Starting phenix.real_space_refine on Thu Mar 5 08:39:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kpx_22991/03_2026/7kpx_22991.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kpx_22991/03_2026/7kpx_22991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kpx_22991/03_2026/7kpx_22991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kpx_22991/03_2026/7kpx_22991.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kpx_22991/03_2026/7kpx_22991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kpx_22991/03_2026/7kpx_22991.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 13241 2.51 5 N 3636 2.21 5 O 3808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20762 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2952 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 17, 'TRANS': 339} Chain breaks: 3 Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2436 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 15, 'TRANS': 274} Chain breaks: 2 Chain: "C" Number of atoms: 8362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1352, 8362 Classifications: {'peptide': 1352} Incomplete info: {'truncation_to_alanine': 830} Link IDs: {'PTRANS': 41, 'TRANS': 1310} Chain breaks: 3 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 2975 Unresolved non-hydrogen angles: 3799 Unresolved non-hydrogen dihedrals: 2479 Unresolved non-hydrogen chiralities: 290 Planarities with less than four sites: {'ASN:plan1': 64, 'ARG:plan': 20, 'ASP:plan': 45, 'PHE:plan': 60, 'GLN:plan1': 43, 'GLU:plan': 50, 'TRP:plan': 8, 'TYR:plan': 32, 'HIS:plan': 17} Unresolved non-hydrogen planarities: 1540 Chain: "D" Number of atoms: 7012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 7012 Classifications: {'peptide': 876} Link IDs: {'PTRANS': 51, 'TRANS': 824} Chain breaks: 2 Time building chain proxies: 4.96, per 1000 atoms: 0.24 Number of scatterers: 20762 At special positions: 0 Unit cell: (123.05, 172.27, 208.65, 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 77 16.00 O 3808 8.00 N 3636 7.00 C 13241 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5588 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 14 sheets defined 53.2% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.758A pdb=" N ALA A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 212 removed outlier: 3.898A pdb=" N GLU A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 259 through 280 removed outlier: 3.733A pdb=" N ASN A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.955A pdb=" N ARG A 331 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 421 through 428 Processing helix chain 'A' and resid 435 through 444 removed outlier: 3.702A pdb=" N LEU A 439 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 34 removed outlier: 4.556A pdb=" N GLN B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 90 Processing helix chain 'B' and resid 92 through 110 removed outlier: 3.728A pdb=" N LEU B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 132 Processing helix chain 'B' and resid 137 through 149 Processing helix chain 'B' and resid 156 through 171 removed outlier: 4.108A pdb=" N VAL B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 removed outlier: 4.032A pdb=" N SER B 183 " --> pdb=" O HIS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 225 through 243 removed outlier: 3.744A pdb=" N ILE B 229 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 279 Processing helix chain 'B' and resid 285 through 300 Processing helix chain 'B' and resid 304 through 317 removed outlier: 4.236A pdb=" N ILE B 308 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 49 removed outlier: 3.833A pdb=" N ASP C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 97 Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.623A pdb=" N HIS C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 152 through 164 Processing helix chain 'C' and resid 166 through 188 Processing helix chain 'C' and resid 198 through 225 removed outlier: 4.105A pdb=" N MET C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 252 removed outlier: 3.917A pdb=" N ARG C 238 " --> pdb=" O ARG C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 272 removed outlier: 3.520A pdb=" N HIS C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET C 272 " --> pdb=" O PHE C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 276 No H-bonds generated for 'chain 'C' and resid 274 through 276' Processing helix chain 'C' and resid 277 through 288 removed outlier: 3.606A pdb=" N HIS C 283 " --> pdb=" O PRO C 279 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.674A pdb=" N CYS C 293 " --> pdb=" O TRP C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 333 removed outlier: 3.800A pdb=" N THR C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER C 333 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 372 removed outlier: 3.616A pdb=" N ASN C 350 " --> pdb=" O ASP C 346 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 357 " --> pdb=" O ILE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 393 Processing helix chain 'C' and resid 399 through 413 Processing helix chain 'C' and resid 419 through 428 removed outlier: 3.694A pdb=" N SER C 424 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C 426 " --> pdb=" O ASN C 422 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG C 427 " --> pdb=" O ASN C 423 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 444 removed outlier: 3.524A pdb=" N ILE C 443 " --> pdb=" O PHE C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 466 removed outlier: 3.587A pdb=" N PHE C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 476 removed outlier: 4.112A pdb=" N GLU C 474 " --> pdb=" O ASP C 470 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP C 476 " --> pdb=" O PRO C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 496 removed outlier: 3.537A pdb=" N LYS C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE C 495 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 517 Processing helix chain 'C' and resid 524 through 543 removed outlier: 4.218A pdb=" N ASP C 528 " --> pdb=" O SER C 524 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU C 529 " --> pdb=" O THR C 525 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 542 " --> pdb=" O ILE C 538 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE C 543 " --> pdb=" O TRP C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 572 removed outlier: 3.521A pdb=" N GLN C 552 " --> pdb=" O ASN C 548 " (cutoff:3.500A) Proline residue: C 561 - end of helix removed outlier: 3.547A pdb=" N LEU C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR C 572 " --> pdb=" O ASN C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 