Starting phenix.real_space_refine on Thu Mar 14 17:16:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dv5_30870/03_2024/7dv5_30870_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dv5_30870/03_2024/7dv5_30870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dv5_30870/03_2024/7dv5_30870.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dv5_30870/03_2024/7dv5_30870.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dv5_30870/03_2024/7dv5_30870_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dv5_30870/03_2024/7dv5_30870_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 56 5.16 5 C 5977 2.51 5 N 1567 2.21 5 O 1719 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 299": "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 PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 792": "NH1" <-> "NH2" Residue "U ARG 832": "NH1" <-> "NH2" Residue "U ARG 860": "NH1" <-> "NH2" Residue "U ARG 957": "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" 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: 9319 Number of models: 1 Model: "" Number of chains: 1 Chain: "U" Number of atoms: 9319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1191, 9319 Unusual residues: {'TCH': 2} Classifications: {'peptide': 1189, 'undetermined': 2} Link IDs: {'PTRANS': 32, 'TRANS': 1156, None: 2} Not linked: pdbres="THR U1315 " pdbres="TCH U1401 " Not linked: pdbres="TCH U1401 " pdbres="TCH U1402 " Chain breaks: 1 Time building chain proxies: 5.52, per 1000 atoms: 0.59 Number of scatterers: 9319 At special positions: 0 Unit cell: (91.91, 157.56, 96.96, 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 56 16.00 O 1719 8.00 N 1567 7.00 C 5977 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: 3.44 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: 59 helices and 3 sheets defined 37.4% 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 56 through 58 No H-bonds generated for 'chain 'U' and resid 56 through 58' Processing helix chain 'U' and resid 75 through 86 removed outlier: 4.652A pdb=" N LEU U 80 " --> pdb=" O GLN U 76 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU U 81 " --> pdb=" O PRO U 77 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE U 82 " --> pdb=" O GLY U 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 89 through 98 removed outlier: 3.853A pdb=" N VAL U 95 " --> pdb=" O ILE U 91 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU U 96 " --> pdb=" O ASP U 92 " (cutoff:3.500A) Processing helix chain 'U' and resid 135 through 153 removed outlier: 3.701A pdb=" N ILE U 139 " --> pdb=" O GLU U 135 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS U 140 " --> pdb=" O SER U 136 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER U 143 " --> pdb=" O ILE U 139 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR U 144 " --> pdb=" O LYS U 140 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA U 146 " --> pdb=" O ALA U 142 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY U 147 " --> pdb=" O SER U 143 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL U 150 " --> pdb=" O ALA U 146 " (cutoff:3.500A) Processing helix chain 'U' and resid 158 through 161 No H-bonds generated for 'chain 'U' and resid 158 through 161' Processing helix chain 'U' and resid 171 through 183 removed outlier: 3.914A pdb=" N LYS U 176 " --> pdb=" O GLN U 172 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE U 179 " --> pdb=" O ARG U 175 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET U 183 " --> pdb=" O PHE U 179 " (cutoff:3.500A) Processing helix chain 'U' and resid 188 through 192 removed outlier: 4.124A pdb=" N CYS U 192 " --> pdb=" O GLY U 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 188 through 192' Processing helix chain 'U' and resid 215 through 235 removed outlier: 3.667A pdb=" N LEU U 219 " --> pdb=" O ASP U 215 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE U 220 " --> pdb=" O GLN U 216 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG U 223 " --> pdb=" O LEU U 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER U 226 " --> pdb=" O GLN U 222 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR U 227 " --> pdb=" O ARG U 223 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS U 229 " --> pdb=" O THR U 225 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE U 231 " --> pdb=" O THR U 227 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY U 234 " --> pdb=" O GLY U 230 " (cutoff:3.500A) Processing helix chain 'U' and resid 239 through 242 No H-bonds generated for 'chain 'U' and resid 239 through 242' Processing helix chain 'U' and resid 245 through 249 Processing helix chain 'U' and resid 251 through 257 removed outlier: 3.777A pdb=" N GLY U 255 " --> pdb=" O LEU U 251 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA U 256 " --> pdb=" O ILE U 252 " (cutoff:3.500A) Processing helix chain 'U' and resid 267 through 274 removed outlier: 3.864A pdb=" N LEU U 271 " --> pdb=" O THR U 267 " (cutoff:3.500A) Processing helix chain 'U' and resid 288 through 294 removed outlier: 3.665A pdb=" N ALA U 292 " --> pdb=" O MET U 288 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA U 293 " --> pdb=" O ARG U 289 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE U 294 " --> pdb=" O THR U 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 288 through 294' Processing helix chain 'U' and resid 297 through 300 No H-bonds generated for 'chain 'U' and resid 297 through 300' Processing helix chain 'U' and resid 302 through 305 No H-bonds generated for 'chain 'U' and resid 302 through 305' Processing helix chain 'U' and resid 321 through 334 removed outlier: 3.834A pdb=" N THR U 326 " --> pdb=" O MET U 322 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY U 327 " --> pdb=" O GLY U 323 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU U 332 " --> pdb=" O PHE U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 343 through 349 removed outlier: 4.114A pdb=" N LEU U 347 " --> pdb=" O TYR U 343 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL U 348 " --> pdb=" O GLY U 344 " (cutoff:3.500A) Processing helix chain 'U' and resid 363 through 376 removed outlier: 3.832A pdb=" N ASN U 372 " --> pdb=" O VAL U 368 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU U 373 " --> pdb=" O GLY U 369 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY U 374 " --> pdb=" O ALA U 370 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA U 376 " --> pdb=" O ASN U 372 " (cutoff:3.500A) Processing helix chain 'U' and resid 382 through 389 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 491 through 497 removed outlier: 3.924A pdb=" N ASP U 496 " --> pdb=" O GLN U 492 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN U 497 " --> pdb=" O TRP U 493 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 534 removed outlier: 3.962A pdb=" N VAL U 529 " --> pdb=" O MET U 525 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN U 530 " --> pdb=" O GLU U 526 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA U 531 " --> pdb=" O ASP U 527 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU U 534 " --> pdb=" O GLN U 530 " (cutoff:3.500A) Processing helix chain 'U' and resid 538 through 542 Processing helix chain 'U' and resid 561 through 573 removed outlier: 4.177A pdb=" N ARG U 566 " --> pdb=" O GLY U 562 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL U 567 " --> pdb=" O GLN U 563 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA U 568 " --> pdb=" O LYS U 564 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE U 569 " --> pdb=" O GLN U 565 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA U 570 " --> pdb=" O ARG U 566 " (cutoff:3.500A) Processing helix chain 'U' and resid 594 through 602 removed outlier: 3.682A pdb=" N VAL U 600 " --> pdb=" O MET U 596 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU U 601 " --> pdb=" O VAL U 597 " (cutoff:3.500A) Processing helix chain 'U' and resid 653 through 655 No H-bonds generated for 'chain 'U' and resid 653 through 655' 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 754 through 764 removed outlier: 3.548A pdb=" N ALA U 762 " --> pdb=" O GLY U 758 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA U 763 " --> pdb=" O SER U 759 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL U 764 " --> pdb=" O VAL U 760 " (cutoff:3.500A) Processing helix chain 'U' and resid 768 through 779 removed outlier: 3.519A pdb=" N TYR U 772 " --> pdb=" O VAL U 768 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA U 773 " --> pdb=" O THR U 769 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE U 774 " --> pdb=" O PRO U 770 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER U 777 " --> pdb=" O ALA U 773 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN U 778 " --> pdb=" O PHE U 774 " (cutoff:3.500A) Processing helix chain 'U' and resid 790 through 793 No H-bonds generated for 'chain 'U' and resid 790 through 793' Processing helix chain 'U' and resid 803 through 818 removed outlier: 3.884A pdb=" N VAL U 808 " --> pdb=" O ALA U 804 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE U 811 " --> pdb=" O CYS U 807 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN U 813 " --> pdb=" O SER U 809 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE U 814 " --> pdb=" O LEU U 810 " (cutoff:3.500A) Processing helix chain 'U' and resid 820 through 840 removed outlier: 3.828A pdb=" N GLY U 824 " --> pdb=" O PHE U 820 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU U 825 " --> pdb=" O ALA U 821 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR U 828 " --> pdb=" O GLY U 824 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG U 830 " --> pdb=" O LEU U 826 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG U 832 " --> pdb=" O THR U 828 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS U 833 " --> pdb=" O LYS U 829 " (cutoff:3.500A) Processing helix chain 'U' and resid 854 through 857 No H-bonds generated for 'chain 'U' and resid 854 through 857' Processing helix chain 'U' and resid 868 through 879 removed outlier: 3.913A pdb=" N ALA U 872 " --> pdb=" O GLN U 869 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLY U 873 " --> pdb=" O GLY U 870 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER U 874 " --> pdb=" O ALA U 871 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN U 875 " --> pdb=" O ALA U 872 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE U 876 " --> pdb=" O GLY U 873 " (cutoff:3.500A) Processing helix chain 'U' and resid 888 through 896 removed outlier: 3.910A pdb=" N PHE U 896 " --> pdb=" O ILE U 892 " (cutoff:3.500A) Processing helix chain 'U' and resid 901 through 906 removed outlier: 3.867A pdb=" N CYS U 906 " --> pdb=" O LEU U 902 " (cutoff:3.500A) Processing helix chain 'U' and resid 909 through 916 removed outlier: 3.539A pdb=" N LEU U 913 " --> pdb=" O PRO U 909 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER U 914 " --> pdb=" O PHE U 910 " (cutoff:3.500A) Processing helix chain 'U' and resid 923 through 925 No H-bonds generated for 'chain 'U' and resid 923 through 925' Processing helix chain 'U' and resid 930 through 932 No H-bonds generated for 'chain 'U' and resid 930 through 932' 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 948 through 951 No H-bonds generated for 'chain 'U' and resid 948 through 951' Processing helix chain 'U' and resid 966 through 972 removed outlier: 3.526A pdb=" N LYS U 969 " --> pdb=" O GLU U 966 " (cutoff:3.500A) Proline residue: U 970 - end of helix No H-bonds generated for 'chain 'U' and resid 966 through 972' Processing helix chain 'U' and resid 981 through 984 No H-bonds generated for 'chain 'U' and resid 981 through 984' Processing helix chain 'U' and resid 992 through 995 No H-bonds generated for 'chain 'U' and resid 992 through 995' Processing helix chain 'U' and resid 997 through 1008 removed outlier: 3.733A pdb=" N ARG U1001 " --> pdb=" O SER U 997 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR U1002 " --> pdb=" O ALA U 998 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU U1006 " --> pdb=" O TYR U1002 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER U1008 " --> pdb=" O GLY U1004 " (cutoff:3.500A) Processing helix chain 'U' and resid 1015 through 1018 No H-bonds generated for 'chain 'U' and resid 1015 through 1018' Processing helix chain 'U' and resid 1030 through 1033 No H-bonds generated for 'chain 'U' and resid 1030 through 1033' Processing helix chain 'U' and resid 1048 through 1055 removed outlier: 3.596A pdb=" N PHE U1052 " --> pdb=" O ALA U1048 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN U1053 " --> pdb=" O ALA U1049 " (cutoff:3.500A) Processing helix chain 'U' and resid 1120 through 1124 Processing helix chain 'U' and resid 1149 through 1153 Processing helix chain 'U' and resid 1170 through 1177 removed