Starting phenix.real_space_refine on Sun Jul 5 21:09:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7py7_13715/07_2026/7py7_13715.cif Found real_map, /net/cci-nas-00/data/ceres_data/7py7_13715/07_2026/7py7_13715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7py7_13715/07_2026/7py7_13715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7py7_13715/07_2026/7py7_13715.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7py7_13715/07_2026/7py7_13715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7py7_13715/07_2026/7py7_13715.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7py7_13715/07_2026/7py7_13715.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7py7_13715/07_2026/7py7_13715.cif" } resolution = 4.1 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= 0.009 sd= 0.063 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 69 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 18500 2.51 5 N 5380 2.21 5 O 5935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30000 Number of models: 1 Model: "" Number of chains: 11 Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 557 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "T" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 630 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 235 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "B" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1699 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Chain: "C" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10388 Classifications: {'peptide': 1335} Link IDs: {'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "G" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 987 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 2447 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 479} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1451 Unresolved non-hydrogen angles: 1853 Unresolved non-hydrogen dihedrals: 1145 Unresolved non-hydrogen chiralities: 145 Planarities with less than four sites: {'ASN:plan1': 19, 'GLU:plan': 56, 'ARG:plan': 33, 'PHE:plan': 14, 'TYR:plan': 6, 'GLN:plan1': 19, 'ASP:plan': 42, 'TRP:plan': 4, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 830 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16061 SG CYS D 88 83.689 109.793 73.304 1.00206.22 S ATOM 21749 SG CYS D 814 92.870 42.365 76.295 1.00151.01 S ATOM 22314 SG CYS D 888 94.486 45.902 76.118 1.00134.73 S ATOM 22365 SG CYS D 895 93.360 44.565 79.349 1.00142.38 S ATOM 22386 SG CYS D 898 96.234 42.910 77.889 1.00135.85 S Time building chain proxies: 6.56, per 1000 atoms: 0.22 Number of scatterers: 30000 At special positions: 0 Unit cell: (187.48, 154.78, 168.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 113 16.00 P 69 15.00 Mg 1 11.99 O 5935 8.00 N 5380 7.00 C 18500 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: 2.92 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " Number of angles added : 6 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7094 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 49 sheets defined 37.4% alpha, 14.0% beta 29 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.841A pdb=" N LEU A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.975A pdb=" N GLU A 162 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 removed outlier: 3.533A pdb=" N ALA A 216 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.843A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.703A pdb=" N LEU B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.672A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.775A pdb=" N ARG C 10 " --> pdb=" O GLU C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 39 Processing helix chain 'C' and resid 42 through 46 removed outlier: 3.792A pdb=" N GLY C 45 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN C 46 " --> pdb=" O PRO C 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 42 through 46' Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.797A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.514A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 480 Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.503A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 4.071A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 614 Processing helix chain 'C' and resid 657 through 661 removed outlier: 3.613A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.681A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.512A pdb=" N ALA C 679 " --> pdb=" O ASP C 675 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 864 removed outlier: 3.824A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 907 removed outlier: 3.545A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 984 removed outlier: 3.732A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY C 982 " --> pdb=" O VAL C 978 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY C 983 " --> pdb=" O LEU C 979 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 984 " --> pdb=" O VAL C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 990 removed outlier: 3.574A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 999 Processing helix chain 'C' and resid 1005 through 1035 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 3.853A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1101 through 1106' Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.862A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.720A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP C1150 " --> pdb=" O GLN C1146 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1175 Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.531A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.786A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 4.095A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP C1310 " --> pdb=" O LYS C1306 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 4.025A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.705A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.667A pdb=" N SER D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 263 through 285 removed outlier: 4.289A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 405 through 416 removed outlier: 4.283A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 