588 Proline residue: C 579 - end of helix removed outlier: 3.782A pdb=" N ILE C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER C 587 " --> pdb=" O ARG C 583 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER C 588 " --> pdb=" O LYS C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 605 removed outlier: 3.636A pdb=" N SER C 596 " --> pdb=" O TYR C 592 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN C 597 " --> pdb=" O LEU C 593 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 624 removed outlier: 4.648A pdb=" N MET C 615 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS C 616 " --> pdb=" O SER C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 651 removed outlier: 3.951A pdb=" N MET C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 664 Processing helix chain 'C' and resid 667 through 685 removed outlier: 4.275A pdb=" N LYS C 671 " --> pdb=" O PRO C 667 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 676 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP C 677 " --> pdb=" O MET C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 704 removed outlier: 3.603A pdb=" N LEU C 695 " --> pdb=" O ASN C 691 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE C 704 " --> pdb=" O LYS C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 721 removed outlier: 3.538A pdb=" N HIS C 711 " --> pdb=" O GLU C 707 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 740 removed outlier: 3.637A pdb=" N LEU C 734 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET C 735 " --> pdb=" O LEU C 731 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP C 736 " --> pdb=" O GLU C 732 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS C 740 " --> pdb=" O ASP C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 747 removed outlier: 4.064A pdb=" N SER C 746 " --> pdb=" O GLN C 742 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN C 747 " --> pdb=" O LYS C 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 742 through 747' Processing helix chain 'C' and resid 748 through 763 Processing helix chain 'C' and resid 773 through 788 Proline residue: C 782 - end of helix Processing helix chain 'C' and resid 791 through 813 removed outlier: 3.501A pdb=" N LYS C 796 " --> pdb=" O PRO C 792 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 803 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU C 804 " --> pdb=" O ASP C 800 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 805 " --> pdb=" O LEU C 801 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS C 813 " --> pdb=" O TYR C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 827 removed outlier: 4.024A pdb=" N LYS C 818 " --> pdb=" O LEU C 814 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 825 " --> pdb=" O ASN C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 854 removed outlier: 4.641A pdb=" N THR C 843 " --> pdb=" O ALA C 839 " (cutoff:3.500A) Proline residue: C 847 - end of helix removed outlier: 3.762A pdb=" N VAL C 852 " --> pdb=" O GLU C 848 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE C 854 " --> pdb=" O PHE C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 878 removed outlier: 4.686A pdb=" N ILE C 864 " --> pdb=" O ASN C 860 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP C 865 " --> pdb=" O SER C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 893 Processing helix chain 'C' and resid 896 through 907 removed outlier: 3.621A pdb=" N LYS C 906 " --> pdb=" O ASP C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 916 Processing helix chain 'C' and resid 918 through 927 removed outlier: 3.585A pdb=" N GLN C 923 " --> pdb=" O PHE C 919 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY C 927 " --> pdb=" O GLN C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 948 removed outlier: 3.815A pdb=" N ASN C 941 " --> pdb=" O ILE C 937 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 948 " --> pdb=" O GLY C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 963 removed outlier: 3.781A pdb=" N PHE C 962 " --> pdb=" O ILE C 958 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 983 Processing helix chain 'C' and resid 986 through 1004 removed outlier: 3.502A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Proline residue: C1000 - end of helix Processing helix chain 'C' and resid 1006 through 1023 removed outlier: 3.793A pdb=" N LEU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN C1015 " --> pdb=" O MET C1011 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1072 through 1083 removed outlier: 4.261A pdb=" N GLU C1076 " --> pdb=" O ILE C1072 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE C1083 " --> pdb=" O VAL C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1087 through 1103 Processing helix chain 'C' and resid 1106 through 1126 removed outlier: 3.749A pdb=" N GLU C1111 " --> pdb=" O ALA C1107 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C1116 " --> pdb=" O ASP C1112 " (cutoff:3.500A) Processing helix chain 'C' and resid 1128 through 1146 Processing helix chain 'C' and resid 1146 through 1172 removed outlier: 3.998A pdb=" N ASN C1169 " --> pdb=" O LYS C1165 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR C1170 " --> pdb=" O ILE C1166 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C1172 " --> pdb=" O ASP C1168 " (cutoff:3.500A) Processing helix chain 'C' and resid 1174 through 1196 removed outlier: 3.547A pdb=" N LEU C1181 " --> pdb=" O ILE C1177 " (cutoff:3.500A) Processing helix chain 'C' and resid 1204 through 1218 removed outlier: 3.614A pdb=" N ARG C1208 " --> pdb=" O ILE C1204 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C1218 " --> pdb=" O ASN C1214 " (cutoff:3.500A) Processing helix chain 'C' and resid 1218 through 1224 Processing helix chain 'C' and resid 1225 through 1239 removed outlier: 4.166A pdb=" N ILE C1239 " --> pdb=" O HIS C1235 " (cutoff:3.500A) Processing helix chain 'C' and resid 1239 through 1251 removed outlier: 4.433A pdb=" N ILE C1243 " --> pdb=" O ILE C1239 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C1245 " --> pdb=" O GLN C1241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP C1250 " --> pdb=" O ASP C1246 " (cutoff:3.500A) Processing helix chain 'C' and resid 1259 through 1272 Processing helix chain 'C' and resid 1276 through 1296 Processing helix chain 'C' and resid 1307 through 1314 Processing helix chain 'C' and resid 1319 through 1326 removed outlier: 3.673A pdb=" N VAL C1323 " --> pdb=" O VAL C1319 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C1326 " --> pdb=" O PHE C1322 " (cutoff:3.500A) Processing helix chain 'C' and resid 1413 through 1417 Processing helix chain 'D' and resid 33 through 