outlier: 3.927A pdb=" N GLY U1177 " --> pdb=" O ASN U1173 " (cutoff:3.500A) Processing helix chain 'U' and resid 1186 through 1190 removed outlier: 3.844A pdb=" N ALA U1190 " --> pdb=" O GLU U1186 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 1186 through 1190' Processing helix chain 'U' and resid 1221 through 1223 No H-bonds generated for 'chain 'U' and resid 1221 through 1223' Processing helix chain 'U' and resid 1225 through 1228 No H-bonds generated for 'chain 'U' and resid 1225 through 1228' Processing helix chain 'U' and resid 1230 through 1233 No H-bonds generated for 'chain 'U' and resid 1230 through 1233' Processing helix chain 'U' and resid 1251 through 1263 removed outlier: 3.717A pdb=" N THR U1256 " --> pdb=" O GLU U1252 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA U1260 " --> pdb=" O THR U1256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP U1262 " --> pdb=" O GLN U1258 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS U1263 " --> pdb=" O VAL U1259 " (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 1314 removed outlier: 4.061A pdb=" N LEU U1313 " --> pdb=" O ALA U1309 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'U' and resid 420 through 422 removed outlier: 3.627A pdb=" N ILE U 420 " --> pdb=" O ILE U 445 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET U 443 " --> pdb=" O PHE U 422 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'U' and resid 498 through 501 removed outlier: 6.483A pdb=" N ILE U 579 " --> pdb=" O GLY U 499 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL U 501 " --> pdb=" O ILE U 579 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU U 581 " --> pdb=" O VAL U 501 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR U 609 " --> pdb=" O LEU U 580 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N LEU U 582 " --> pdb=" O THR U 609 " (cutoff:3.500A) removed outlier: 7.150A 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: 6.586A pdb=" N ILE U1239 " --> pdb=" O GLY U1157 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL U1159 " --> pdb=" O ILE U1239 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU U1241 " --> pdb=" O VAL U1159 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 125 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: 2.25 Time building geometry restraints manager: 3.78 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: 2531 1.33 - 1.45: 1907 1.45 - 1.57: 4975 1.57 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 9503 Sorted by residual: bond pdb=" CG1 ILE U 171 " pdb=" CD1 ILE U 171 " ideal model delta sigma weight residual 1.513 1.365 0.148 3.90e-02 6.57e+02 1.43e+01 bond pdb=" O3S TCH U1401 " pdb=" S26 TCH U1401 " ideal model delta sigma weight residual 1.475 1.548 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" O3S TCH U1402 " pdb=" S26 TCH U1402 " ideal model delta sigma weight residual 1.475 1.547 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" N VAL U 348 " pdb=" CA VAL U 348 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.22e-02 6.72e+03 9.19e+00 bond pdb=" N ILE U1280 " pdb=" CA ILE U1280 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.25e-02 6.40e+03 8.69e+00 ... (remaining 9498 not shown) Histogram of bond angle deviations from ideal: 75.84 - 90.96: 2 90.96 - 106.08: 202 106.08 - 121.21: 10162 121.21 - 136.33: 2498 136.33 - 151.45: 2 Bond angle restraints: 12866 Sorted by residual: angle pdb=" N ARG U 920 " pdb=" CA ARG U 920 " pdb=" C ARG U 920 " ideal model delta sigma weight residual 110.80 151.45 -40.65 2.13e+00 2.20e-01 3.64e+02 angle pdb=" N ILE U 112 " pdb=" CA ILE U 112 " pdb=" C ILE U 112 " ideal model delta sigma weight residual 110.62 132.26 -21.64 1.14e+00 7.69e-01 3.60e+02 angle pdb=" C ARG U 920 " pdb=" CA ARG U 920 " pdb=" CB ARG U 920 " ideal model delta sigma weight residual 110.42 75.84 34.58 1.99e+00 2.53e-01 3.02e+02 angle pdb=" N THR U 111 " pdb=" CA THR U 111 " pdb=" C THR U 111 " ideal model delta sigma weight residual 108.00 82.83 25.17 1.48e+00 4.57e-01 2.89e+02 angle pdb=" C THR U 111 " pdb=" CA THR U 111 " pdb=" CB THR U 111 " ideal model delta sigma weight residual 116.34 137.97 -21.63 1.40e+00 5.10e-01 2.39e+02 ... (remaining 12861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.37: 5479 24.37 - 48.75: 250 48.75 - 73.12: 22 73.12 - 97.49: 8 97.49 - 121.87: 3 Dihedral angle restraints: 5762 sinusoidal: 2351 harmonic: 3411 Sorted by residual: dihedral pdb=" C THR U1279 " pdb=" N THR U1279 " pdb=" CA THR U1279 " pdb=" CB THR U1279 " ideal model delta harmonic sigma weight residual -122.00 -98.92 -23.08 0 2.50e+00 1.60e-01 8.52e+01 dihedral pdb=" C ARG U 920 " pdb=" N ARG U 920 " pdb=" CA ARG U 920 " pdb=" CB ARG U 920 " ideal model delta harmonic sigma weight residual -122.60 -100.02 -22.58 0 2.50e+00 1.60e-01 8.16e+01 dihedral pdb=" N MET U 921 " pdb=" C MET U 921 " pdb=" CA MET U 921 " pdb=" CB MET U 921 " ideal model delta harmonic sigma weight residual 122.80 102.72 20.08 0 2.50e+00 1.60e-01 6.45e+01 ... (remaining 5759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 1441 0.194 - 0.388: 27 0.388 - 0.581: 1 0.581 - 0.775: 3 0.775 - 0.969: 1 Chirality restraints: 1473 Sorted by residual: chirality pdb=" CA ARG U 920 " pdb=" N ARG U 920 " pdb=" C ARG U 920 " pdb=" CB ARG U 920 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CA THR U1279 " pdb=" N THR U1279 " pdb=" C THR U1279 " pdb=" CB THR U1279 " both_signs ideal model delta sigma weight residual False 2.53 3.22 -0.69 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA ILE U 112 " pdb=" N ILE U 112 " pdb=" C ILE U 112 " pdb=" CB ILE U 112 " both_signs ideal model delta sigma weight residual False 2.43 1.76 0.67 2.00e-01 2.50e+01 1.14e+01 ... (remaining 1470 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C23 TCH U1401 " -0.113 2.00e-02 2.50e+03 1.26e-01 1.99e+02 pdb=" C24 TCH U1401 " 0.043 2.00e-02 2.50e+03 pdb=" C25 TCH U1401 " -0.153 2.00e-02 2.50e+03 pdb=" N24 TCH U1401 " 0.203 2.00e-02 2.50e+03 pdb=" O24 TCH U1401 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR U 769 " -0.049 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO U 770 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO U 770 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO U 770 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS U 969 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.35e+00 pdb=" N PRO U 970 