505 through 513 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.800A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.680A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN D 593 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.619A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU D 658 " --> pdb=" O ILE D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 704 removed outlier: 4.013A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU D 704 " --> pdb=" O ASN D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.116A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.556A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.545A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1068 through 1073 removed outlier: 3.683A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1244 removed outlier: 3.921A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL D1226 " --> pdb=" O ARG D1222 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N HIS D1227 " --> pdb=" O LEU D1223 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA D1228 " --> pdb=" O ARG D1224 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.368A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D1261 " --> pdb=" O VAL D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1319 through 1325 Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 4.267A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.666A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.511A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 90 Processing helix chain 'G' and resid 18 through 34 Processing helix chain 'G' and resid 76 through 85 Processing helix chain 'G' and resid 104 through 119 removed outlier: 3.528A pdb=" N VAL G 108 " --> pdb=" O SER G 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 10 Processing helix chain 'F' and resid 19 through 39 removed outlier: 3.943A pdb=" N ALA F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 128 removed outlier: 4.007A pdb=" N GLN F 112 " --> pdb=" O GLN F 108 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL F 115 " --> pdb=" O LYS F 111 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU F 120 " --> pdb=" O GLN F 116 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL F 126 " --> pdb=" O GLU F 122 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP F 128 " --> pdb=" O ALA F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 134 removed outlier: 3.873A pdb=" N GLU F 134 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 208 removed outlier: 4.357A pdb=" N LEU F 205 " --> pdb=" O LYS F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 266 removed outlier: 3.719A pdb=" N GLU F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 314 removed outlier: 3.670A pdb=" N LEU F 314 " --> pdb=" O ALA F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 329 Processing helix chain 'F' and resid 342 through 351 removed outlier: 4.556A pdb=" N HIS F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 362 removed outlier: 4.078A pdb=" N ALA F 355 " --> pdb=" O GLU F 351 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE F 359 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR F 360 " --> pdb=" O ILE F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 370 removed outlier: 3.711A pdb=" N PHE F 369 " --> pdb=" O ASP F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 404 removed outlier: 4.047A pdb=" N GLU F 404 " --> pdb=" O PRO F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 425 removed outlier: 4.033A pdb=" N SER F 424 " --> pdb=" O GLN F 421 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU F 425 " --> pdb=" O GLU F 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 421 through 425' Processing helix chain 'F' and resid 443 through 447 removed outlier: 3.918A pdb=" N PHE F 446 " --> pdb=" O ASP F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 459 removed outlier: 4.387A pdb=" N ASP F 458 " --> pdb=" O THR F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 479 removed outlier: 3.632A pdb=" N ALA F 478 " --> pdb=" O THR F 474 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY F 479 " --> pdb=" O ASP F 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 474 through 479' Processing helix chain 'F' and resid 479 through 487 removed outlier: 4.089A pdb=" N MET F 483 " --> pdb=" O GLY F 479 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA F 484 " --> pdb=" O ALA F 480 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA F 485 " --> pdb=" O LEU F 481 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG F 486 " --> pdb=" O ILE F 482 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN F 487 " --> pdb=" O MET F 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 479 through 487' Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 4.159A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 104 removed outlier: 3.777A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 140 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.766A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 17 removed outlier: 6.911A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 28 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU B 201 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 104 removed outlier: 7.892A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.629A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.864A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.807A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 284 through 285 removed outlier: 4.893A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.763A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 301 through 303 removed outlier: 6.775A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 599 through 606 removed outlier: 6.256A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AC1, first strand: chain 'C' and resid 749 through 752 removed outlier: 4.098A pdb=" N ILE C 732 " --> pdb=" O TYR C 751 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY C 722 " --> pdb=" O VAL C 777 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.702A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.464A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.738A pdb=" N GLY C 846 