155 (mtmt) REVERT: U 1271 ILE cc_start: 0.9184 (mm) cc_final: 0.8807 (mm) REVERT: U 1299 THR cc_start: 0.3989 (OUTLIER) cc_final: 0.3762 (m) REVERT: U 1304 MET cc_start: 0.7470 (mpt) cc_final: 0.7058 (mpp) outliers start: 35 outliers final: 19 residues processed: 155 average time/residue: 0.1869 time to fit residues: 42.3852 Evaluate side-chains 135 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 171 ILE Chi-restraints excluded: chain U residue 335 LEU Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 380 LEU Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 524 THR Chi-restraints excluded: chain U residue 567 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 587 SER Chi-restraints excluded: chain U residue 656 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 794 GLN Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 888 VAL Chi-restraints excluded: chain U residue 1013 HIS Chi-restraints excluded: chain U residue 1014 PHE Chi-restraints excluded: chain U residue 1079 ASP Chi-restraints excluded: chain U residue 1199 ASP Chi-restraints excluded: chain U residue 1299 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.0980 chunk 81 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 515 ASN ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 9465 Z= 0.350 Angle : 0.712 19.014 12806 Z= 0.355 Chirality : 0.044 0.144 1462 Planarity : 0.004 0.061 1631 Dihedral : 7.568 75.629 1358 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 4.76 % Allowed : 15.69 % Favored : 79.55 % 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: -4.82 (0.21), residues: 1185 helix: -3.33 (0.16), residues: 644 sheet: -2.83 (1.14), residues: 25 loop : -2.88 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP U 314 HIS 0.004 0.001 HIS U1142 PHE 0.012 0.002 PHE U1014 TYR 0.015 0.002 TYR U 178 ARG 0.004 0.000 ARG U 517 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 109 time to evaluate : 1.106 Fit side-chains REVERT: U 154 ILE cc_start: 0.8380 (tp) cc_final: 0.8022 (tp) REVERT: U 177 PHE cc_start: 0.8158 (t80) cc_final: 0.7832 (t80) REVERT: U 205 ASP cc_start: 0.8623 (t0) cc_final: 0.8414 (t0) REVERT: U 217 MET cc_start: 0.8196 (tpp) cc_final: 0.7771 (tpt) REVERT: U 246 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.9024 (mt) REVERT: U 252 ILE cc_start: 0.7557 (tt) cc_final: 0.7139 (tt) REVERT: U 290 THR cc_start: 0.8914 (p) cc_final: 0.8709 (t) REVERT: U 335 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6915 (mt) REVERT: U 359 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8842 (tt) REVERT: U 380 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8271 (tt) REVERT: U 413 LEU cc_start: 0.8789 (tt) cc_final: 0.8413 (mp) REVERT: U 453 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7589 (tt) REVERT: U 629 PHE cc_start: 0.6952 (p90) cc_final: 0.6434 (p90) REVERT: U 656 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7035 (mt) REVERT: U 891 ILE cc_start: 0.8299 (mm) cc_final: 0.8035 (mt) REVERT: U 1111 PHE cc_start: 0.8629 (m-10) cc_final: 0.8049 (m-10) REVERT: U 1221 ARG cc_start: 0.8140 (ptt-90) cc_final: 0.7753 (ptt-90) REVERT: U 1224 LYS cc_start: 0.8710 (mtmm) cc_final: 0.8317 (mtmt) REVERT: U 1225 GLN cc_start: 0.8667 (tp-100) cc_final: 0.8200 (tp-100) REVERT: U 1271 ILE cc_start: 0.9254 (mm) cc_final: 0.8940 (mm) REVERT: U 1299 THR cc_start: 0.3952 (OUTLIER) cc_final: 0.3727 (m) REVERT: U 1304 MET cc_start: 0.7625 (mpt) cc_final: 0.7208 (mpp) outliers start: 47 outliers final: 21 residues processed: 145 average time/residue: 0.1815 time to fit residues: 38.9275 Evaluate side-chains 128 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 246 ILE Chi-restraints excluded: chain U residue 335 LEU Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 380 LEU Chi-restraints excluded: chain U residue 453 LEU Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 524 THR Chi-restraints excluded: chain U residue 567 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 587 SER Chi-restraints excluded: chain U residue 656 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 