37 removed outlier: 4.050A pdb=" N GLN D 36 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN D 37 " --> pdb=" O LYS D 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 33 through 37' Processing helix chain 'D' and resid 39 through 50 removed outlier: 3.971A pdb=" N PHE D 46 " --> pdb=" O ILE D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 125 removed outlier: 3.952A pdb=" N LYS D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 179 through 184 Processing helix chain 'D' and resid 216 through 222 removed outlier: 3.681A pdb=" N THR D 220 " --> pdb=" O GLU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.845A pdb=" N ALA D 300 " --> pdb=" O CYS D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 822 removed outlier: 3.658A pdb=" N ARG D 822 " --> pdb=" O PRO D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 859 removed outlier: 4.133A pdb=" N THR D 859 " --> pdb=" O GLU D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 893 Processing helix chain 'D' and resid 900 through 904 removed outlier: 3.955A pdb=" N THR D 904 " --> pdb=" O ASN D 900 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 900 through 904' Processing helix chain 'D' and resid 958 through 975 removed outlier: 3.649A pdb=" N CYS D 962 " --> pdb=" O PHE D 958 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER D 964 " --> pdb=" O GLU D 960 " (cutoff:3.500A) Proline residue: D 967 - end of helix Processing helix chain 'D' and resid 1001 through 1019 Processing helix chain 'D' and resid 1042 through 1059 removed outlier: 3.607A pdb=" N ALA D1059 " --> pdb=" O ASN D1055 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1078 Processing helix chain 'D' and resid 1085 through 1095 removed outlier: 3.679A pdb=" N VAL D1089 " --> pdb=" O GLN D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1188 through 1207 removed outlier: 3.876A pdb=" N ASP D1192 " --> pdb=" O ARG D1188 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP D1199 " --> pdb=" O CYS D1195 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1236 removed outlier: 3.587A pdb=" N LEU D1229 " --> pdb=" O PRO D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1265 through 1271 removed outlier: 4.055A pdb=" N ASP D1271 " --> pdb=" O PRO D1267 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1364 removed outlier: 3.622A pdb=" N LEU D1350 " --> pdb=" O ASP D1346 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN D1360 " --> pdb=" O GLU D1356 " (cutoff:3.500A) Processing helix chain 'D' and resid 1365 through 1367 No H-bonds generated for 'chain 'D' and resid 1365 through 1367' Processing helix chain 'D' and resid 1379 through 1392 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 81 removed outlier: 6.803A pdb=" N LYS A 91 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TYR A 80 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL A 89 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 88 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 180 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 224 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 242 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.596A pdb=" N ILE C 119 " --> pdb=" O ILE C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 1373 through 1377 removed outlier: 6.838A pdb=" N ILE C1366 " --> pdb=" O VAL C1375 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR C1377 " --> pdb=" O TRP C1364 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TRP C1364 " --> pdb=" O THR C1377 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C1365 " --> pdb=" O ARG D1289 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU D1287 " --> pdb=" O TYR C1367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 153 Processing sheet with id=AA6, first strand: chain 'D' and resid 56 through 59 removed outlier: 4.626A pdb=" N LEU D 56 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=AA8, first strand: chain 'D' and resid 171 through 172 removed outlier: 11.998A pdb=" N HIS D 186 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N LEU D 199 " --> pdb=" O HIS D 186 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU D 188 " --> pdb=" O MET D 197 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 839 through 842 Processing sheet with id=AB1, first strand: chain 'D' and resid 905 through 910 removed outlier: 5.294A pdb=" N SER D1317 " --> pdb=" O PHE D1300 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ARG D1316 " --> pdb=" O LEU D1339 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU D1339 " --> pdb=" O ARG D1316 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D1244 " --> pdb=" O LEU D1340 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N SER D1150 " --> pdb=" O CYS D1214 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE D1216 " --> pdb=" O SER D1150 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D1152 " --> pdb=" O ILE D1216 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR D1218 " --> pdb=" O ILE D1152 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU D1154 " --> pdb=" O THR D1218 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 905 through 910 removed outlier: 5.294A pdb=" N SER D1317 " --> pdb=" O PHE D1300 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ARG D1316 " --> pdb=" O LEU D1339 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU D1339 " --> pdb=" O ARG D1316 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D1244 " --> pdb=" O LEU D1340 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE D1213 " --> pdb=" O HIS D1241 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 915 through 919 Processing sheet with id=AB4, first strand: chain 'D' and resid 950 through 953 removed outlier: 6.659A pdb=" N LYS D 950 " --> pdb=" O LEU D1030 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE D1032 " --> pdb=" O LYS D 950 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU D 952 " --> pdb=" O ILE D1032 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE D1029 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LYS D1069 " --> pdb=" O ILE D1029 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE D1031 " --> pdb=" O LYS D1069 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE D1071 " --> pdb=" O ILE D1031 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU D1033 " --> pdb=" O ILE D1071 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 1256 through 1257 1076 hydrogen bonds defined for protein. 