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.149A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AC9, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.728A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA D 467 " --> pdb=" O ASN D 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN D 424 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.728A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 4.032A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1338 Processing sheet with id=AD5, first strand: chain 'D' and resid 103 through 112 removed outlier: 4.066A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.819A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.402A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 159 through 160 removed outlier: 3.736A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 252 through 253 Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.547A pdb=" N LYS D 566 " --> pdb=" O GLU D 554 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.687A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 849 through 850 removed outlier: 3.744A pdb=" N ASP D 855 " --> pdb=" O LYS D 850 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 949 through 951 removed outlier: 6.928A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 991 through 996 removed outlier: 3.677A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 4.241A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 4.270A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1046 through 1050 Processing sheet with id=AE8, first strand: chain 'D' and resid 1187 through 1190 Processing sheet with id=AE9, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.803A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 42 through 43 removed outlier: 3.852A pdb=" N LEU G 70 " --> pdb=" O MET G 43 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY G 91 " --> pdb=" O GLN G 13 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 47 through 49 Processing sheet with id=AF3, first strand: chain 'F' and resid 138 through 141 removed outlier: 3.740A pdb=" N GLY F 181 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 152 through 154 removed outlier: 3.577A pdb=" N ALA F 158 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N VAL F 197 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL F 161 " --> pdb=" O VAL F 197 " (cutoff:3.500A) 1104 hydrogen bonds defined for protein. 3060 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 7.64 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9389 1.33 - 1.46: 4679 1.46 - 1.58: 16153 1.58 - 1.70: 134 1.70 - 1.82: 198 Bond restraints: 30553 Sorted by residual: bond pdb=" C ARG A 166 " pdb=" N PRO A 167 " ideal model delta sigma weight residual 1.330 1.382 -0.051 1.19e-02 7.06e+03 1.87e+01 bond pdb=" N PRO G 45 " pdb=" CA PRO G 45 " ideal model delta sigma weight residual 1.469 1.514 -0.045 1.22e-02 6.72e+03 1.37e+01 bond pdb=" C VAL G 44 " pdb=" N PRO G 45 " ideal model delta sigma weight residual 1.333 1.373 -0.040 1.17e-02 7.31e+03 1.16e+01 bond pdb=" C1' DT N 23 " pdb=" N1 DT N 23 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.86e+00 bond pdb=" C3' DC T 3 " pdb=" O3' DC T 3 " ideal model delta sigma weight residual 1.435 1.475 -0.040 1.30e-02 5.92e+03 9.45e+00 ... (remaining 30548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 41210 2.59 - 5.17: 389 5.17 - 7.76: 51 7.76 - 10.34: 4 10.34 - 12.93: 3 Bond angle restraints: 41657 Sorted by residual: angle pdb=" C VAL G 44 " pdb=" N PRO G 45 " pdb=" CA PRO G 45 " ideal model delta sigma weight residual 119.90 126.68 -6.78 1.05e+00 9.07e-01 4.17e+01 angle pdb=" O4' DG N 25 " pdb=" C4' DG N 25 " pdb=" C3' DG N 25 " ideal model delta sigma weight residual 106.00 103.38 2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" CB MET C 239 " pdb=" CG MET C 239 " pdb=" SD MET C 239 " ideal model delta sigma weight residual 112.70 99.77 12.93 3.00e+00 1.11e-01 1.86e+01 angle pdb=" N3 DT T 8 " pdb=" C4 DT T 8 " pdb=" O4 DT T 8 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT N 11 " pdb=" C4 DT N 11 " pdb=" O4 DT N 11 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 41652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 18067 35.44 - 70.89: 439 70.89 - 106.33: 24 106.33 - 141.78: 2 141.78 - 177.22: 2 Dihedral angle restraints: 18534 sinusoidal: 7531 harmonic: 11003 Sorted by residual: dihedral pdb=" CA LYS C1035 " pdb=" C LYS C1035 " pdb=" N ILE C1036 " pdb=" CA ILE C1036 " ideal model delta harmonic sigma weight residual -180.00 -143.83 -36.17 0 5.00e+00 4.00e-02 5.23e+01 dihedral pdb=" CA LYS G 7 " pdb=" C LYS G 7 " pdb=" N ARG G 8 " pdb=" CA ARG G 8 " ideal model delta harmonic sigma weight residual -180.00 -155.30 -24.70 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA GLU C 44 " pdb=" C GLU C 44 " pdb=" N GLY C 45 " pdb=" CA GLY C 45 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 18531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3401 0.042 - 0.083: 1001 0.083 - 0.125: 380 0.125 - 0.166: 40 0.166 - 0.208: 6 Chirality restraints: 4828 Sorted by residual: chirality pdb=" C3' DC T 3 " pdb=" C4' DC T 3 " pdb=" O3' DC T 3 " pdb=" C2' DC T 3 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE C 572 " pdb=" CA ILE C 572 " pdb=" CG1 ILE C 572 " pdb=" CG2 ILE C 572 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CA MET C 488 " pdb=" N MET C 488 " pdb=" C MET C 488 " pdb=" CB MET C 488 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 4825 not shown) Planarity restraints: 5268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C1229 " -0.021 2.00e-02 2.50e+03 2.31e-02 1.07e+01 pdb=" CG TYR C1229 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR C1229 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR C1229 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR C1229 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C1229 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR C1229 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C1229 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 165 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C GLU A 165 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU A 165 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 166 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 