794 GLN Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 888 VAL Chi-restraints excluded: chain U residue 1013 HIS Chi-restraints excluded: chain U residue 1014 PHE Chi-restraints excluded: chain U residue 1051 PHE Chi-restraints excluded: chain U residue 1072 ASP Chi-restraints excluded: chain U residue 1121 THR Chi-restraints excluded: chain U residue 1199 ASP Chi-restraints excluded: chain U residue 1299 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9465 Z= 0.194 Angle : 0.635 18.918 12806 Z= 0.309 Chirality : 0.041 0.133 1462 Planarity : 0.003 0.049 1631 Dihedral : 7.079 77.273 1358 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.64 % Allowed : 18.52 % Favored : 77.83 % 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: -4.44 (0.21), residues: 1185 helix: -3.03 (0.17), residues: 635 sheet: -2.57 (1.18), residues: 25 loop : -2.72 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 314 HIS 0.006 0.001 HIS U1142 PHE 0.013 0.001 PHE U 363 TYR 0.010 0.001 TYR U 650 ARG 0.002 0.000 ARG U1221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 110 time to evaluate : 1.010 Fit side-chains REVERT: U 154 ILE cc_start: 0.8312 (tp) cc_final: 0.7962 (tp) REVERT: U 177 PHE cc_start: 0.8042 (t80) cc_final: 0.7682 (t80) REVERT: U 183 MET cc_start: 0.8657 (mmm) cc_final: 0.8344 (mmm) REVERT: U 197 GLU cc_start: 0.7987 (tp30) cc_final: 0.7568 (tp30) REVERT: U 217 MET cc_start: 0.7835 (tpp) cc_final: 0.7511 (tpt) REVERT: U 252 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7086 (tt) REVERT: U 335 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6945 (mt) REVERT: U 359 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8709 (tt) REVERT: U 373 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8449 (tt) REVERT: U 380 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8211 (tt) REVERT: U 413 LEU cc_start: 0.8729 (tt) cc_final: 0.8377 (mp) REVERT: U 453 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7619 (tt) REVERT: U 596 MET cc_start: 0.9012 (mmm) cc_final: 0.8780 (mmm) REVERT: U 629 PHE cc_start: 0.6987 (p90) cc_final: 0.6465 (p90) REVERT: U 656 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7171 (mt) REVERT: U 891 ILE cc_start: 0.8306 (mm) cc_final: 0.8059 (mt) REVERT: U 1111 PHE cc_start: 0.8695 (m-10) cc_final: 0.8152 (m-10) REVERT: U 1202 MET cc_start: 0.4766 (mmm) cc_final: 0.3776 (mtm) REVERT: U 1221 ARG cc_start: 0.8168 (ptt-90) cc_final: 0.7890 (ptt-90) REVERT: U 1224 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8092 (tmtt) REVERT: U 1225 GLN cc_start: 0.8623 (tp-100) cc_final: 0.8271 (tp-100) REVERT: U 1304 MET cc_start: 0.7622 (mpt) cc_final: 0.7124 (mpp) outliers start: 36 outliers final: 20 residues processed: 138 average time/residue: 0.1795 time to fit residues: 36.7622 Evaluate side-chains 130 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 171 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 252 ILE Chi-restraints excluded: chain U residue 335 LEU Chi-restraints excluded: chain U residue 358 THR Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 380 LEU Chi-restraints excluded: chain U residue 422 PHE Chi-restraints excluded: chain U residue 453 LEU Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 582 LEU Chi-restraints excluded: chain U residue 587 SER Chi-restraints excluded: chain U residue 656 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 888 VAL Chi-restraints excluded: chain U residue 1013 HIS Chi-restraints excluded: chain U residue 1014 PHE Chi-restraints excluded: chain U residue 1051 PHE Chi-restraints excluded: chain U residue 1072 ASP Chi-restraints excluded: chain U residue 1121 THR Chi-restraints excluded: chain U residue 1199 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 115 optimal weight: 0.0270 chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 111 optimal weight: 0.5980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 546 GLN ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9465 Z= 0.147 Angle : 0.611 18.420 12806 Z= 0.292 Chirality : 0.040 0.151 1462 Planarity : 0.003 0.041 1631 Dihedral : 6.608 74.872 1357 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.25 % Allowed : 18.93 % Favored : 76.82 % 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: -4.10 (0.22), residues: 1185 helix: -2.78 (0.18), residues: 632 sheet: -2.58 (1.01), residues: 32 loop : -2.50 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 493 HIS 0.005 0.001 HIS U1142 PHE 0.012 0.001 PHE U 363 TYR 0.011 0.001 TYR U 650 ARG 0.002 0.000 ARG U 743 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 114 time to evaluate : 1.038 Fit side-chains REVERT: U 154 ILE cc_start: 0.8391 (tp) cc_final: 0.8017 (tp) REVERT: U 177 PHE cc_start: 0.7966 (t80) cc_final: 0.7597 (t80) REVERT: U 197 GLU cc_start: 0.8058 (tp30) cc_final: 0.7559 (tp30) REVERT: U 217 MET cc_start: 0.7687 (tpp) cc_final: 0.7410 (tpt) REVERT: U 335 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6921 (mt) REVERT: U 373 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8366 (tt) REVERT: U 413 LEU cc_start: 0.8697 (tt) cc_final: 0.8382 (mp) REVERT: U 443 MET cc_start: 0.8466 (ppp) cc_final: 0.8198 (ppp) REVERT: U 629 PHE cc_start: 0.6952 (p90) cc_final: 0.6389 (p90) REVERT: U 656 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7213 (mt) REVERT: U 891 ILE cc_start: 0.8324 (mm) cc_final: 0.8108 (mt) REVERT: U 1111 PHE cc_start: 0.8682 (m-10) cc_final: 0.7860 (m-10) REVERT: U 1202 MET cc_start: 0.5042 (mmm) cc_final: 0.4091 (mtm) REVERT: U 1221 ARG cc_start: 0.8199 (ptt-90) cc_final: 0.7944 (ptt-90) REVERT: U 1224 LYS cc_start: 0.8629 (mtmm) cc_final: 0.8024 (tmtt) REVERT: U 1225 GLN cc_start: 0.8587 (tp-100) cc_final: 0.8221 (tp-100) REVERT: U 1304 MET cc_start: 0.7619 (mpt) cc_final: 0.7133 (mpp) outliers start: 42 outliers final: 21 residues processed: 148 average time/residue: 0.1887 time to fit residues: 40.4413 Evaluate side-chains 125 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 171 ILE Chi-restraints excluded: chain U residue 233 LEU Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 246 ILE Chi-restraints excluded: chain U residue 290 THR Chi-restraints excluded: chain U residue 335 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 422 PHE Chi-restraints excluded: chain U residue 442 ASN Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 587 SER Chi-restraints excluded: chain U residue 619 THR Chi-restraints excluded: chain U residue 656 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 888 VAL Chi-restraints excluded: chain U residue 1013 HIS Chi-restraints excluded: chain U residue 1014 PHE Chi-restraints excluded: chain U residue 1026 LEU Chi-restraints excluded: chain U residue 1072 ASP Chi-restraints excluded: chain U residue 1139 ILE Chi-restraints excluded: chain U residue 1199 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 114 optimal weight: 0.0970 chunk 71 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9465 Z= 0.147 Angle : 0.625 18.198 12806 Z= 0.293 Chirality : 0.040 0.157 1462 Planarity : 0.003 0.037 1631 Dihedral : 6.390 72.808 1357 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.74 % Allowed : 20.04 % Favored : 76.21 % 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: -3.73 (0.23), residues: 1185 helix: -2.50 (0.18), residues: 629 sheet: -2.51 (1.00), residues: 32 loop : -2.29 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP U 493 HIS 0.005 0.001 HIS U1142 PHE 0.011 0.001 PHE U 363 TYR 0.011 0.001 TYR U 650 ARG 0.002 0.000 ARG U1268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 110 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: U 123 MET cc_start: 0.0322 (mmm) cc_final: -0.0623 (mmp) REVERT: U 154 ILE cc_start: 0.8378 (tp) cc_final: 0.8018 (mt) REVERT: U 177 PHE cc_start: 0.7940 (t80) cc_final: 0.7555 (t80) REVERT: U 197 GLU cc_start: 0.8100 (tp30) cc_final: 0.7563 (tp30) REVERT: U 217 MET cc_start: 0.7728 (tpp) cc_final: 0.7405 (tpt) REVERT: U 335 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6895 (mt) REVERT: U 373 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8462 (tt) REVERT: U 629 PHE cc_start: 0.6825 (p90) cc_final: 0.6348 (p90) REVERT: U 