3153 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: 4.07 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3707 1.32 - 1.45: 5256 1.45 - 1.57: 12102 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 21185 Sorted by residual: bond pdb=" C LEU C 661 " pdb=" O LEU C 661 " ideal model delta sigma weight residual 1.237 1.296 -0.059 1.17e-02 7.31e+03 2.56e+01 bond pdb=" C ARG C 802 " pdb=" O ARG C 802 " ideal model delta sigma weight residual 1.237 1.293 -0.056 1.17e-02 7.31e+03 2.30e+01 bond pdb=" C GLY C 944 " pdb=" O GLY C 944 " ideal model delta sigma weight residual 1.234 1.290 -0.056 1.20e-02 6.94e+03 2.20e+01 bond pdb=" C VAL C 808 " pdb=" O VAL C 808 " ideal model delta sigma weight residual 1.237 1.288 -0.050 1.17e-02 7.31e+03 1.85e+01 bond pdb=" C ILE C 912 " pdb=" O ILE C 912 " ideal model delta sigma weight residual 1.237 1.283 -0.046 1.17e-02 7.31e+03 1.56e+01 ... (remaining 21180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 28400 3.29 - 6.58: 416 6.58 - 9.88: 80 9.88 - 13.17: 7 13.17 - 16.46: 2 Bond angle restraints: 28905 Sorted by residual: angle pdb=" N LEU C 494 " pdb=" CA LEU C 494 " pdb=" C LEU C 494 " ideal model delta sigma weight residual 111.14 127.60 -16.46 1.08e+00 8.57e-01 2.32e+02 angle pdb=" N ILE C 495 " pdb=" CA ILE C 495 " pdb=" C ILE C 495 " ideal model delta sigma weight residual 113.20 124.91 -11.71 9.60e-01 1.09e+00 1.49e+02 angle pdb=" N PRO D1027 " pdb=" CA PRO D1027 " pdb=" C PRO D1027 " ideal model delta sigma weight residual 110.70 123.97 -13.27 1.22e+00 6.72e-01 1.18e+02 angle pdb=" N ASP C1073 " pdb=" CA ASP C1073 " pdb=" C ASP C1073 " ideal model delta sigma weight residual 111.28 123.07 -11.79 1.09e+00 8.42e-01 1.17e+02 angle pdb=" C PRO D1027 " pdb=" N PRO D1028 " pdb=" CA PRO D1028 " ideal model delta sigma weight residual 119.76 109.94 9.82 1.03e+00 9.43e-01 9.10e+01 ... (remaining 28900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11378 17.94 - 35.88: 903 35.88 - 53.83: 330 53.83 - 71.77: 90 71.77 - 89.71: 13 Dihedral angle restraints: 12714 sinusoidal: 4172 harmonic: 8542 Sorted by residual: dihedral pdb=" CA LEU D 59 " pdb=" C LEU D 59 " pdb=" N LEU D 60 " pdb=" CA LEU D 60 " ideal model delta harmonic sigma weight residual 180.00 151.79 28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" N PRO C 613 " pdb=" C PRO C 613 " pdb=" CA PRO C 613 " pdb=" CB PRO C 613 " ideal model delta harmonic sigma weight residual 115.10 129.00 -13.90 0 2.50e+00 1.60e-01 3.09e+01 dihedral pdb=" CA ASP D 12 " pdb=" C ASP D 12 " pdb=" N VAL D 13 " pdb=" CA VAL D 13 " ideal model delta harmonic sigma weight residual 180.00 152.21 27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 12711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3171 0.122 - 0.245: 193 0.245 - 0.367: 28 0.367 - 0.490: 7 0.490 - 0.612: 2 Chirality restraints: 3401 Sorted by residual: chirality pdb=" CA LEU C 494 " pdb=" N LEU C 494 " pdb=" C LEU C 494 " pdb=" CB LEU C 494 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.37e+00 chirality pdb=" CA PRO C 613 " pdb=" N PRO C 613 " pdb=" C PRO C 613 " pdb=" CB PRO C 613 " both_signs ideal model delta sigma weight residual False 2.72 2.18 0.54 2.00e-01 2.50e+01 7.21e+00 chirality pdb=" CA PRO C1255 " pdb=" N PRO C1255 " pdb=" C PRO C1255 " pdb=" CB PRO C1255 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.75e+00 ... (remaining 3398 not shown) Planarity restraints: 3735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 340 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C GLU C 340 " 0.070 2.00e-02 2.50e+03 pdb=" O GLU C 340 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN C 341 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C1082 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ASP C1082 " -0.061 2.00e-02 2.50e+03 pdb=" O ASP C1082 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE C1083 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 667 " 0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C PRO C 667 " -0.061 2.00e-02 2.50e+03 pdb=" O PRO C 667 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU C 668 " 0.020 2.00e-02 2.50e+03 ... (remaining 3732 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 101 2.50 - 3.10: 14092 3.10 - 3.70: 31653 3.70 - 4.30: 39545 4.30 - 4.90: 66371 Nonbonded interactions: 151762 Sorted by model distance: nonbonded pdb=" O SER C 373 " pdb=" O PHE C1317 " model vdw 1.894 3.040 nonbonded pdb=" O SER C 373 " pdb=" CA GLN C1318 " model vdw 2.132 3.470 nonbonded pdb=" O SER C 373 " pdb=" CB GLN C1318 " model vdw 2.157 3.440 nonbonded pdb=" N ASP B 65 " pdb=" OD1 ASP B 65 " model vdw 2.193 3.120 nonbonded pdb=" O LEU B 66 " pdb=" ND1 HIS B 67 " model vdw 2.270 3.120 ... (remaining 151757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 6.060 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.610 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 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 : 0.006 0.068 21185 Z= 0.366 Angle : 1.066 16.459 28905 Z= 0.739 Chirality : 0.071 0.612 3401 Planarity : 0.007 0.082 3735 Dihedral : 16.336 89.712 7126 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.76 % Favored : 91.89 % Rotamer: Outliers : 17.46 % Allowed : 13.77 % Favored : 68.76 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.15), residues: 2847 helix: 0.63 (0.15), residues: 1358 sheet: -2.28 (0.32), residues: 211 loop : -3.17 (0.15), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 19 TYR 0.026 0.002 TYR C 178 PHE 0.023 0.002 PHE D 294 TRP 0.026 0.002 TRP B 14 HIS 0.010 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00571 (21185) covalent geometry : angle 1.06648 (28905) hydrogen bonds : bond 0.18603 ( 1053) hydrogen bonds : angle 6.28228 ( 3153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 322 poor density : 393 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 VAL cc_start: 0.2279 (OUTLIER) cc_final: 0.2015 (p) REVERT: A 211 CYS cc_start: 0.7930 (t) cc_final: 0.7490 (t) REVERT: A 232 VAL cc_start: 0.7456 (OUTLIER) cc_final: 0.6719 (m) REVERT: A 278 HIS cc_start: 0.8794 (OUTLIER) cc_final: 0.8534 (m-70) REVERT: A 325 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8809 (p) REVERT: A 347 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8264 (m-30) REVERT: A 350 SER cc_start: 0.9213 (m) cc_final: 0.9008 (p) REVERT: A 446 TYR cc_start: 0.6469 (OUTLIER) cc_final: 0.5951 (p90) REVERT: B 45 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.6894 (t70) REVERT: B 185 LYS cc_start: 0.9473 (OUTLIER) cc_final: 0.8899 (ttmt) REVERT: B 212 ILE cc_start: 0.9692 (mt) cc_final: 0.9471 (mt) REVERT: B 233 CYS cc_start: 0.9227 (m) cc_final: 0.8987 (m) REVERT: B 237 THR cc_start: 0.9003 (m) cc_final: 0.8420 (t) REVERT: B 269 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7987 (tp40) REVERT: B 280 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.8237 (mm) REVERT: B 281 VAL cc_start: 0.9195 (OUTLIER) cc_final: 0.8713 (m) REVERT: C 16 LEU cc_start: 0.8614 (tp) cc_final: 0.8369 (mp) REVERT: C 164 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.5922 (m-80) REVERT: C 203 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7560 (t-90) REVERT: C 218 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7849 (tptp) REVERT: C 337 ILE cc_start: 0.6295 (OUTLIER) cc_final: 0.5417 (tp) REVERT: C 392 PHE cc_start: 0.7923 (m-80) cc_final: 0.7686 (m-10) REVERT: C 406 MET cc_start: 0.9406 (ttm) cc_final: 0.8494 (tmm) REVERT: C 409 LYS cc_start: 0.9161 (tptt) cc_final: 0.8734 (ttmt) REVERT: C 1425 ASN cc_start: 0.8827 (m-40) cc_final: 0.8198 (m110) REVERT: D 25 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8094 (ptmm) REVERT: D 26 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8561 (tt) REVERT: D 34 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7219 (tptp) REVERT: D 45 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: D 47 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8215 (tpp) REVERT: D 113 LEU cc_start: 0.9343 (tp) cc_final: 0.9119 (tt) REVERT: D 858 VAL cc_start: 0.9393 (OUTLIER) cc_final: 0.9073 (p) REVERT: D 861 TYR cc_start: 0.7939 (m-80) cc_final: 0.7565 (m-10) REVERT: D 1068 LEU cc_start: 0.8821 (tp) cc_final: 0.8570 (tt) REVERT: D 1083 VAL cc_start: 0.9311 (OUTLIER) cc_final: 0.9036 (t) REVERT: D 1388 MET cc_start: 0.8510 (mtm) cc_final: 0.8295 (mtt) outliers start: 322 outliers final: 65 residues processed: 645 average time/residue: 0.1383 time to fit residues: 139.1035 Evaluate side-chains 301 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 214 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS A 312 HIS A 381 GLN B 100 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN B 291 GLN C 17 HIS C 56 HIS C 85 GLN ** C 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS D 198 HIS ** D 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1200 ASN D1221 ASN D1296 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.072337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.055952 restraints weight = 117517.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.057369 restraints weight = 68835.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.058332 restraints weight = 47662.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.058968 restraints weight = 36913.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.059350 restraints weight = 31058.193| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 21185 Z= 0.257 Angle : 0.781 10.198 28905 Z= 0.417 Chirality : 0.048 0.310 3401 Planarity : 0.005 0.074 3735 Dihedral : 5.976 39.047 3030 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.01 % Favored : 91.85 % Rotamer: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.63 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.15), residues: 2847 helix: 0.94 (0.13), residues: 1421 sheet: -2.05 (0.32), residues: 214 loop : -3.05 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 118 TYR 0.026 0.002 TYR A 462 PHE 0.030 0.002 PHE D 819 TRP 0.036 0.003 TRP D1332 HIS 0.012 0.002 HIS C 149 Details of bonding type rmsd covalent geometry : bond 0.00550 (21185) covalent geometry : angle 0.78138 (28905) hydrogen bonds : bond 0.04851 ( 1053) hydrogen bonds : angle 4.75845 ( 3153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 CYS cc_start: 0.8771 (t) cc_final: 0.8316 (p) REVERT: A 453 ASP cc_start: 0.8465 (p0) cc_final: 0.8123 (p0) REVERT: B 163 PHE cc_start: 0.8983 (t80) cc_final: 0.8657 (t80) REVERT: B 214 ASP cc_start: 0.8999 (t0) cc_final: 0.8723 (t0) REVERT: B 292 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8674 (tp30) REVERT: B 307 TRP cc_start: 0.7715 (t60) cc_final: 0.7452 (t60) REVERT: B 311 LEU cc_start: 0.9614 (mt) cc_final: 0.9389 (mt) REVERT: C 16 LEU cc_start: 0.8993 (tp) cc_final: 0.8692 (mt) REVERT: C 388 LYS cc_start: 0.9155 (mtpt) cc_final: 0.8791 (mttp) REVERT: D 158 ASP cc_start: 0.8335 (m-30) cc_final: 0.8092 (m-30) REVERT: D 1096 MET cc_start: 0.8987 (mmm) cc_final: 0.8593 (mmm) REVERT: D 1214 CYS cc_start: 0.8672 (t) cc_final: 0.8393 (t) REVERT: D 1223 ILE cc_start: 0.8939 (tt) cc_final: 0.8508 (pt) REVERT: D 1352 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8758 (tp30) REVERT: D 1388 MET cc_start: 0.8808 (mtm) cc_final: 0.8518 (mtt) outliers start: 1 outliers final: 1 residues processed: 234 average time/residue: 0.1238 time to fit residues: 47.8331 Evaluate side-chains 164 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 164 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 256 optimal weight: 3.9990 chunk 175 optimal weight: 40.0000 chunk 93 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 182 optimal weight: 20.0000 chunk 243 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN D 148 GLN D 921 HIS ** D 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 988 ASN D1221 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.069323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.053214 restraints weight = 118054.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.054602 restraints weight = 68576.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.055553 restraints weight = 47248.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.056191 restraints weight = 36375.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.056570 restraints weight = 30384.088| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21185 Z= 0.228 Angle : 0.720 14.080 28905 Z= 0.380 Chirality : 0.046 0.214 3401 Planarity : 0.005 0.071 3735 Dihedral : 5.536 32.849 3030 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.39 % Favored : 91.46 % Rotamer: Outliers : 0.22 % Allowed : 5.86 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.16), residues: 2847 helix: 1.35 (0.14), residues: 1403 sheet: -1.67 (0.35), residues: 211 loop : -2.90 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1158 TYR 0.039 0.003 TYR B 72 PHE 0.021 0.002 PHE D 819 TRP 0.037 0.002 TRP D1332 HIS 0.011 0.002 HIS D 247 Details of bonding type rmsd covalent geometry : bond 0.00499 (21185) covalent geometry : angle 0.71975 (28905) hydrogen bonds : bond 0.04263 ( 1053) hydrogen bonds : angle 4.45314 ( 3153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 197 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 CYS cc_start: 0.8843 (t) cc_final: 0.8209 (t) REVERT: A 262 MET cc_start: 0.9041 (tpp) cc_final: 0.8727 (tpp) REVERT: A 350 SER cc_start: 0.9504 (m) cc_final: 0.9269 (p) REVERT: A 453 ASP cc_start: 0.8594 (p0) cc_final: 0.8342 (p0) REVERT: B 44 MET cc_start: 0.4970 (tpt) cc_final: 0.4672 (tpt) REVERT: B 214 ASP cc_start: 0.9059 (t0) cc_final: 0.8819 (t0) REVERT: B 292 