551 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO C 552 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 552 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 552 " 0.027 5.00e-02 4.00e+02 ... (remaining 5265 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 559 2.66 - 3.22: 28807 3.22 - 3.78: 46999 3.78 - 4.34: 59839 4.34 - 4.90: 93981 Nonbonded interactions: 230185 Sorted by model distance: nonbonded pdb=" OG1 THR C1286 " pdb=" OE2 GLU D 479 " model vdw 2.097 3.040 nonbonded pdb=" N CYS D 72 " pdb="ZN ZN D1502 " model vdw 2.151 2.310 nonbonded pdb=" O LYS C 324 " pdb=" OG SER C 328 " model vdw 2.156 3.040 nonbonded pdb=" OE1 GLN C1268 " pdb=" OG SER D 350 " model vdw 2.162 3.040 nonbonded pdb=" OH TYR D1186 " pdb=" OE1 GLU D1188 " model vdw 2.181 3.040 ... (remaining 230180 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 158 or resid 170 through 234)) selection = (chain 'B' and resid 7 through 234) } 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 36.060 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 : 0.003 0.051 30558 Z= 0.211 Angle : 0.663 12.928 41663 Z= 0.382 Chirality : 0.045 0.208 4828 Planarity : 0.004 0.049 5268 Dihedral : 15.171 177.220 11440 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.67 % Favored : 94.23 % Rotamer: Outliers : 0.04 % Allowed : 0.28 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.49 (0.13), residues: 3812 helix: -0.02 (0.15), residues: 1219 sheet: -0.67 (0.24), residues: 436 loop : -1.67 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 12 TYR 0.056 0.001 TYR C1229 PHE 0.033 0.001 PHE C1025 TRP 0.016 0.002 TRP D 115 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.21 (30553) covalent geometry : angle 0.66148 / 0.38 (41657) hydrogen bonds : bond 0.20040 / 21.84 ( 1179) hydrogen bonds : angle 7.13482 / 7.67 ( 3216) metal coordination : bond 0.01646 / 1.43 ( 5) metal coordination : angle 4.05894 / 8.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7930 (p) cc_final: 0.7309 (p) REVERT: C 130 MET cc_start: 0.8735 (mmm) cc_final: 0.8414 (mmm) REVERT: C 239 MET cc_start: 0.8807 (mmm) cc_final: 0.8355 (mmm) REVERT: C 315 MET cc_start: 0.8633 (ttp) cc_final: 0.8276 (ptm) REVERT: C 403 MET cc_start: 0.9220 (tmm) cc_final: 0.8851 (tmm) REVERT: C 681 MET cc_start: 0.8803 (ttp) cc_final: 0.7697 (ptp) REVERT: C 685 MET cc_start: 0.8914 (ptp) cc_final: 0.8260 (ptp) REVERT: C 704 MET cc_start: 0.8787 (mmp) cc_final: 0.8577 (mmp) REVERT: C 760 ASN cc_start: 0.8165 (m110) cc_final: 0.7781 (m110) REVERT: C 1034 ARG cc_start: 0.9110 (tmm160) cc_final: 0.8815 (ttp80) REVERT: C 1151 LEU cc_start: 0.8633 (tp) cc_final: 0.8400 (tp) REVERT: D 343 LEU cc_start: 0.9523 (mt) cc_final: 0.9101 (mt) REVERT: D 484 MET cc_start: 0.7829 (mpp) cc_final: 0.7420 (mpp) REVERT: D 625 MET cc_start: 0.8640 (ttp) cc_final: 0.8350 (tmm) REVERT: D 644 MET cc_start: 0.8384 (mpp) cc_final: 0.7663 (mpp) REVERT: D 1156 LEU cc_start: 0.9199 (mp) cc_final: 0.8917 (mp) REVERT: D 1189 MET cc_start: 0.8974 (tpp) cc_final: 0.8639 (mmm) REVERT: E 43 ASN cc_start: 0.9146 (t0) cc_final: 0.8904 (t0) REVERT: E 62 GLN cc_start: 0.9753 (tt0) cc_final: 0.9099 (tm-30) REVERT: G 29 HIS cc_start: 0.8778 (m90) cc_final: 0.8475 (m90) REVERT: G 35 MET cc_start: 0.6600 (mpp) cc_final: 0.6159 (mpp) outliers start: 1 outliers final: 0 residues processed: 261 average time/residue: 0.1800 time to fit residues: 80.3209 Evaluate side-chains 194 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 GLN C 276 GLN C 513 GLN C 573 ASN C 649 GLN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS D 448 GLN D 700 ASN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.089220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.060489 restraints weight = 139055.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.062327 restraints weight = 71498.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.063529 restraints weight = 45787.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.064388 restraints weight = 33780.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.064869 restraints weight = 27436.930| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 30558 Z= 0.220 Angle : 0.636 13.905 41663 Z= 0.341 Chirality : 0.044 0.396 4828 Planarity : 0.004 0.053 5268 Dihedral : 12.843 178.873 4896 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.75 % Favored : 94.18 % Rotamer: Outliers : 0.07 % Allowed : 5.56 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.41 (0.13), residues: 3812 helix: 0.20 (0.14), residues: 1272 sheet: -0.81 (0.23), residues: 470 loop : -1.73 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 275 TYR 0.051 0.002 TYR C1229 PHE 0.015 0.001 PHE C 405 TRP 0.009 0.001 TRP D 580 HIS 0.010 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.22 (30553) covalent geometry : angle 0.63414 / 0.34 (41657) hydrogen bonds : bond 0.04581 / 4.94 ( 1179) hydrogen bonds : angle 5.53120 / 5.87 ( 3216) metal coordination : bond 0.01231 / 1.16 ( 5) metal coordination : angle 4.36940 / 9.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 240 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.8009 (p) cc_final: 0.7504 (p) REVERT: C 130 MET cc_start: 0.8681 (mmm) cc_final: 0.8283 (mmm) REVERT: C 239 MET cc_start: 0.8984 (mmm) cc_final: 0.8524 (mmm) REVERT: C 403 MET cc_start: 0.9125 (tmm) cc_final: 0.8766 (tmm) REVERT: C 488 MET cc_start: 0.8957 (tpt) cc_final: 0.8613 (tpt) REVERT: C 632 ASP cc_start: 0.8269 (p0) cc_final: 0.8067 (p0) REVERT: C 674 ASP cc_start: 0.9226 (m-30) cc_final: 0.8891 (m-30) REVERT: C 681 MET cc_start: 0.8918 (ttp) cc_final: 0.7858 (ptp) REVERT: C 685 MET cc_start: 0.8831 (ptp) cc_final: 0.8349 (ptp) REVERT: C 704 MET cc_start: 0.8773 (mmp) cc_final: 0.8560 (mmp) REVERT: C 760 ASN cc_start: 0.8291 (m110) cc_final: 0.8049 (m110) REVERT: C 764 CYS cc_start: 0.9325 (t) cc_final: 0.9046 (t) REVERT: C 1034 ARG cc_start: 0.9071 (tmm160) cc_final: 0.8738 (ttp80) REVERT: C 1151 LEU cc_start: 0.8607 (tp) cc_final: 0.8336 (tp) REVERT: C 1275 VAL cc_start: 0.9320 (t) cc_final: 0.9093 (t) REVERT: C 1290 MET cc_start: 0.9251 (tpp) cc_final: 0.8708 (mmp) REVERT: C 1292 THR cc_start: 0.8838 (m) cc_final: 0.8388 (p) REVERT: C 1319 MET cc_start: 0.8804 (tmm) cc_final: 0.7947 (tmm) REVERT: D 343 LEU