656 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7190 (mt) REVERT: U 743 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.8021 (mmm-85) REVERT: U 891 ILE cc_start: 0.8298 (mm) cc_final: 0.8073 (mt) REVERT: U 1202 MET cc_start: 0.5122 (mmm) cc_final: 0.3988 (mtm) REVERT: U 1221 ARG cc_start: 0.8192 (ptt-90) cc_final: 0.7869 (ptt-90) REVERT: U 1224 LYS cc_start: 0.8598 (mtmm) cc_final: 0.8009 (tmtt) outliers start: 37 outliers final: 27 residues processed: 138 average time/residue: 0.1823 time to fit residues: 36.9528 Evaluate side-chains 132 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 171 ILE Chi-restraints excluded: chain U residue 233 LEU Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 246 ILE Chi-restraints excluded: chain U residue 290 THR Chi-restraints excluded: chain U residue 335 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 422 PHE Chi-restraints excluded: chain U residue 442 ASN Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 479 VAL Chi-restraints excluded: chain U residue 524 THR Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 619 THR Chi-restraints excluded: chain U residue 656 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 811 PHE Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 888 VAL Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 1013 HIS Chi-restraints excluded: chain U residue 1014 PHE Chi-restraints excluded: chain U residue 1026 LEU Chi-restraints excluded: chain U residue 1051 PHE Chi-restraints excluded: chain U residue 1072 ASP Chi-restraints excluded: chain U residue 1139 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 546 GLN ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 9465 Z= 0.389 Angle : 0.732 16.432 12806 Z= 0.358 Chirality : 0.046 0.150 1462 Planarity : 0.004 0.050 1631 Dihedral : 7.026 72.222 1357 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 4.35 % Allowed : 20.65 % Favored : 75.00 % 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: -3.99 (0.22), residues: 1185 helix: -2.73 (0.18), residues: 634 sheet: -2.54 (1.03), residues: 32 loop : -2.38 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP U 493 HIS 0.004 0.001 HIS U 72 PHE 0.013 0.002 PHE U1014 TYR 0.015 0.002 TYR U 157 ARG 0.004 0.000 ARG U 621 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 111 time to evaluate : 1.039 Fit side-chains REVERT: U 87 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.9064 (m) REVERT: U 123 MET cc_start: 0.0265 (mmm) cc_final: -0.0109 (mmp) REVERT: U 153 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8125 (tp) REVERT: U 154 ILE cc_start: 0.8330 (tp) cc_final: 0.8010 (tp) REVERT: U 177 PHE cc_start: 0.8089 (t80) cc_final: 0.7713 (t80) REVERT: U 197 GLU cc_start: 0.8304 (tp30) cc_final: 0.7927 (tp30) REVERT: U 217 MET cc_start: 0.8290 (tpp) cc_final: 0.8081 (tpt) REVERT: U 224 MET cc_start: 0.7881 (tpp) cc_final: 0.7606 (tpt) REVERT: U 335 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7026 (mt) REVERT: U 371 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8019 (mp) REVERT: U 373 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8511 (tt) REVERT: U 629 PHE cc_start: 0.7143 (p90) cc_final: 0.6659 (p90) REVERT: U 656 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7069 (mt) REVERT: U 878 MET cc_start: 0.8267 (tpp) cc_final: 0.7338 (tmm) REVERT: U 891 ILE cc_start: 0.8359 (mm) cc_final: 0.8098 (mt) REVERT: U 1111 PHE cc_start: 0.8393 (m-10) cc_final: 0.8163 (m-10) REVERT: U 1202 MET cc_start: 0.5069 (mmm) cc_final: 0.3914 (mtm) REVERT: U 1221 ARG cc_start: 0.8192 (ptt-90) cc_final: 0.7888 (ptt-90) REVERT: U 1224 LYS cc_start: 0.8699 (mtmm) cc_final: 0.8127 (tmtt) outliers start: 43 outliers final: 27 residues processed: 142 average time/residue: 0.2077 time to fit residues: 42.4885 Evaluate side-chains 140 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 107 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 153 LEU Chi-restraints excluded: chain U residue 171 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 246 ILE Chi-restraints excluded: chain U residue 290 