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8703 (tp30) REVERT: C 1422 GLU cc_start: 0.8660 (tp30) cc_final: 0.8444 (tp30) REVERT: D 158 ASP cc_start: 0.8530 (m-30) cc_final: 0.8288 (m-30) REVERT: D 228 ILE cc_start: 0.8805 (pt) cc_final: 0.8459 (mm) REVERT: D 861 TYR cc_start: 0.7870 (m-80) cc_final: 0.7523 (m-10) REVERT: D 959 LYS cc_start: 0.8147 (tmtt) cc_final: 0.7804 (tptp) REVERT: D 1223 ILE cc_start: 0.8942 (tt) cc_final: 0.8528 (pt) REVERT: D 1279 ASP cc_start: 0.8776 (m-30) cc_final: 0.7889 (t0) REVERT: D 1280 MET cc_start: 0.8427 (ptt) cc_final: 0.8030 (ppp) outliers start: 4 outliers final: 2 residues processed: 201 average time/residue: 0.1164 time to fit residues: 39.8414 Evaluate side-chains 146 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 147 optimal weight: 20.0000 chunk 238 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 195 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN A 435 HIS A 460 HIS B 90 ASN B 186 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1384 HIS D 36 GLN ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1095 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.066758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.051141 restraints weight = 119241.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.052496 restraints weight = 68920.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.053387 restraints weight = 47288.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.054013 restraints weight = 36484.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.054380 restraints weight = 30487.547| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.143 21185 Z= 0.266 Angle : 0.749 8.761 28905 Z= 0.398 Chirality : 0.047 0.231 3401 Planarity : 0.005 0.068 3735 Dihedral : 5.667 30.688 3030 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.45 % Favored : 90.41 % Rotamer: Outliers : 0.22 % Allowed : 5.97 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.16), residues: 2847 helix: 1.24 (0.14), residues: 1425 sheet: -1.60 (0.36), residues: 206 loop : -2.91 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 264 TYR 0.029 0.002 TYR D 118 PHE 0.042 0.003 PHE D 182 TRP 0.048 0.002 TRP D1332 HIS 0.011 0.002 HIS D 922 Details of bonding type rmsd covalent geometry : bond 0.00568 (21185) covalent geometry : angle 0.74940 (28905) hydrogen bonds : bond 0.04209 ( 1053) hydrogen bonds : angle 4.54837 ( 3153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 178 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 CYS cc_start: 0.8929 (t) cc_final: 0.8333 (t) REVERT: A 350 SER cc_start: 0.9530 (m) cc_final: 0.9298 (p) REVERT: B 214 ASP cc_start: 0.9055 (t0) cc_final: 0.8851 (t0) REVERT: C 1422 GLU cc_start: 0.8631 (tp30) cc_final: 0.8384 (tp30) REVERT: D 223 SER cc_start: 0.8772 (t) cc_final: 0.8427 (p) REVERT: D 228 ILE cc_start: 0.8942 (pt) cc_final: 0.8673 (mm) REVERT: D 959 LYS cc_start: 0.7962 (tmtt) cc_final: 0.7573 (tptp) outliers start: 4 outliers final: 3 residues processed: 182 average time/residue: 0.1171 time to fit residues: 35.8394 Evaluate side-chains 126 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 78 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 250 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN B 186 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 HIS ** C 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1362 GLN ** C1384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1051 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.067037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.051406 restraints weight = 117799.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.052767 restraints weight = 68314.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.053675 restraints weight = 46985.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.054306 restraints weight = 36186.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.054729 restraints weight = 30096.628| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21185 Z= 0.193 Angle : 0.675 9.211 28905 Z= 0.356 Chirality : 0.046 0.268 3401 Planarity : 0.004 0.066 3735 Dihedral : 5.409 28.210 3030 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.54 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 2847 helix: 1.54 (0.14), residues: 1429 sheet: -1.59 (0.36), residues: 208 loop : -2.83 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1420 TYR 0.020 0.002 TYR D 118 PHE 0.027 0.002 PHE B 80 TRP 0.039 0.002 TRP D1332 HIS 0.009 0.001 HIS C1384 Details of bonding type rmsd covalent geometry : bond 0.00423 (21185) covalent geometry : angle 0.67455 (28905) hydrogen bonds : bond 0.03840 ( 1053) hydrogen bonds : angle 4.33821 ( 3153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 CYS cc_start: 0.8934 (t) cc_final: 0.8380 (t) REVERT: A 293 MET cc_start: 0.8323 (mmt) cc_final: 0.7863 (mmp) REVERT: C 1422 GLU cc_start: 0.8639 (tp30) cc_final: 0.8375 (tp30) REVERT: D 223 SER cc_start: 0.8749 (t) cc_final: 0.8403 (p) REVERT: D 228 ILE cc_start: 0.8933 (pt) cc_final: 0.8664 (mm) REVERT: D 959 LYS cc_start: 0.7980 (tmtt) cc_final: 0.7592 (tptp) REVERT: D 1068 LEU cc_start: 0.9417 (tp) cc_final: 0.9207 (tp) REVERT: D 1278 MET cc_start: 0.6867 (mmp) cc_final: 0.6654 (mmm) REVERT: D 1279 ASP cc_start: 0.8668 (m-30) cc_final: 0.7959 (t0) REVERT: D 1280 MET cc_start: 0.8249 (ptt) cc_final: 0.8016 (ppp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1231 time to fit residues: 35.9279 Evaluate side-chains 127 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 122 optimal weight: 7.9990 chunk 231 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 155 optimal weight: 30.0000 chunk 124 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 249 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 131 optimal weight: 40.0000 chunk 130 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN C 149 HIS C 270 ASN C1390 ASN ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 205 GLN ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1153 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.065714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.049856 restraints weight = 120956.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.051121 restraints weight = 72788.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.051962 restraints weight = 51526.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.052545 restraints weight = 40626.