cc_start: 0.9509 (mt) cc_final: 0.9112 (mt) REVERT: D 347 VAL cc_start: 0.9589 (m) cc_final: 0.9359 (t) REVERT: D 484 MET cc_start: 0.8159 (mpp) cc_final: 0.7758 (mpp) REVERT: D 625 MET cc_start: 0.8736 (ttp) cc_final: 0.8292 (tmm) REVERT: D 644 MET cc_start: 0.8483 (mpp) cc_final: 0.7747 (mpp) REVERT: D 1260 MET cc_start: 0.8813 (mmm) cc_final: 0.8393 (tpp) REVERT: E 43 ASN cc_start: 0.9078 (t0) cc_final: 0.8797 (t0) REVERT: G 29 HIS cc_start: 0.8958 (m90) cc_final: 0.8549 (m90) REVERT: G 35 MET cc_start: 0.6841 (mpp) cc_final: 0.6282 (mpp) REVERT: G 43 MET cc_start: 0.6472 (mmm) cc_final: 0.6033 (mmm) outliers start: 2 outliers final: 1 residues processed: 242 average time/residue: 0.1707 time to fit residues: 71.1526 Evaluate side-chains 192 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 293 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 211 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 329 optimal weight: 0.0470 chunk 275 optimal weight: 0.0010 chunk 88 optimal weight: 1.9990 chunk 305 optimal weight: 0.7980 chunk 212 optimal weight: 2.9990 overall best weight: 0.6886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS C 573 ASN C 649 GLN C 760 ASN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 GLN ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN E 75 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.091352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.062596 restraints weight = 138317.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.064493 restraints weight = 70389.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.065688 restraints weight = 44674.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.066428 restraints weight = 32965.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.067050 restraints weight = 27132.573| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 30558 Z= 0.114 Angle : 0.566 10.229 41663 Z= 0.301 Chirality : 0.044 0.329 4828 Planarity : 0.004 0.061 5268 Dihedral : 12.872 177.115 4896 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.22 (0.13), residues: 3812 helix: 0.40 (0.15), residues: 1273 sheet: -0.71 (0.24), residues: 440 loop : -1.64 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 275 TYR 0.057 0.001 TYR C1229 PHE 0.013 0.001 PHE G 65 TRP 0.007 0.001 TRP D 580 HIS 0.007 0.001 HIS G 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (30553) covalent geometry : angle 0.56592 / 0.30 (41657) hydrogen bonds : bond 0.03986 / 4.33 ( 1179) hydrogen bonds : angle 5.13123 / 5.36 ( 3216) metal coordination : bond 0.00425 / 0.47 ( 5) metal coordination : angle 2.18110 / 4.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7992 (p) cc_final: 0.7559 (p) REVERT: C 47 TYR cc_start: 0.2063 (m-80) cc_final: 0.0967 (m-80) REVERT: C 130 MET cc_start: 0.8630 (mmm) cc_final: 0.8205 (mmm) REVERT: C 315 MET cc_start: 0.8591 (ttp) cc_final: 0.8212 (ptm) REVERT: C 403 MET cc_start: 0.9071 (tmm) cc_final: 0.8699 (tmm) REVERT: C 488 MET cc_start: 0.8962 (tpt) cc_final: 0.8503 (tpt) REVERT: C 632 ASP cc_start: 0.8372 (p0) cc_final: 0.8074 (p0) REVERT: C 681 MET cc_start: 0.8952 (ttp) cc_final: 0.7916 (ptp) REVERT: C 685 MET cc_start: 0.8854 (ptp) cc_final: 0.8330 (ptp) REVERT: C 704 MET cc_start: 0.8639 (mmp) cc_final: 0.8388 (mmp) REVERT: C 788 SER cc_start: 0.8793 (m) cc_final: 0.8010 (t) REVERT: C 1034 ARG cc_start: 0.9055 (tmm160) cc_final: 0.8689 (ttp80) REVERT: C 1151 LEU cc_start: 0.8520 (tp) cc_final: 0.8247 (tp) REVERT: C 1243 MET cc_start: 0.9119 (tmm) cc_final: 0.8705 (tmm) REVERT: C 1290 MET cc_start: 0.8846 (tpp) cc_final: 0.8609 (mmp) REVERT: C 1319 MET cc_start: 0.8762 (tmm) cc_final: 0.8017 (tmm) REVERT: D 298 MET cc_start: 0.9194 (ttp) cc_final: 0.8973 (ttp) REVERT: D 347 VAL cc_start: 0.9619 (m) cc_final: 0.9378 (t) REVERT: D 484 MET cc_start: 0.8116 (mpp) cc_final: 0.7649 (mpp) REVERT: D 625 MET cc_start: 0.8752 (ttp) cc_final: 0.8264 (tmm) REVERT: D 644 MET cc_start: 0.8257 (mpp) cc_final: 0.7636 (mpp) REVERT: D 1156 LEU cc_start: 0.9241 (mp) cc_final: 0.8982 (mp) REVERT: D 1260 MET cc_start: 0.8731 (mmm) cc_final: 0.8481 (tpp) REVERT: D 1349 GLU cc_start: 0.8155 (pm20) cc_final: 0.7703 (pm20) REVERT: E 43 ASN cc_start: 0.9068 (t0) cc_final: 0.8758 (t0) REVERT: G 29 HIS cc_start: 0.8958 (m90) cc_final: 0.8505 (m90) REVERT: G 43 MET cc_start: 0.6632 (mmm) cc_final: 0.6162 (mmm) outliers start: 1 outliers final: 0 residues processed: 276 average time/residue: 0.1618 time to fit residues: 75.7255 Evaluate side-chains 197 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 152 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 335 optimal weight: 30.0000 chunk 138 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 263 optimal weight: 0.0370 chunk 230 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 253 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 overall best weight: 2.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 628 HIS C 649 GLN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN D1326 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.089926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.061207 restraints weight = 137367.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.063043 restraints weight = 70473.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.064285 restraints weight = 45115.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.065023 restraints weight = 33209.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.065622 restraints weight = 27202.188| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30558 Z= 0.165 Angle : 0.583 12.375 41663 Z= 0.310 Chirality : 0.043 0.327 4828 Planarity : 0.004 0.058 5268 Dihedral : 12.935 176.803 4896 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.62 % Rotamer: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.20 (0.13), residues: 3812 helix: 0.47 (0.15), residues: 1276 sheet: -0.78 (0.24), residues: 443 loop : -1.66 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 275 TYR 0.032 0.002 TYR C1229 PHE 0.019 0.001 PHE A 35 TRP 0.008 0.001 TRP D 580 HIS 0.010 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (30553) covalent geometry : angle 0.58177 / 0.31 (41657) hydrogen bonds : bond 0.03798 / 4.10 ( 1179) hydrogen bonds : angle 5.06753 / 5.31 ( 3216) metal coordination : bond 0.00902 / 0.95 ( 5) metal coordination : angle 3.14285 / 7.