Starting phenix.real_space_refine on Tue Nov 14 19:04:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dv5_30870/11_2023/7dv5_30870_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dv5_30870/11_2023/7dv5_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_30870/11_2023/7dv5_30870.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dv5_30870/11_2023/7dv5_30870.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dv5_30870/11_2023/7dv5_30870_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dv5_30870/11_2023/7dv5_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-1.21rc1-5144/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: 5.39, per 1000 atoms: 0.58 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: 3.36 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: 2.52 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: 3.70 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 - 20.22: 5254 20.22 - 40.44: 315 40.44 - 60.66: 37 60.66 - 80.88: 16 80.88 - 101.10: 2 Dihedral angle restraints: 5624 sinusoidal: 2213 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 5621 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: 0.350 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: 2.300 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.100 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.030 ------------------------------------------------------------------------------- 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 : 13.902 101.104 3434 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 *********************** 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 : 0.957 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 206 average time/residue: 0.2619 time to fit residues: 70.8966 Evaluate side-chains 115 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 0.936 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1341 time to fit residues: 3.3741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 0.0670 chunk 48 optimal weight: 6.9990 chunk 93 optimal weight: 0.1980 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: 0.6130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 110 ASN U 372 ASN ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 867 GLN U 946 ASN U1097 ASN U1107 GLN U1124 GLN U1258 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2522 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= 0.162 Angle : 0.663 8.612 12866 Z= 0.337 Chirality : 0.042 0.164 1473 Planarity : 0.005 0.079 1632 Dihedral : 7.361 80.929 1295 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.43 % Allowed : 13.87 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.77 (0.17), residues: 1185 helix: -4.17 (0.11), residues: 643 sheet: -3.82 (0.67), residues: 26 loop : -3.20 (0.23), residues: 516 *********************** 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 168 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 5 residues processed: 162 average time/residue: 0.2348 time to fit residues: 52.0903 Evaluate side-chains 118 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2269 time to fit residues: 2.9903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 0.0050 chunk 73 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 116 optimal weight: 0.0980 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 72 HIS ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 946 ASN U1124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9503 Z= 0.224 Angle : 0.640 8.261 12866 Z= 0.325 Chirality : 0.043 0.143 1473 Planarity : 0.004 0.041 1632 Dihedral : 7.053 82.005 1295 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.14 % Allowed : 14.68 % Favored : 82.19 % 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: -5.16 (0.19), residues: 1185 helix: -3.60 (0.15), residues: 638 sheet: -3.69 (0.65), residues: 26 loop : -3.04 (0.24), residues: 521 *********************** 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 149 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 118 time to evaluate : 0.939 Fit side-chains outliers start: 31 outliers final: 16 residues processed: 144 average time/residue: 0.2221 time to fit residues: 44.5278 Evaluate side-chains 123 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0877 time to fit residues: 3.9077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 424 ASN ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 563 GLN ** 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: 0.7762 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9503 Z= 0.246 Angle : 0.634 9.650 12866 Z= 0.321 Chirality : 0.043 0.140 1473 Planarity : 0.004 0.038 1632 Dihedral : 6.897 82.203 1295 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 3.04 % Allowed : 15.89 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.20), residues: 1185 helix: -3.31 (0.16), residues: 658 sheet: -3.53 (0.59), residues: 26 loop : -3.02 (0.25), residues: 501 *********************** 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 155 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 10 residues processed: 149 average time/residue: 0.2283 time to fit residues: 47.0454 Evaluate side-chains 120 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0879 time to fit residues: 3.0373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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: 0.7802 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9503 Z= 0.301 Angle : 0.659 10.057 12866 Z= 0.332 Chirality : 0.045 0.137 1473 Planarity : 0.004 0.035 1632 Dihedral : 6.894 82.991 1295 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 1.82 % Allowed : 17.91 % Favored : 80.26 % 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: -4.59 (0.21), residues: 1185 helix: -3.08 (0.17), residues: 644 sheet: -3.58 (0.52), residues: 26 loop : -2.83 (0.25), residues: 515 *********************** 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 132 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 1.037 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 127 