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.052932 restraints weight = 34515.995| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.6549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 21185 Z= 0.255 Angle : 0.732 9.633 28905 Z= 0.384 Chirality : 0.046 0.238 3401 Planarity : 0.005 0.065 3735 Dihedral : 5.503 27.194 3030 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.01 % Favored : 89.85 % Rotamer: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.16), residues: 2847 helix: 1.41 (0.14), residues: 1432 sheet: -1.81 (0.34), residues: 219 loop : -2.82 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 196 TYR 0.024 0.002 TYR D 118 PHE 0.021 0.002 PHE A 179 TRP 0.058 0.002 TRP D1332 HIS 0.011 0.002 HIS D 922 Details of bonding type rmsd covalent geometry : bond 0.00556 (21185) covalent geometry : angle 0.73212 (28905) hydrogen bonds : bond 0.04001 ( 1053) hydrogen bonds : angle 4.51706 ( 3153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 CYS cc_start: 0.8989 (t) cc_final: 0.8498 (t) REVERT: C 409 LYS cc_start: 0.9225 (tppt) cc_final: 0.8944 (ttmt) REVERT: C 1422 GLU cc_start: 0.8740 (tp30) cc_final: 0.8376 (tp30) REVERT: D 223 SER cc_start: 0.9017 (t) cc_final: 0.8577 (p) REVERT: D 228 ILE cc_start: 0.8926 (pt) cc_final: 0.8637 (mm) REVERT: D 236 LEU cc_start: 0.8392 (tt) cc_final: 0.7783 (mt) REVERT: D 889 MET cc_start: 0.8823 (tpp) cc_final: 0.8569 (tpp) REVERT: D 935 ILE cc_start: 0.9412 (tp) cc_final: 0.9162 (tp) REVERT: D 1068 LEU cc_start: 0.9390 (tp) cc_final: 0.9156 (tp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1280 time to fit residues: 33.6917 Evaluate side-chains 122 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 114 optimal weight: 30.0000 chunk 171 optimal weight: 1.9990 chunk 134 optimal weight: 20.0000 chunk 216 optimal weight: 0.7980 chunk 279 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 273 optimal weight: 0.7980 chunk 164 optimal weight: 7.9990 chunk 236 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 174 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.066750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.051238 restraints weight = 117553.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.052500 restraints weight = 70495.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.053369 restraints weight = 49362.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.053955 restraints weight = 38722.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.054297 restraints weight = 32717.597| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.6700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21185 Z= 0.166 Angle : 0.654 10.744 28905 Z= 0.343 Chirality : 0.045 0.222 3401 Planarity : 0.004 0.067 3735 Dihedral : 5.292 25.698 3030 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.61 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.16), residues: 2847 helix: 1.70 (0.14), residues: 1422 sheet: -1.89 (0.33), residues: 229 loop : -2.74 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1077 TYR 0.031 0.002 TYR C 178 PHE 0.017 0.001 PHE C 179 TRP 0.045 0.002 TRP D1332 HIS 0.006 0.001 HIS C1384 Details of bonding type rmsd covalent geometry : bond 0.00368 (21185) covalent geometry : angle 0.65406 (28905) hydrogen bonds : bond 0.03627 ( 1053) hydrogen bonds : angle 4.26482 ( 3153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 CYS cc_start: 0.8864 (t) cc_final: 0.8357 (t) REVERT: A 293 MET cc_start: 0.8406 (mmt) cc_final: 0.7969 (mmp) REVERT: B 116 ASN cc_start: 0.8119 (t0) cc_final: 0.7686 (t0) REVERT: C 59 MET cc_start: 0.8621 (pmm) cc_final: 0.8349 (ptp) REVERT: C 409 LYS cc_start: 0.9252 (tppt) cc_final: 0.8990 (ttmt) REVERT: C 1422 GLU cc_start: 0.8648 (tp30) cc_final: 0.8377 (tp30) REVERT: D 223 SER cc_start: 0.8985 (t) cc_final: 0.8635 (p) REVERT: D 228 ILE cc_start: 0.8927 (pt) cc_final: 0.8697 (mm) REVERT: D 889 MET cc_start: 0.8726 (tpp) cc_final: 0.8440 (tpp) REVERT: D 935 ILE cc_start: 0.9450 (tp) cc_final: 0.9180 (tp) REVERT: D 959 LYS cc_start: 0.8047 (tmtt) cc_final: 0.7620 (tptp) REVERT: D 1068 LEU cc_start: 0.9401 (tp) cc_final: 0.9186 (tp) REVERT: D 1280 MET cc_start: 0.8288 (ptt) cc_final: 0.7965 (ppp) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1319 time to fit residues: 35.0296 Evaluate side-chains 123 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 176 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 193 optimal weight: 5.9990 chunk 165 optimal weight: 20.0000 chunk 186 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 253 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 chunk 218 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN B 67 HIS ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.066940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.051458 restraints weight = 117863.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.052843 restraints weight = 68064.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.053764 restraints weight = 46594.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.054411 restraints weight = 35932.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.054784 restraints weight = 29913.189| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.6819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21185 Z= 0.130 Angle : 0.623 10.943 28905 Z= 0.324 Chirality : 0.044 0.211 3401 Planarity : 0.004 0.065 3735 Dihedral : 5.042 25.855 3030 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.75 % Favored : 91.11 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2847 helix: 1.91 (0.14), residues: 1419 sheet: -1.81 (0.33), residues: 229 loop : -2.58 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 169 TYR 0.026 0.002 TYR C 178 PHE 0.019 0.001 PHE C 179 TRP 0.044 0.002 TRP D1332 HIS 0.010 0.001 HIS D 29 Details of bonding type rmsd covalent geometry : bond 0.00287 (21185) covalent geometry : angle 0.62317 (28905) hydrogen bonds : bond 0.03362 ( 1053) hydrogen bonds : angle 4.09112 ( 3153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.7994 (tpp) cc_final: 0.7759 (tpp) REVERT: A 67 MET cc_start: 0.8095 (pmm) cc_final: 0.7857 (mmt) REVERT: A 211 CYS cc_start: 0.8957 (t) cc_final: 0.8441 (t) REVERT: A 262 MET cc_start: 0.9024 (tpp) cc_final: 0.8733 (tpt) REVERT: A 293 MET cc_start: 0.8350 (mmt) cc_final: 0.7865 (mmp) REVERT: B 116 ASN cc_start: 0.8068 (t0) cc_final: 0.7644 (t0) REVERT: C 8 TYR cc_start: 0.6040 (m-80) cc_final: 0.5302 (m-10) REVERT: C 59 MET cc_start: 0.8681 (pmm) cc_final: 0.8321 (ptp) REVERT: C 223 MET cc_start: 0.8423 (tmm) cc_final: 0.7781 (tmm) REVERT: C 1422 GLU cc_start: 0.8654 (tp30) cc_final: 0.8360 (tp30) REVERT: D 223 SER cc_start: 0.8922 (t) cc_final: 0.8577 (p) REVERT: D 228 ILE cc_start: 0.8995 (pt) cc_final: 0.8710 (mm) REVERT: D 935 ILE cc_start: 0.9443 (tp) cc_final: 0.9177 (tp) REVERT: D 959 LYS cc_start: 0.7925 (tmtt) cc_final: 0.7597 (tptp) REVERT: D 1068 LEU cc_start: 0.9356 (tp) cc_final: 0.9083 (tp) REVERT: D 1278 MET cc_start: 0.6941 (mmp) cc_final: 0.6723 (mmm) REVERT: D 1280 MET cc_start: 0.8333 (ptt) cc_final: 0.7950 (ppp) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1264 time to fit residues: 35.7940 Evaluate side-chains 123 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 95 optimal weight: 0.0670 chunk 251 optimal weight: 8.9990 chunk 90 optimal weight: 0.6980 chunk 257 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 129 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 225 optimal weight: 5.9990 chunk 190 optimal weight: 20.0000 overall best weight: 2.