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.8107 (p) cc_final: 0.7699 (p) REVERT: C 47 TYR cc_start: 0.2253 (m-80) cc_final: 0.1741 (m-80) REVERT: C 130 MET cc_start: 0.8631 (mmm) cc_final: 0.8145 (mmm) REVERT: C 315 MET cc_start: 0.8566 (ttp) cc_final: 0.8246 (ptm) REVERT: C 403 MET cc_start: 0.9110 (tmm) cc_final: 0.8696 (tmm) REVERT: C 488 MET cc_start: 0.8963 (tpt) cc_final: 0.8537 (tpt) REVERT: C 674 ASP cc_start: 0.9207 (m-30) cc_final: 0.8834 (m-30) REVERT: C 681 MET cc_start: 0.9022 (ttp) cc_final: 0.7856 (ptp) REVERT: C 685 MET cc_start: 0.8843 (ptp) cc_final: 0.8349 (ptp) REVERT: C 704 MET cc_start: 0.8751 (mmp) cc_final: 0.8532 (mmp) REVERT: C 764 CYS cc_start: 0.9378 (t) cc_final: 0.9143 (t) REVERT: C 788 SER cc_start: 0.8814 (m) cc_final: 0.8056 (t) REVERT: C 796 LEU cc_start: 0.9219 (mt) cc_final: 0.8936 (mt) REVERT: C 962 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7820 (tm-30) REVERT: C 1034 ARG cc_start: 0.9064 (tmm160) cc_final: 0.8689 (ttp80) REVERT: C 1107 MET cc_start: 0.8158 (mpp) cc_final: 0.7934 (mmt) REVERT: C 1151 LEU cc_start: 0.8636 (tp) cc_final: 0.8349 (tp) REVERT: C 1281 TYR cc_start: 0.8005 (m-10) cc_final: 0.7733 (m-10) REVERT: C 1319 MET cc_start: 0.8785 (tmm) cc_final: 0.7956 (tmm) REVERT: D 130 MET cc_start: 0.8645 (tmm) cc_final: 0.8423 (tmm) REVERT: D 298 MET cc_start: 0.9231 (ttp) cc_final: 0.9021 (ttp) REVERT: D 372 MET cc_start: 0.8528 (mmp) cc_final: 0.8293 (mmp) REVERT: D 484 MET cc_start: 0.8273 (mpp) cc_final: 0.7781 (mpp) REVERT: D 513 MET cc_start: 0.8821 (mmt) cc_final: 0.8527 (tpp) REVERT: D 581 MET cc_start: 0.8474 (ttm) cc_final: 0.8202 (ttm) REVERT: D 625 MET cc_start: 0.8726 (ttp) cc_final: 0.8313 (tmm) REVERT: D 644 MET cc_start: 0.8378 (mpp) cc_final: 0.7766 (mpp) REVERT: D 743 MET cc_start: 0.8170 (ppp) cc_final: 0.7699 (ppp) REVERT: D 1349 GLU cc_start: 0.8157 (pm20) cc_final: 0.7904 (pm20) REVERT: E 43 ASN cc_start: 0.8999 (t0) cc_final: 0.8531 (t0) REVERT: E 70 GLN cc_start: 0.9686 (tm-30) cc_final: 0.9437 (pt0) REVERT: G 29 HIS cc_start: 0.8977 (m90) cc_final: 0.8450 (m90) REVERT: G 75 MET cc_start: 0.9006 (mmm) cc_final: 0.8787 (tpt) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.1763 time to fit residues: 76.1683 Evaluate side-chains 198 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 383 optimal weight: 40.0000 chunk 359 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 209 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 326 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 249 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 649 GLN C1146 GLN C1288 GLN D 700 ASN E 75 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.089839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.061186 restraints weight = 137923.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.063045 restraints weight = 70430.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.064255 restraints weight = 44801.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.064997 restraints weight = 32964.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.065584 restraints weight = 27034.799| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30558 Z= 0.151 Angle : 0.576 11.964 41663 Z= 0.304 Chirality : 0.043 0.320 4828 Planarity : 0.004 0.059 5268 Dihedral : 12.989 176.042 4896 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.81 % Rotamer: Outliers : 0.11 % Allowed : 3.10 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.15 (0.13), residues: 3812 helix: 0.53 (0.15), residues: 1275 sheet: -0.78 (0.24), residues: 443 loop : -1.64 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 275 TYR 0.029 0.001 TYR C1229 PHE 0.014 0.001 PHE C1025 TRP 0.008 0.001 TRP D 580 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (30553) covalent geometry : angle 0.57514 / 0.30 (41657) hydrogen bonds : bond 0.03553 / 3.83 ( 1179) hydrogen bonds : angle 4.93687 / 5.19 ( 3216) metal coordination : bond 0.00818 / 0.87 ( 5) metal coordination : angle 2.84798 / 6.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 262 time to evaluate : 1.104 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 54 CYS cc_start: 0.8086 (p) cc_final: 0.7725 (p) REVERT: C 130 MET cc_start: 0.8666 (mmm) cc_final: 0.8207 (mmm) REVERT: C 315 MET cc_start: 0.8538 (ttp) cc_final: 0.8238 (ptm) REVERT: C 403 MET cc_start: 0.9072 (tmm) cc_final: 0.8670 (tmm) REVERT: C 488 MET cc_start: 0.9005 (tpt) cc_final: 0.8708 (tpt) REVERT: C 674 ASP cc_start: 0.9186 (m-30) cc_final: 0.8805 (m-30) REVERT: C 681 MET cc_start: 0.9010 (ttp) cc_final: 0.7944 (ptm) REVERT: C 685 MET cc_start: 0.8823 (ptp) cc_final: 0.8349 (ptp) REVERT: C 704 MET cc_start: 0.8707 (mmp) cc_final: 0.8492 (mmp) REVERT: C 764 CYS cc_start: 0.9351 (t) cc_final: 0.9109 (t) REVERT: C 788 SER cc_start: 0.8806 (m) cc_final: 0.8064 (t) REVERT: C 796 LEU cc_start: 0.9200 (mt) cc_final: 0.8824 (mt) REVERT: C 1034 ARG cc_start: 0.9036 (tmm160) cc_final: 0.8641 (ttp80) REVERT: C 1151 LEU cc_start: 0.8606 (tp) cc_final: 0.8303 (tp) REVERT: C 1319 MET cc_start: 0.8776 (tmm) cc_final: 0.8086 (tmm) REVERT: D 484 MET cc_start: 0.8090 (mpp) cc_final: 0.7492 (mpp) REVERT: D 581 MET cc_start: 0.8490 (ttm) cc_final: 0.8185 (ttm) REVERT: D 625 MET cc_start: 0.8637 (ttp) cc_final: 0.8312 (tmm) REVERT: D 1260 MET cc_start: 0.8829 (tpp) cc_final: 0.8549 (tpp) REVERT: D 1349 GLU cc_start: 0.8148 (pm20) cc_final: 0.7676 (pm20) REVERT: E 43 ASN cc_start: 0.8932 (t0) cc_final: 0.8424 (t0) REVERT: G 29 HIS cc_start: 0.8988 (m90) cc_final: 0.8479 (m90) outliers start: 3 outliers final: 1 residues processed: 263 average time/residue: 0.1701 time to fit residues: 76.1727 Evaluate side-chains 198 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 332 optimal weight: 8.9990 chunk 232 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 339 optimal weight: 50.0000 chunk 154 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 362 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 377 optimal weight: 50.0000 chunk 108 optimal weight: 0.9990 chunk 350 optimal weight: 50.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN C 573 ASN C 649 GLN C 832 HIS ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.087824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.061255 restraints weight = 124276.