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO U 970 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO U 970 " -0.041 5.00e-02 4.00e+02 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 57 2.53 - 3.12: 6646 3.12 - 3.71: 13788 3.71 - 4.31: 18940 4.31 - 4.90: 30840 Nonbonded interactions: 70271 Sorted by model distance: nonbonded pdb=" O ARG U 920 " pdb=" CB ARG U 920 " model vdw 1.936 2.752 nonbonded pdb=" OD1 ASP U 350 " pdb=" N GLU U 351 " model vdw 2.014 2.520 nonbonded pdb=" N THR U 111 " pdb=" O THR U 111 " model vdw 2.079 2.496 nonbonded pdb=" N THR U1279 " pdb=" O THR U1279 " model vdw 2.257 2.496 nonbonded pdb=" C SER U1278 " pdb=" O THR U1279 " model vdw 2.272 3.270 ... (remaining 70266 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: 0.380 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: 2.310 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.140 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 0.148 9503 Z= 0.674 Angle : 1.462 40.646 12866 Z= 0.824 Chirality : 0.083 0.969 1473 Planarity : 0.008 0.126 1632 Dihedral : 14.003 121.866 3572 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.73 % Favored : 88.19 % Rotamer: Outliers : 2.23 % Allowed : 8.81 % Favored : 88.97 % Cbeta Deviations : 0.55 % 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: -6.60 (0.15), residues: 1185 helix: -4.90 (0.07), residues: 634 sheet: -4.65 (0.54), residues: 26 loop : -3.52 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP U 163 HIS 0.009 0.002 HIS U 72 PHE 0.026 0.003 PHE U 629 TYR 0.028 0.003 TYR U 981 ARG 0.014 0.001 ARG U1001 *********************** 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 211 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 189 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: U 268 ASP cc_start: 0.7978 (m-30) cc_final: 0.7694 (t0) REVERT: U 424 ASN cc_start: 0.5405 (p0) cc_final: 0.4738 (p0) REVERT: U 426 THR cc_start: 0.7168 (t) cc_final: 0.6866 (p) REVERT: U 478 MET cc_start: 0.6556 (ppp) cc_final: 0.5941 (mmt) REVERT: U 516 ILE cc_start: 0.9009 (mt) cc_final: 0.8714 (mm) REVERT: U 533 LYS cc_start: 0.7873 (tttm) cc_final: 0.7367 (pttt) REVERT: U 913 LEU cc_start: 0.8530 (tm) cc_final: 0.8062 (mt) REVERT: U 918 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.5912 (tp-100) REVERT: U 925 PHE cc_start: 0.5698 (OUTLIER) cc_final: 0.3421 (p90) REVERT: U 946 ASN cc_start: 0.8606 (p0) cc_final: 0.8400 (p0) REVERT: U 1033 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7449 (ttp80) REVERT: U 1037 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.6996 (m-10) REVERT: U 1145 LYS cc_start: 0.8217 (mmmm) cc_final: 0.7573 (ptmt) REVERT: U 1161 GLN cc_start: 0.6938 (tt0) cc_final: 0.6568 (tp40) REVERT: U 1221 ARG cc_start: 0.6777 (ttp-170) cc_final: 0.6565 (ttp-170) REVERT: U 1261 LEU cc_start: 0.8459 (mp) cc_final: 0.8224 (mt) outliers start: 22 outliers final: 10 residues processed: 206 average time/residue: 0.2626 time to fit residues: 70.9716 Evaluate side-chains 128 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 343 TYR Chi-restraints excluded: chain U residue 347 LEU Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 651 PHE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 921 MET Chi-restraints excluded: chain U residue 925 PHE Chi-restraints excluded: chain U residue 1029 THR Chi-restraints excluded: chain U residue 1033 ARG Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1126 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 48 optimal weight: 7.9990 chunk 93 optimal weight: 0.0040 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.0030 chunk 69 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 overall best weight: 1.1006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 72 HIS U 110 ASN U 372 ASN ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 867 GLN U1097 ASN U1107 GLN U1258 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9503 Z= 0.181 Angle : 0.675 8.212 12866 Z= 0.345 Chirality : 0.042 0.156 1473 Planarity : 0.004 0.049 1632 Dihedral : 10.153 133.967 1464 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.34 % Allowed : 13.26 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.82 (0.17), residues: 1185 helix: -4.24 (0.11), residues: 638 sheet: -3.94 (0.64), residues: 26 loop : -3.20 (0.23), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP U 493 HIS 0.003 0.001 HIS U1142 PHE 0.012 0.001 PHE U 651 TYR 0.018 0.001 TYR U 157 ARG 0.003 0.000 ARG U 920 *********************** 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 172 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 144 TYR cc_start: 0.8136 (m-10) cc_final: 0.7891 (m-80) REVERT: U 154 ILE cc_start: 0.8853 (tp) cc_final: 0.8374 (tp) REVERT: U 173 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8440 (mtmm) REVERT: U 424 ASN cc_start: 0.5346 (p0) cc_final: 0.4901 (p0) REVERT: U 472 TYR cc_start: 0.8536 (m-80) cc_final: 0.8299 (m-80) REVERT: U 478 MET cc_start: 0.6447 (ppp) cc_final: 0.5890 (mmt) REVERT: U 533 LYS cc_start: 0.7754 (tttm) cc_final: 0.7327 (pttt) REVERT: U 576 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7468 (t0) REVERT: U 610 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.7985 (mp) REVERT: U 636 GLU cc_start: 0.6907 (tm-30) cc_final: 0.6482 (tt0) REVERT: U 878 MET cc_start: 0.8174 (tmm) cc_final: 0.7923 (tmm) REVERT: U 913 LEU cc_start: 0.8565 (tm) cc_final: 0.8153 (mp) REVERT: U 918 GLN cc_start: 0.6674 (OUTLIER) cc_final: 0.5822 (tp-100) REVERT: U 920 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.5114 (mtt90) REVERT: U 921 MET cc_start: 0.5911 (OUTLIER) cc_final: 0.4556 (ttp) REVERT: U 928 ARG cc_start: 0.7258 (tpt170) cc_final: 0.6043 (ptp90) REVERT: U 946 ASN cc_start: 0.8445 (p0) cc_final: 0.8160 (p0) REVERT: U 966 GLU cc_start: 0.7751 (tp30) cc_final: 0.7527 (tp30) REVERT: U 1037 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.7045 (m-10) REVERT: U 1145 LYS cc_start: 0.8131 (mmmm) cc_final: 0.7482 (ptmt) REVERT: U 1161 GLN cc_start: 0.6903 (tt0) cc_final: 0.6517 (tp40) REVERT: U 1171 MET cc_start: 0.8079 (tmm) cc_final: 0.7770 (tmm) REVERT: U 1270 CYS cc_start: 0.7548 (t) cc_final: 0.7084 (m) outliers start: 33 outliers final: 10 residues processed: 163 average time/residue: 0.2535 time to fit residues: 56.1818 Evaluate side-chains 131 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 347 LEU Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 921 