average time/residue: 0.2303 time to fit residues: 40.7730 Evaluate side-chains 119 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1403 time to fit residues: 3.4124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 484 HIS U 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9503 Z= 0.276 Angle : 0.640 9.628 12866 Z= 0.324 Chirality : 0.044 0.189 1473 Planarity : 0.004 0.035 1632 Dihedral : 6.810 82.856 1295 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 1.82 % Allowed : 19.03 % Favored : 79.15 % 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: -4.42 (0.21), residues: 1185 helix: -2.90 (0.17), residues: 643 sheet: -3.53 (0.52), residues: 26 loop : -2.81 (0.25), residues: 516 *********************** 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 136 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.932 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 129 average time/residue: 0.2302 time to fit residues: 41.3858 Evaluate side-chains 119 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0961 time to fit residues: 3.1180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 0.0870 chunk 84 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 64 optimal weight: 0.1980 chunk 114 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 563 GLN U 946 ASN U1281 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.101 9503 Z= 0.156 Angle : 0.563 8.571 12866 Z= 0.286 Chirality : 0.040 0.167 1473 Planarity : 0.003 0.032 1632 Dihedral : 6.294 80.821 1295 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 1.21 % Allowed : 19.43 % Favored : 79.35 % 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: -4.12 (0.21), residues: 1185 helix: -2.61 (0.18), residues: 640 sheet: -3.28 (0.59), residues: 26 loop : -2.75 (0.25), residues: 519 *********************** 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 137 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 133 average time/residue: 0.2363 time to fit residues: 43.8245 Evaluate side-chains 112 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1120 time to fit residues: 1.8483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 0.0980 chunk 56 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 497 GLN U 563 GLN U 946 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 9503 Z= 0.190 Angle : 0.580 8.170 12866 Z= 0.293 Chirality : 0.041 0.168 1473 Planarity : 0.003 0.031 1632 Dihedral : 6.217 81.302 1295 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 1.01 % Allowed : 21.36 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.22), residues: 1185 helix: -2.46 (0.19), residues: 644 sheet: -3.06 (0.64), residues: 26 loop : -2.75 (0.25), residues: 515 *********************** 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 131 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 125 average time/residue: 0.2420 time to fit residues: 41.9059 Evaluate side-chains 118 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0985 time to fit residues: 1.8886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 96 optimal weight: 0.0570 chunk 101 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 946 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 9503 Z= 0.243 Angle : 0.598 8.145 12866 Z= 0.305 Chirality : 0.043 0.165 1473 Planarity : 0.003 0.032 1632 Dihedral : 6.257 82.253 1295 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 0.71 % Allowed : 22.06 % Favored : 77.23 % 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: -3.90 (0.22), residues: 1185 helix: -2.41 (0.19), residues: 634 sheet: -3.22 (0.65), residues: 27 loop : -2.67 (0.25), residues: 524 *********************** 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 122 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 120 average time/residue: 0.2360 time to fit residues: 39.0268 Evaluate side-chains 114 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0832 time to fit residues: 1.6488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 118 optimal weight: 0.0470 chunk 109 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 946 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4164 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= 0.176 Angle : 0.587 8.598 12866 Z= 0.295 Chirality : 0.041 0.164 1473 Planarity : 0.003 0.031 1632 Dihedral : 6.005 81.702 1295 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.51 % Allowed : 22.27 % Favored : 77.23 % 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: -3.74 (0.22), residues: 1185 helix: -2.28 (0.19), residues: 636 sheet: -3.31 (0.63), residues: 32 loop : -2.57 (0.26), residues: 517 ********************** 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 122 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 120 average time/residue: 0.2696 time to fit residues: 44.4726 Evaluate side-chains 114 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0896 time to fit residues: 1.7928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 97 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 5 optimal weight: 0.0770 chunk 68 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 563 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.180527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.138042 restraints weight = 13069.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138512 restraints weight = 9916.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.139165 restraints weight = 7554.526| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9503 Z= 0.134 Angle : 0.557 8.615 12866 Z= 0.279 Chirality : 0.040 0.167 1473 Planarity : 0.003 0.029 1632 Dihedral : 5.525 79.924 1295 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.20 % Allowed : 22.67 % Favored : 77.13 % 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: -3.47 (0.22), residues: 1185 helix: -1.97 (0.20), residues: 637 sheet: -2.67 (0.75), residues: 39 loop : -2.60 (0.25), residues: 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1895.73 seconds wall clock time: 35 minutes 28.08 seconds (2128.08 seconds total)