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.062925 restraints weight = 66842.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.064077 restraints weight = 43588.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.064862 restraints weight = 32289.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.065309 restraints weight = 26410.795| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30558 Z= 0.201 Angle : 0.619 13.634 41663 Z= 0.326 Chirality : 0.044 0.314 4828 Planarity : 0.004 0.060 5268 Dihedral : 13.078 173.343 4896 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % 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: -1.21 (0.13), residues: 3812 helix: 0.52 (0.15), residues: 1266 sheet: -0.89 (0.23), residues: 444 loop : -1.66 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 368 TYR 0.063 0.002 TYR C1229 PHE 0.016 0.001 PHE C1025 TRP 0.009 0.001 TRP D 580 HIS 0.006 0.001 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (30553) covalent geometry : angle 0.61801 / 0.33 (41657) hydrogen bonds : bond 0.03804 / 4.09 ( 1179) hydrogen bonds : angle 5.00293 / 5.33 ( 3216) metal coordination : bond 0.01190 / 1.19 ( 5) metal coordination : angle 3.45524 / 7.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 248 time to evaluate : 1.104 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: C 130 MET cc_start: 0.8584 (mmm) cc_final: 0.8132 (mmm) REVERT: C 403 MET cc_start: 0.8919 (tmm) cc_final: 0.8581 (tmm) REVERT: C 423 ASP cc_start: 0.8589 (p0) cc_final: 0.8385 (p0) REVERT: C 488 MET cc_start: 0.8869 (tpt) cc_final: 0.8583 (tpt) REVERT: C 674 ASP cc_start: 0.9122 (m-30) cc_final: 0.8692 (m-30) REVERT: C 681 MET cc_start: 0.8988 (ttp) cc_final: 0.7929 (ptm) REVERT: C 685 MET cc_start: 0.8669 (ptp) cc_final: 0.8224 (ptp) REVERT: C 704 MET cc_start: 0.8636 (mmp) cc_final: 0.8392 (mmp) REVERT: C 764 CYS cc_start: 0.9255 (t) cc_final: 0.8994 (t) REVERT: C 1034 ARG cc_start: 0.8913 (tmm160) cc_final: 0.8554 (ttp80) REVERT: C 1107 MET cc_start: 0.8156 (mpp) cc_final: 0.7917 (mmt) REVERT: C 1151 LEU cc_start: 0.8515 (tp) cc_final: 0.8222 (tp) REVERT: C 1319 MET cc_start: 0.8827 (tmm) cc_final: 0.8152 (tmm) REVERT: D 625 MET cc_start: 0.8832 (tmm) cc_final: 0.8610 (tmm) REVERT: D 788 LEU cc_start: 0.9557 (tp) cc_final: 0.9350 (tp) REVERT: D 1325 PHE cc_start: 0.8806 (t80) cc_final: 0.8475 (t80) REVERT: E 39 VAL cc_start: 0.9000 (t) cc_final: 0.8790 (t) REVERT: E 43 ASN cc_start: 0.8834 (t0) cc_final: 0.8329 (t0) REVERT: E 70 GLN cc_start: 0.9640 (tm-30) cc_final: 0.9432 (tm-30) REVERT: G 29 HIS cc_start: 0.9040 (m90) cc_final: 0.8418 (m90) REVERT: G 77 ASP cc_start: 0.6250 (t70) cc_final: 0.5487 (t0) REVERT: G 81 HIS cc_start: 0.8681 (OUTLIER) cc_final: 0.8170 (m90) outliers start: 2 outliers final: 0 residues processed: 248 average time/residue: 0.1728 time to fit residues: 72.4728 Evaluate side-chains 195 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 2 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 322 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 303 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 649 GLN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN D 700 ASN E 75 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.090282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.064422 restraints weight = 117903.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.066131 restraints weight = 61826.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.067350 restraints weight = 39728.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.068074 restraints weight = 29014.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.068658 restraints weight = 23666.240| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30558 Z= 0.147 Angle : 0.588 12.182 41663 Z= 0.307 Chirality : 0.044 0.316 4828 Planarity : 0.004 0.060 5268 Dihedral : 13.083 174.657 4896 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 0.07 % Allowed : 1.97 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % 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: -1.15 (0.13), residues: 3812 helix: 0.56 (0.15), residues: 1270 sheet: -0.85 (0.23), residues: 443 loop : -1.63 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 275 TYR 0.026 0.001 TYR C1231 PHE 0.016 0.001 PHE C1025 TRP 0.011 0.001 TRP C1276 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (30553) covalent geometry : angle 0.58743 / 0.31 (41657) hydrogen bonds : bond 0.03511 / 3.76 ( 1179) hydrogen bonds : angle 4.86921 / 5.18 ( 3216) metal coordination : bond 0.00778 / 0.80 ( 5) metal coordination : angle 2.64874 / 5.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 257 time to evaluate : 1.563 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 54 CYS cc_start: 0.7960 (p) cc_final: 0.7614 (p) REVERT: C 130 MET cc_start: 0.8621 (mmm) cc_final: 0.8193 (mmm) REVERT: C 403 MET cc_start: 0.8919 (tmm) cc_final: 0.8570 (tmm) REVERT: C 419 ILE cc_start: 0.9593 (pt) cc_final: 0.8883 (mm) REVERT: C 423 ASP cc_start: 0.8604 (p0) cc_final: 0.8389 (p0) REVERT: C 488 MET cc_start: 0.8814 (tpt) cc_final: 0.8503 (tpp) REVERT: C 659 GLN cc_start: 0.8789 (pp30) cc_final: 0.8581 (pp30) REVERT: C 674 ASP cc_start: 0.9107 (m-30) cc_final: 0.8639 (m-30) REVERT: C 681 MET cc_start: 0.8973 (ttp) cc_final: 0.7776 (ptm) REVERT: C 685 MET cc_start: 0.8675 (ptp) cc_final: 0.8217 (ptp) REVERT: C 704 MET cc_start: 0.8589 (mmp) cc_final: 0.8337 (mmp) REVERT: C 764 CYS cc_start: 0.9251 (t) cc_final: 0.8995 (t) REVERT: C 1107 MET cc_start: 0.8079 (mpp) cc_final: 0.7849 (mmt) REVERT: C 1151 LEU cc_start: 0.8499 (tp) cc_final: 0.8187 (tp) REVERT: C 1319 MET cc_start: 0.8779 (tmm) cc_final: 0.8298 (tmm) REVERT: D 581 MET cc_start: 0.8398 (ttm) cc_final: 0.8163 (ttm) REVERT: D 788 LEU cc_start: 0.9552 (tp) cc_final: 0.9337 (tp) REVERT: D 1260 MET cc_start: 0.8513 (tpp) cc_final: 0.8235 (tpp) REVERT: D 1325 PHE cc_start: 0.8832 (t80) cc_final: 0.8423 (t80) REVERT: D 1349 GLU cc_start: 0.8006 (pm20) cc_final: 0.7229 (pm20) REVERT: E 43 ASN cc_start: 0.8807 (t0) cc_final: 0.8286 (t0) REVERT: E 70 GLN cc_start: 0.9597 (tm-30) cc_final: 0.9388 (tm-30) REVERT: G 29 HIS cc_start: 0.8994 (m90) cc_final: 0.8369 (m90) outliers start: 2 outliers final: 0 residues processed: 258 average time/residue: 0.1767 time to fit residues: 77.6090 Evaluate side-chains 197 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 83 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 368 optimal weight: 4.9990 chunk 266 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 316 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 357 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 649 GLN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 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 = 0.3831 r_free = 0.3831 target = 0.089813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.061059 restraints weight = 138141.