MET Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 992 MET Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 116 optimal weight: 0.2980 chunk 96 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U1281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9503 Z= 0.151 Angle : 0.593 8.105 12866 Z= 0.301 Chirality : 0.041 0.142 1473 Planarity : 0.003 0.037 1632 Dihedral : 9.191 135.382 1451 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.85 % Allowed : 14.57 % Favored : 81.58 % 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: -3.56 (0.15), residues: 639 sheet: -3.70 (0.63), residues: 26 loop : -3.11 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 846 HIS 0.003 0.001 HIS U1142 PHE 0.010 0.001 PHE U 783 TYR 0.013 0.001 TYR U1176 ARG 0.005 0.000 ARG U 792 *********************** 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 168 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 130 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 144 TYR cc_start: 0.8044 (m-10) cc_final: 0.7772 (m-80) REVERT: U 154 ILE cc_start: 0.8822 (tp) cc_final: 0.8331 (tp) REVERT: U 173 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8405 (mtmm) REVERT: U 371 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8568 (mt) REVERT: U 424 ASN cc_start: 0.5441 (p0) cc_final: 0.4936 (p0) REVERT: U 478 MET cc_start: 0.6422 (ppp) cc_final: 0.5850 (mmt) REVERT: U 517 ARG cc_start: 0.6236 (ttm170) cc_final: 0.6004 (ttm110) REVERT: U 533 LYS cc_start: 0.7645 (tttm) cc_final: 0.7272 (pttt) REVERT: U 576 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7334 (t0) REVERT: U 610 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7910 (mp) REVERT: U 878 MET cc_start: 0.8106 (tmm) cc_final: 0.7846 (tmm) REVERT: U 913 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8106 (mp) REVERT: U 918 GLN cc_start: 0.6525 (OUTLIER) cc_final: 0.5863 (tp-100) REVERT: U 920 ARG cc_start: 0.6234 (OUTLIER) cc_final: 0.5039 (mtt90) REVERT: U 921 MET cc_start: 0.5520 (tpt) cc_final: 0.4598 (ttp) REVERT: U 928 ARG cc_start: 0.7387 (tpt170) cc_final: 0.6185 (ptp90) REVERT: U 946 ASN cc_start: 0.8486 (p0) cc_final: 0.8258 (p0) REVERT: U 966 GLU cc_start: 0.7735 (tp30) cc_final: 0.7453 (tp30) REVERT: U 1031 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8489 (tt) REVERT: U 1037 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.7050 (m-10) REVERT: U 1145 LYS cc_start: 0.8048 (mmmm) cc_final: 0.7416 (ptmt) REVERT: U 1161 GLN cc_start: 0.7014 (tt0) cc_final: 0.6382 (tp40) REVERT: U 1171 MET cc_start: 0.8027 (tmm) cc_final: 0.7753 (tmm) REVERT: U 1270 CYS cc_start: 0.7431 (t) cc_final: 0.7083 (m) outliers start: 38 outliers final: 16 residues processed: 159 average time/residue: 0.2404 time to fit residues: 52.3812 Evaluate side-chains 142 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 347 LEU Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 960 ILE Chi-restraints excluded: chain U residue 992 MET Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1152 LEU Chi-restraints excluded: chain U residue 1279 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 640 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 9503 Z= 0.487 Angle : 0.758 9.414 12866 Z= 0.389 Chirality : 0.049 0.145 1473 Planarity : 0.005 0.050 1632 Dihedral : 9.671 133.286 1448 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 6.17 % Allowed : 15.28 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.09 (0.19), residues: 1185 helix: -3.48 (0.15), residues: 654 sheet: -3.94 (0.54), residues: 26 loop : -3.04 (0.24), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP U 846 HIS 0.003 0.001 HIS U 484 PHE 0.017 0.002 PHE U 53 TYR 0.016 0.002 TYR U1176 ARG 0.005 0.001 ARG U 832 *********************** 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 187 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 126 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 154 ILE cc_start: 0.8907 (tp) cc_final: 0.8395 (tp) REVERT: U 373 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8858 (tp) REVERT: U 478 MET cc_start: 0.6743 (ppp) cc_final: 0.6023 (mmt) REVERT: U 533 LYS cc_start: 0.7802 (tttm) cc_final: 0.7374 (pttt) REVERT: U 610 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8100 (mp) REVERT: U 852 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7953 (p0) REVERT: U 913 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8076 (mp) REVERT: U 918 GLN cc_start: 0.6757 (OUTLIER) cc_final: 0.5861 (tp-100) REVERT: U 920 ARG cc_start: 0.6233 (OUTLIER) cc_final: 0.4917 (mtt90) REVERT: U 928 ARG cc_start: 0.7379 (tpt170) cc_final: 0.6154 (ptp90) REVERT: U 933 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8076 (tt) REVERT: U 1031 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8600 (tt) REVERT: U 1037 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.7274 (m-10) REVERT: U 1145 LYS cc_start: 0.8189 (mmmm) cc_final: 0.7538 (ptmt) REVERT: U 1161 GLN cc_start: 0.7058 (tt0) cc_final: 0.6505 (tp40) REVERT: U 1171 MET cc_start: 0.7927 (tmm) cc_final: 0.7659 (tmm) REVERT: U 1185 MET cc_start: 0.5088 (tpp) cc_final: 0.4792 (tpt) REVERT: U 1238 LYS cc_start: 0.7446 (mmpt) cc_final: 0.7060 (mttt) REVERT: U 1270 CYS cc_start: 0.7739 (t) cc_final: 0.7120 (m) outliers start: 61 outliers final: 27 residues processed: 175 average time/residue: 0.2104 time to fit residues: 50.8925 Evaluate side-chains 154 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 118 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 347 LEU Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 407 SER Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 426 THR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 600 VAL Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 800 LEU Chi-restraints excluded: chain U residue 808 VAL Chi-restraints excluded: chain U residue 852 ASN Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1021 ILE Chi-restraints excluded: chain U residue 1025 VAL Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1265 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 0 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 29 optimal weight: 0.2980 chunk 38 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9503 Z= 0.166 Angle : 0.600 9.570 12866 Z= 0.302 Chirality : 0.041 0.166 1473 Planarity : 0.003 0.033 1632 Dihedral : 8.989 134.824 1448 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.95 % Allowed : 17.51 