THR Chi-restraints excluded: chain U residue 335 LEU Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 479 VAL Chi-restraints excluded: chain U residue 524 THR Chi-restraints excluded: chain U residue 567 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 587 SER Chi-restraints excluded: chain U residue 656 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 888 VAL Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 1013 HIS Chi-restraints excluded: chain U residue 1014 PHE Chi-restraints excluded: chain U residue 1051 PHE Chi-restraints excluded: chain U residue 1072 ASP Chi-restraints excluded: chain U residue 1121 THR Chi-restraints excluded: chain U residue 1139 ILE Chi-restraints excluded: chain U residue 1199 ASP Chi-restraints excluded: chain U residue 1285 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 113 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 546 GLN ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9465 Z= 0.151 Angle : 0.643 17.403 12806 Z= 0.302 Chirality : 0.040 0.148 1462 Planarity : 0.003 0.037 1631 Dihedral : 6.491 76.371 1357 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.94 % Allowed : 22.47 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.71 (0.23), residues: 1185 helix: -2.45 (0.18), residues: 637 sheet: -2.19 (1.24), residues: 25 loop : -2.36 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP U 493 HIS 0.004 0.001 HIS U1013 PHE 0.013 0.001 PHE U 363 TYR 0.010 0.001 TYR U 650 ARG 0.002 0.000 ARG U1268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 1.040 Fit side-chains REVERT: U 123 MET cc_start: 0.0169 (mmm) cc_final: -0.0135 (mmp) REVERT: U 154 ILE cc_start: 0.8370 (tp) cc_final: 0.8033 (tp) REVERT: U 177 PHE cc_start: 0.7838 (t80) cc_final: 0.7408 (t80) REVERT: U 197 GLU cc_start: 0.8295 (tp30) cc_final: 0.7905 (tp30) REVERT: U 217 MET cc_start: 0.7792 (tpp) cc_final: 0.7545 (tpt) REVERT: U 232 LEU cc_start: 0.8754 (tt) cc_final: 0.8211 (mm) REVERT: U 335 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6914 (mt) REVERT: U 371 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7983 (mp) REVERT: U 373 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8454 (tt) REVERT: U 461 LYS cc_start: 0.7603 (ptpp) cc_final: 0.7151 (mmmt) REVERT: U 629 PHE cc_start: 0.6891 (p90) cc_final: 0.6499 (p90) REVERT: U 656 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7168 (mt) REVERT: U 743 ARG cc_start: 0.8300 (mmm-85) cc_final: 0.8045 (mmm-85) REVERT: U 878 MET cc_start: 0.8235 (tpp) cc_final: 0.7289 (tmm) REVERT: U 891 ILE cc_start: 0.8228 (mm) cc_final: 0.8000 (mt) REVERT: U 1146 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8141 (mmtm) REVERT: U 1171 MET cc_start: 0.5726 (tpt) cc_final: 0.5335 (tpt) REVERT: U 1202 MET cc_start: 0.5131 (mmm) cc_final: 0.4024 (mtm) REVERT: U 1224 LYS cc_start: 0.8615 (mtmm) cc_final: 0.8078 (tmtt) outliers start: 29 outliers final: 23 residues processed: 127 average time/residue: 0.1970 time to fit residues: 36.1641 Evaluate side-chains 127 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 171 ILE Chi-restraints excluded: chain U residue 176 LYS Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 246 ILE Chi-restraints excluded: chain U residue 290 THR Chi-restraints excluded: chain U residue 335 LEU Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 422 PHE Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 587 SER Chi-restraints excluded: chain U residue 656 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 787 ASP Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 888 VAL Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 1013 HIS Chi-restraints excluded: chain U residue 1014 PHE Chi-restraints excluded: chain U residue 1051 PHE Chi-restraints excluded: chain U residue 1072 ASP Chi-restraints excluded: chain U residue 1121 THR Chi-restraints excluded: chain U residue 1139 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 chunk 109 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 0.0050 chunk 57 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 546 GLN ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9465 Z= 0.233 Angle : 0.657 16.779 12806 Z= 0.312 Chirality : 0.043 0.180 1462 Planarity : 0.003 0.040 1631 Dihedral : 6.580 73.565 1357 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 3.24 % Allowed : 21.96 % Favored : 74.80 % 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: -3.63 (0.23), residues: 1185 helix: -2.38 (0.19), residues: 641 sheet: -2.32 (1.01), residues: 32 loop : -2.31 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP U 493 HIS 0.003 0.001 HIS U1013 PHE 0.011 0.001 PHE U1014 TYR 0.010 0.001 TYR U 650 ARG 0.002 0.000 ARG U 621 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 105 time to evaluate : 1.077 Fit side-chains REVERT: U 87 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8982 (m) REVERT: U 154 ILE cc_start: 0.8402 (tp) cc_final: 0.7987 (mt) REVERT: U 177 PHE cc_start: 0.7962 (t80) cc_final: 0.7551 (t80) REVERT: U 184 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7830 (mtt180) REVERT: U 197 GLU cc_start: 0.8364 (tp30) cc_final: 0.7969 (tp30) REVERT: U 217 MET cc_start: 0.8010 (tpp) cc_final: 0.7572 (tpt) REVERT: U 335 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7037 (mt) REVERT: U 373 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8522 (tt) REVERT: U 422 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6747 (m-10) REVERT: U 461 LYS cc_start: 0.7558 (ptpp) cc_final: 0.7174 (mmmt) REVERT: U 629 PHE cc_start: 0.6928 (p90) cc_final: 0.6610 (p90) REVERT: U 656 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7123 (mt) REVERT: U 878 MET cc_start: 0.8131 (tpp) cc_final: 0.7292 (tmm) REVERT: U 891 ILE cc_start: 0.8327 (mm) cc_final: 0.8096 (mt) REVERT: U 1171 MET cc_start: 0.5773 (tpt) cc_final: 0.5395 (tpt) REVERT: U 1202 MET cc_start: 0.5312 (mmm) cc_final: 0.4143 (mtm) REVERT: U 1224 LYS cc_start: 0.8492 (mtmm) cc_final: 0.8056 (tmtt) outliers start: 32 outliers final: 23 residues processed: 129 average time/residue: 0.1984 time to fit residues: 36.6473 Evaluate side-chains 127 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 171 ILE Chi-restraints excluded: chain U residue 176 LYS Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 246 ILE Chi-restraints excluded: chain U residue 252 ILE Chi-restraints excluded: chain U residue 290 THR Chi-restraints excluded: chain U residue 335 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 422 PHE Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 524 THR Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 587 SER Chi-restraints excluded: chain U residue 656 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 787 ASP Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 888 VAL Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 1013 HIS Chi-restraints excluded: chain U residue 1014 PHE Chi-restraints excluded: chain U residue 1051 PHE Chi-restraints excluded: chain U residue 1072 ASP Chi-restraints excluded: chain U residue 1121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 546 GLN ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.181414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.127549 restraints weight = 13612.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.125635 restraints weight = 7363.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.125322 restraints weight = 7233.859| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9465 Z= 0.152 Angle : 0.638 17.134 12806 Z= 0.298 Chirality : 0.041 0.201 1462 Planarity : 0.003 0.035 1631 Dihedral : 6.306 74.458 1357 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.04 % Allowed : 22.27 % Favored : 74.70 % 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: -3.46 (0.23), residues: 1185 helix: -2.17 (0.19), residues: 646 sheet: -2.01 (1.03), residues: 32 loop : -2.34 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 493 HIS 0.004 0.001 HIS U1013 PHE 0.016 0.001 PHE U 363 TYR 0.010 0.001 TYR U 650 ARG 0.003 0.000 ARG U1268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1900.33 seconds wall clock time: 35 minutes 0.71 seconds (2100.71 seconds total)