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.065265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.049604 restraints weight = 121942.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.050861 restraints weight = 73103.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.051646 restraints weight = 51456.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.052249 restraints weight = 40849.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.052639 restraints weight = 34697.432| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.7180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 21185 Z= 0.233 Angle : 0.711 11.307 28905 Z= 0.373 Chirality : 0.046 0.213 3401 Planarity : 0.005 0.061 3735 Dihedral : 5.308 26.373 3030 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.15 % Favored : 89.71 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.16), residues: 2847 helix: 1.63 (0.14), residues: 1445 sheet: -1.70 (0.34), residues: 209 loop : -2.68 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 7 TYR 0.037 0.002 TYR D 258 PHE 0.035 0.002 PHE D1358 TRP 0.064 0.002 TRP D1332 HIS 0.019 0.002 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00510 (21185) covalent geometry : angle 0.71121 (28905) hydrogen bonds : bond 0.03901 ( 1053) hydrogen bonds : angle 4.38714 ( 3153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 208 MET cc_start: 0.8997 (ptp) cc_final: 0.8600 (ptp) REVERT: A 211 CYS cc_start: 0.9050 (t) cc_final: 0.8594 (t) REVERT: A 262 MET cc_start: 0.9040 (tpp) cc_final: 0.8769 (tpt) REVERT: B 223 LEU cc_start: 0.9429 (mp) cc_final: 0.9174 (mm) REVERT: C 409 LYS cc_start: 0.9243 (tppt) cc_final: 0.8960 (ttmt) REVERT: C 1422 GLU cc_start: 0.8635 (tp30) cc_final: 0.8369 (tp30) REVERT: D 223 SER cc_start: 0.9009 (t) cc_final: 0.8603 (p) REVERT: D 228 ILE cc_start: 0.8968 (pt) cc_final: 0.8671 (mm) REVERT: D 1278 MET cc_start: 0.7008 (mmp) cc_final: 0.6773 (mmm) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1175 time to fit residues: 29.0794 Evaluate side-chains 119 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 201 optimal weight: 0.9990 chunk 236 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 155 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 86 optimal weight: 0.4980 chunk 215 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.066307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.050690 restraints weight = 121131.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.051968 restraints weight = 71869.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.052868 restraints weight = 50505.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.053455 restraints weight = 39239.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.053700 restraints weight = 33138.322| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.7265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21185 Z= 0.149 Angle : 0.640 11.926 28905 Z= 0.334 Chirality : 0.045 0.195 3401 Planarity : 0.004 0.061 3735 Dihedral : 5.098 25.208 3030 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.64 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2847 helix: 1.86 (0.14), residues: 1428 sheet: -1.55 (0.34), residues: 206 loop : -2.61 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 113 TYR 0.023 0.002 TYR D 258 PHE 0.022 0.001 PHE C 179 TRP 0.055 0.002 TRP D1332 HIS 0.017 0.001 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00329 (21185) covalent geometry : angle 0.64020 (28905) hydrogen bonds : bond 0.03458 ( 1053) hydrogen bonds : angle 4.13628 ( 3153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8041 (tpp) cc_final: 0.7772 (tpp) REVERT: A 211 CYS cc_start: 0.9023 (t) cc_final: 0.8497 (t) REVERT: A 262 MET cc_start: 0.9035 (tpp) cc_final: 0.8747 (tpt) REVERT: A 293 MET cc_start: 0.8552 (mmt) cc_final: 0.8069 (mmp) REVERT: B 116 ASN cc_start: 0.8167 (t0) cc_final: 0.7871 (t0) REVERT: C 223 MET cc_start: 0.8412 (tmm) cc_final: 0.7764 (tmm) REVERT: C 1422 GLU cc_start: 0.8660 (tp30) cc_final: 0.8399 (tp30) REVERT: D 223 SER cc_start: 0.9028 (t) cc_final: 0.8643 (p) REVERT: D 228 ILE cc_start: 0.8988 (pt) cc_final: 0.8693 (mm) REVERT: D 959 LYS cc_start: 0.7949 (tmtt) cc_final: 0.7602 (tptp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1188 time to fit residues: 30.8838 Evaluate side-chains 114 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 124 optimal weight: 8.9990 chunk 7 optimal weight: 0.0170 chunk 147 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 chunk 283 optimal weight: 1.9990 chunk 125 optimal weight: 0.3980 chunk 30 optimal weight: 0.4980 chunk 243 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1408 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.067441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.051777 restraints weight = 120225.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.053126 restraints weight = 70686.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.054044 restraints weight = 48997.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.054667 restraints weight = 37884.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.055080 restraints weight = 31801.844| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.7330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21185 Z= 0.117 Angle : 0.615 12.116 28905 Z= 0.318 Chirality : 0.044 0.207 3401 Planarity : 0.004 0.058 3735 Dihedral : 4.769 22.815 3030 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.25 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.17), residues: 2847 helix: 2.09 (0.14), residues: 1424 sheet: -1.63 (0.33), residues: 224 loop : -2.42 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 169 TYR 0.037 0.002 TYR D1284 PHE 0.020 0.001 PHE C 179 TRP 0.041 0.002 TRP C 264 HIS 0.016 0.001 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00255 (21185) covalent geometry : angle 0.61478 (28905) hydrogen bonds : bond 0.03103 ( 1053) hydrogen bonds : angle 3.93031 ( 3153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3009.04 seconds wall clock time: 52 minutes 53.44 seconds (3173.44 seconds total)