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.21), residues: 1185 helix: -3.05 (0.17), residues: 640 sheet: -3.33 (0.59), residues: 26 loop : -2.86 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP U 846 HIS 0.003 0.000 HIS U1142 PHE 0.010 0.001 PHE U 783 TYR 0.016 0.001 TYR U 538 ARG 0.003 0.000 ARG U 792 *********************** 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 166 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8416 (mm) REVERT: U 154 ILE cc_start: 0.8764 (tp) cc_final: 0.8170 (tp) REVERT: U 373 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8761 (tp) REVERT: U 478 MET cc_start: 0.6533 (ppp) cc_final: 0.5845 (mmt) REVERT: U 533 LYS cc_start: 0.7708 (tttm) cc_final: 0.7312 (pttt) REVERT: U 913 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8011 (mp) REVERT: U 918 GLN cc_start: 0.6530 (OUTLIER) cc_final: 0.5775 (tp-100) REVERT: U 920 ARG cc_start: 0.6141 (OUTLIER) cc_final: 0.4943 (mtt90) REVERT: U 921 MET cc_start: 0.6084 (tpt) cc_final: 0.4674 (ttp) REVERT: U 928 ARG cc_start: 0.7367 (tpt170) cc_final: 0.6035 (ptp90) REVERT: U 1031 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8454 (tt) REVERT: U 1037 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.7363 (m-10) REVERT: U 1145 LYS cc_start: 0.8092 (mmmm) cc_final: 0.7470 (ptmt) REVERT: U 1161 GLN cc_start: 0.7095 (tt0) cc_final: 0.6347 (tp40) REVERT: U 1221 ARG cc_start: 0.7177 (tmm160) cc_final: 0.6683 (ppt170) REVERT: U 1238 LYS cc_start: 0.7367 (mmpt) cc_final: 0.6964 (mttm) REVERT: U 1270 CYS cc_start: 0.7659 (t) cc_final: 0.7142 (m) outliers start: 39 outliers final: 22 residues processed: 156 average time/residue: 0.2293 time to fit residues: 48.8620 Evaluate side-chains 145 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 800 LEU Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1025 VAL Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1158 ILE Chi-restraints excluded: chain U residue 1279 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 67 optimal weight: 0.0570 chunk 28 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 484 HIS ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9503 Z= 0.261 Angle : 0.628 10.785 12866 Z= 0.317 Chirality : 0.043 0.167 1473 Planarity : 0.004 0.035 1632 Dihedral : 8.940 134.797 1446 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 5.36 % Allowed : 17.81 % 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: -4.36 (0.21), residues: 1185 helix: -2.90 (0.17), residues: 632 sheet: -3.16 (0.64), residues: 26 loop : -2.75 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP U 846 HIS 0.002 0.001 HIS U1142 PHE 0.012 0.001 PHE U 783 TYR 0.014 0.001 TYR U1005 ARG 0.003 0.000 ARG U 299 *********************** 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 173 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 120 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8518 (mm) REVERT: U 154 ILE cc_start: 0.8840 (tp) cc_final: 0.8268 (tp) REVERT: U 373 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8794 (tp) REVERT: U 478 MET cc_start: 0.6540 (ppp) cc_final: 0.5841 (mmt) REVERT: U 533 LYS cc_start: 0.7695 (tttm) cc_final: 0.7305 (pttt) REVERT: U 610 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8021 (mp) REVERT: U 913 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8028 (mp) REVERT: U 918 GLN cc_start: 0.6548 (OUTLIER) cc_final: 0.5785 (tp-100) REVERT: U 920 ARG cc_start: 0.6179 (OUTLIER) cc_final: 0.4963 (mtt90) REVERT: U 921 MET cc_start: 0.6084 (tpt) cc_final: 0.4488 (ttp) REVERT: U 928 ARG cc_start: 0.7484 (tpt170) cc_final: 0.5950 (ptp90) REVERT: U 933 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7933 (tt) REVERT: U 946 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8410 (p0) REVERT: U 1031 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8467 (tt) REVERT: U 1037 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7372 (m-10) REVERT: U 1145 LYS cc_start: 0.8066 (mmmm) cc_final: 0.7497 (ptmt) REVERT: U 1161 GLN cc_start: 0.7118 (tt0) cc_final: 0.6342 (tp40) REVERT: U 1221 ARG cc_start: 0.7187 (tmm160) cc_final: 0.6630 (ppt170) REVERT: U 1238 LYS cc_start: 0.7396 (mmpt) cc_final: 0.7000 (mttm) REVERT: U 1270 CYS cc_start: 0.7926 (t) cc_final: 0.7299 (m) outliers start: 53 outliers final: 34 residues processed: 157 average time/residue: 0.2434 time to fit residues: 51.8852 Evaluate side-chains 161 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 117 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 426 THR Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 582 LEU Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 767 THR Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 808 VAL Chi-restraints excluded: chain U residue 846 TRP Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 946 ASN Chi-restraints excluded: chain U residue 992 MET Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1021 ILE Chi-restraints excluded: chain U residue 1025 VAL Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1143 ASP Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1152 LEU Chi-restraints excluded: chain U residue 1158 ILE Chi-restraints excluded: chain U residue 1174 ILE Chi-restraints excluded: chain U residue 1265 ARG Chi-restraints excluded: chain U residue 1288 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 71 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 0.0370 overall best weight: 1.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 946 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9503 Z= 0.196 Angle : 0.597 9.554 12866 Z= 0.301 Chirality : 0.042 0.154 1473 Planarity : 0.003 0.033 1632 Dihedral : 8.746 134.937 1446 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.57 % Allowed : 18.32 % Favored : 76.11 % 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: -4.22 (0.21), residues: 1185 helix: -2.72 (0.18), residues: 638 sheet: -3.04 (0.67), residues: 27 loop : -2.77 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP U 846 HIS 0.002 0.000 HIS U1142 PHE 0.009 0.001 PHE U 783 TYR 0.011 0.001 TYR U1176 ARG 0.003 0.000 ARG U 299 *********************** 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 174 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 119 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8496 (mm) REVERT: U 154 ILE cc_start: 0.8738 (tp) cc_final: 0.8105 (tp) REVERT: U 373 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8765 (tp) REVERT: U 478 MET cc_start: 0.6544 (ppp) cc_final: 0.5826 (mmt) REVERT: U 533 LYS cc_start: 0.7696 (tttm) cc_final: 0.7311 (pttt) REVERT: U 583 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6504 (p0) REVERT: U 610 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7993 (mp) REVERT: U 913 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.7969 (mp) REVERT: U 918 GLN cc_start: 0.6434 (OUTLIER) cc_final: 0.5680 (tp-100) REVERT: U 920 ARG cc_start: 0.6103 (OUTLIER) cc_final: 0.4792 (mtt90) REVERT: U 928 ARG cc_start: 0.7458 (tpt170) cc_final: 0.5875 (ptp90) REVERT: U 933 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7663 (tt) REVERT: U 1031 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8425 (tt) REVERT: U 1037 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7337 (m-10) REVERT: U 1138 MET cc_start: 0.6669 (ttp) cc_final: 0.6141 (mmt) REVERT: U 1145 LYS cc_start: 0.8046 (mmmm) cc_final: 0.7479 (ptmt) REVERT: U 1161 GLN cc_start: 0.7188 (tt0) cc_final: 0.6392 (tp40) REVERT: U 1221 ARG cc_start: 0.7037 (tmm160) cc_final: 0.6530 (ppt170) REVERT: U 1270 CYS cc_start: 0.7879 (t) cc_final: 0.7262 (m) outliers start: 55 outliers final: 35 residues processed: 159 average time/residue: 0.2276 time to fit residues: 50.0919 Evaluate side-chains 159 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 114 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 185 MET Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 426 THR Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 583 ASP Chi-restraints excluded: chain U residue 600 VAL Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 767 THR Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 808 VAL Chi-restraints excluded: chain U residue 846 TRP Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 992 MET Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1143 ASP Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1152 LEU Chi-restraints excluded: chain U residue 1158 ILE Chi-restraints excluded: chain U residue 1174 ILE Chi-restraints excluded: chain U residue 1201 VAL Chi-restraints excluded: chain U residue 1265 ARG Chi-restraints excluded: chain U residue 1288 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 946 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 9503 Z= 0.185 Angle : 0.581 9.196 12866 Z= 0.293 Chirality : 0.041 0.147 1473 Planarity : 0.003 0.031 1632 Dihedral : 8.506 135.038 1446 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 5.26 % Allowed : 19.74 % 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: -4.00 (0.22), residues: 1185 helix: -2.47 (0.18), residues: 645 sheet: -2.81 (0.73), residues: 27 loop : -2.77 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP U 846 HIS 0.002 0.000 HIS U1142 PHE 0.009 0.001 PHE U 783 TYR 0.016 0.001 TYR U1005 ARG 0.003 0.000 ARG U 299 *********************** 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 173 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 121 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8503 (mm) REVERT: U 154 ILE cc_start: 0.8730 (tp) cc_final: 0.8270 (tp) REVERT: U 371 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8534 (mt) REVERT: U 373 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8754 (tp) REVERT: U 478 MET cc_start: 0.6571 (ppp) cc_final: 0.5909 (mmt) REVERT: U 533 LYS cc_start: 0.7611 (tttm) cc_final: 0.7301 (pttt) REVERT: U 583 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6477 (p0) REVERT: U 610 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8001 (mp) REVERT: U 913 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7913 (mt) REVERT: U 918 GLN cc_start: 0.6375 (OUTLIER) cc_final: 0.5593 (tp-100) REVERT: U 920 ARG cc_start: 0.6017 (OUTLIER) cc_final: 0.4719 (mtt90) REVERT: U 928 ARG cc_start: 0.7448 (tpt170) cc_final: 0.5894 (ptp90) REVERT: U 933 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7636 (tt) REVERT: U 1031 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8436 (tt) REVERT: U 1037 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7292 (m-10) REVERT: U 1138 MET cc_start: 0.6688 (ttp) cc_final: 0.5866 (mmt) REVERT: U 1145 LYS cc_start: 0.8029 (mmmm) cc_final: 0.7473 (ptmt) REVERT: U 1161 GLN cc_start: 0.7132 (tt0) cc_final: 0.6361 (tp40) REVERT: U 1221 ARG cc_start: 0.6971 (tmm160) cc_final: 0.6492 (ppt170) REVERT: U 1270 CYS cc_start: 0.7876 (t) cc_final: 0.7239 (m) outliers start: 52 outliers final: 32 residues processed: 160 average time/residue: 0.2318 time to fit residues: 50.1232 Evaluate side-chains 157 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 114 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 185 MET Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 582 LEU Chi-restraints excluded: chain U residue 583 ASP Chi-restraints excluded: chain U residue 600 VAL Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 767 THR Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 808 VAL Chi-restraints excluded: chain U residue 846 TRP Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 992 MET Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1143 ASP Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1152 LEU Chi-restraints excluded: chain U residue 1158 ILE Chi-restraints excluded: chain U residue 1174 ILE Chi-restraints excluded: chain U residue 1201 VAL Chi-restraints excluded: chain U residue 1265 ARG Chi-restraints excluded: chain U residue 1288 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 0.1980 chunk 70 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 497 GLN ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 9503 Z= 0.171 Angle : 0.573 8.708 12866 Z= 0.289 Chirality : 0.040 0.143 1473 Planarity : 0.003 0.029 1632 Dihedral : 8.330 134.895 1446 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.35 % Allowed : 21.26 % Favored : 74.39 % 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: -3.75 (0.22), residues: 1185 helix: -2.27 (0.19), residues: 638 sheet: -2.69 (0.76), residues: 27 loop : -2.66 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP U 846 HIS 0.002 0.000 HIS U1142 PHE 0.007 0.001 PHE U 783 TYR 0.022 0.001 TYR U 538 ARG 0.003 0.000 ARG U 299 *********************** 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 167 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 124 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8532 (mm) REVERT: U 154 ILE cc_start: 0.8744 (tp) cc_final: 0.8285 (tp) REVERT: U 371 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8486 (mt) REVERT: U 478 MET cc_start: 0.6447 (ppp) cc_final: 0.5803 (mmt) REVERT: U 533 LYS cc_start: 0.7616 (tttm) cc_final: 0.7301 (pttt) REVERT: U 583 ASP cc_start: 0.6747 (OUTLIER) cc_final: 0.6339 (p0) REVERT: U 596 MET cc_start: 0.6564 (tpt) cc_final: 0.5772 (ptm) REVERT: U 913 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7861 (mt) REVERT: U 918 GLN cc_start: 0.6313 (OUTLIER) cc_final: 0.5494 (tp-100) REVERT: U 920 ARG cc_start: 0.6083 (OUTLIER) cc_final: 0.4758 (mtt90) REVERT: U 928 ARG cc_start: 0.7366 (tpt170) cc_final: 0.5874 (ptp90) REVERT: U 933 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7598 (tt) REVERT: U 1037 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7193 (m-10) REVERT: U 1145 LYS cc_start: 0.8094 (mmmm) cc_final: 0.7459 (ptmt) REVERT: U 1221 ARG cc_start: 0.6928 (tmm160) cc_final: 0.6476 (ppt170) REVERT: U 1270 CYS cc_start: 0.7769 (t) cc_final: 0.7122 (m) outliers start: 43 outliers final: 28 residues processed: 158 average time/residue: 0.2351 time to fit residues: 50.3906 Evaluate side-chains 152 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 116 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 583 ASP Chi-restraints excluded: chain U residue 600 VAL Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 946 ASN Chi-restraints excluded: chain U residue 992 MET Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1021 ILE Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1143 ASP Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1152 LEU Chi-restraints excluded: chain U residue 1158 ILE Chi-restraints excluded: chain U residue 1174 ILE Chi-restraints excluded: chain U residue 1201 VAL Chi-restraints excluded: chain U residue 1265 ARG Chi-restraints excluded: chain U residue 1288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.0670 chunk 78 optimal weight: 0.0040 chunk 118 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 0.4980 chunk 74 optimal weight: 8.9990 chunk 100 optimal weight: 0.0060 chunk 28 optimal weight: 2.9990 overall best weight: 0.7148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 946 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.192 9503 Z= 0.198 Angle : 0.578 8.315 12866 Z= 0.290 Chirality : 0.041 0.250 1473 Planarity : 0.003 0.029 1632 Dihedral : 8.253 134.788 1445 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 4.15 % Allowed : 21.76 % Favored : 74.09 % Cbeta Deviations : 0.09 % 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: -3.53 (0.22), residues: 1185 helix: -2.10 (0.19), residues: 631 sheet: -2.37 (0.77), residues: 39 loop : -2.54 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 493 HIS 0.003 0.000 HIS U1142 PHE 0.018 0.001 PHE U1014 TYR 0.012 0.001 TYR U 538 ARG 0.002 0.000 ARG U 637 ********************** 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 160 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 119 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 154 ILE cc_start: 0.8722 (tp) cc_final: 0.8256 (tp) REVERT: U 373 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8721 (tp) REVERT: U 478 MET cc_start: 0.6478 (ppp) cc_final: 0.5836 (mmt) REVERT: U 533 LYS cc_start: 0.7643 (tttm) cc_final: 0.7318 (pttt) REVERT: U 566 ARG cc_start: 0.7336 (ptp-170) cc_final: 0.6414 (mtm-85) REVERT: U 583 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.5985 (p0) REVERT: U 584 MET cc_start: 0.4493 (mpp) cc_final: 0.4243 (mpp) REVERT: U 596 MET cc_start: 0.6536 (tpt) cc_final: 0.5800 (ptm) REVERT: U 610 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7930 (mp) REVERT: U 913 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7886 (mt) REVERT: U 918 GLN cc_start: 0.6368 (OUTLIER) cc_final: 0.5556 (tp-100) REVERT: U 920 ARG cc_start: 0.6125 (OUTLIER) cc_final: 0.4782 (mtt90) REVERT: U 928 ARG cc_start: 0.7396 (tpt170) cc_final: 0.6027 (ptp90) REVERT: U 933 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7521 (tt) REVERT: U 1031 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8408 (tt) REVERT: U 1037 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7222 (m-10) REVERT: U 1145 LYS cc_start: 0.8174 (mmmm) cc_final: 0.7614 (ptmt) REVERT: U 1161 GLN cc_start: 0.7061 (tt0) cc_final: 0.6450 (tp40) REVERT: U 1221 ARG cc_start: 0.6912 (tmm160) cc_final: 0.6462 (ppt170) REVERT: U 1270 CYS cc_start: 0.7774 (t) cc_final: 0.7166 (m) outliers start: 41 outliers final: 30 residues processed: 154 average time/residue: 0.2426 time to fit residues: 50.6925 Evaluate side-chains 154 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 115 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 583 ASP Chi-restraints excluded: chain U residue 600 VAL Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 745 LEU Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 946 ASN Chi-restraints excluded: chain U residue 992 MET Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1021 ILE Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1143 ASP Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1152 LEU Chi-restraints excluded: chain U residue 1158 ILE Chi-restraints excluded: chain U residue 1174 ILE Chi-restraints excluded: chain U residue 1201 VAL Chi-restraints excluded: chain U residue 1265 ARG Chi-restraints excluded: chain U residue 1288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 946 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.175357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.133240 restraints weight = 13115.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131432 restraints weight = 7673.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131628 restraints weight = 6515.008| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 9503 Z= 0.164 Angle : 0.569 8.742 12866 Z= 0.286 Chirality : 0.040 0.148 1473 Planarity : 0.003 0.029 1632 Dihedral : 8.158 134.591 1445 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.05 % Allowed : 21.66 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.38 (0.23), residues: 1185 helix: -1.92 (0.20), residues: 632 sheet: -2.33 (0.77), residues: 40 loop : -2.55 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 493 HIS 0.003 0.000 HIS U1142 PHE 0.020 0.001 PHE U1014 TYR 0.017 0.001 TYR U1005 ARG 0.003 0.000 ARG U 948 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1960.12 seconds wall clock time: 35 minutes 58.65 seconds (2158.65 seconds total)