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.062858 restraints weight = 70374.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.064111 restraints weight = 45001.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.064842 restraints weight = 33051.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.065443 restraints weight = 27130.086| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30558 Z= 0.134 Angle : 0.587 11.523 41663 Z= 0.306 Chirality : 0.043 0.315 4828 Planarity : 0.004 0.060 5268 Dihedral : 13.069 174.600 4896 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 0.04 % Allowed : 1.20 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % 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: -1.09 (0.13), residues: 3812 helix: 0.62 (0.15), residues: 1261 sheet: -0.84 (0.24), residues: 443 loop : -1.58 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG C 275 TYR 0.030 0.001 TYR D1363 PHE 0.017 0.001 PHE C1025 TRP 0.011 0.001 TRP C1276 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (30553) covalent geometry : angle 0.58655 / 0.31 (41657) hydrogen bonds : bond 0.03414 / 3.66 ( 1179) hydrogen bonds : angle 4.81316 / 5.12 ( 3216) metal coordination : bond 0.00624 / 0.67 ( 5) metal coordination : angle 2.31730 / 5.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 1.192 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 54 CYS cc_start: 0.8104 (p) cc_final: 0.7712 (p) REVERT: C 130 MET cc_start: 0.8643 (mmm) cc_final: 0.8181 (mmm) REVERT: C 403 MET cc_start: 0.9102 (tmm) cc_final: 0.8705 (tmm) REVERT: C 419 ILE cc_start: 0.9574 (pt) cc_final: 0.8756 (mm) REVERT: C 423 ASP cc_start: 0.8699 (p0) cc_final: 0.8491 (p0) REVERT: C 488 MET cc_start: 0.8940 (tpt) cc_final: 0.8618 (tpp) REVERT: C 659 GLN cc_start: 0.8841 (pp30) cc_final: 0.8246 (pp30) REVERT: C 674 ASP cc_start: 0.9176 (m-30) cc_final: 0.8767 (m-30) REVERT: C 681 MET cc_start: 0.9031 (ttp) cc_final: 0.7767 (ptm) REVERT: C 685 MET cc_start: 0.8814 (ptp) cc_final: 0.8325 (ptp) REVERT: C 704 MET cc_start: 0.8745 (mmp) cc_final: 0.8502 (mmp) REVERT: C 764 CYS cc_start: 0.9344 (t) cc_final: 0.9104 (t) REVERT: C 1107 MET cc_start: 0.8031 (mpp) cc_final: 0.7762 (mmt) REVERT: C 1151 LEU cc_start: 0.8617 (tp) cc_final: 0.8276 (tp) REVERT: C 1319 MET cc_start: 0.8743 (tmm) cc_final: 0.8299 (tmm) REVERT: D 479 GLU cc_start: 0.8693 (pp20) cc_final: 0.8437 (pp20) REVERT: D 484 MET cc_start: 0.7775 (mpp) cc_final: 0.7369 (mpp) REVERT: D 581 MET cc_start: 0.8462 (ttm) cc_final: 0.8127 (ttm) REVERT: D 625 MET cc_start: 0.8828 (tmm) cc_final: 0.8533 (tmm) REVERT: D 743 MET cc_start: 0.8137 (ppp) cc_final: 0.7618 (ppp) REVERT: D 788 LEU cc_start: 0.9559 (tp) cc_final: 0.9349 (tp) REVERT: D 822 MET cc_start: 0.8443 (tpt) cc_final: 0.8168 (tpp) REVERT: D 1260 MET cc_start: 0.8778 (tpp) cc_final: 0.8467 (tpp) REVERT: D 1325 PHE cc_start: 0.8810 (t80) cc_final: 0.8306 (t80) REVERT: D 1349 GLU cc_start: 0.8221 (pm20) cc_final: 0.7377 (pm20) REVERT: E 43 ASN cc_start: 0.8944 (t0) cc_final: 0.8433 (t0) REVERT: G 29 HIS cc_start: 0.9102 (m90) cc_final: 0.8456 (m90) REVERT: G 31 LYS cc_start: 0.6490 (pttp) cc_final: 0.6256 (pttm) outliers start: 1 outliers final: 0 residues processed: 255 average time/residue: 0.1705 time to fit residues: 74.9533 Evaluate side-chains 200 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 329 optimal weight: 20.0000 chunk 105 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 232 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 353 optimal weight: 50.0000 chunk 145 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 383 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 649 GLN ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS D 700 ASN ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN E 75 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.087559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.061097 restraints weight = 121773.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.062778 restraints weight = 65098.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.063905 restraints weight = 42282.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.064632 restraints weight = 31335.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.065161 restraints weight = 25777.070| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30558 Z= 0.255 Angle : 0.682 15.203 41663 Z= 0.355 Chirality : 0.045 0.312 4828 Planarity : 0.004 0.052 5268 Dihedral : 13.198 173.829 4896 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.66 % Favored : 93.28 % Rotamer: Outliers : 0.07 % Allowed : 0.60 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % 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: -1.35 (0.13), residues: 3812 helix: 0.41 (0.15), residues: 1267 sheet: -1.05 (0.23), residues: 456 loop : -1.74 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 275 TYR 0.024 0.002 TYR A 177 PHE 0.020 0.002 PHE C 464 TRP 0.018 0.002 TRP C1276 HIS 0.007 0.002 HIS C 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.25 (30553) covalent geometry : angle 0.68127 / 0.36 (41657) hydrogen bonds : bond 0.03993 / 4.30 ( 1179) hydrogen bonds : angle 5.08008 / 5.51 ( 3216) metal coordination : bond 0.01559 / 1.50 ( 5) metal coordination : angle 3.46220 / 7.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 1.225 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 54 CYS cc_start: 0.7950 (p) cc_final: 0.7598 (p) REVERT: C 130 MET cc_start: 0.8612 (mmm) cc_final: 0.8241 (mmm) REVERT: C 403 MET cc_start: 0.8950 (tmm) cc_final: 0.8580 (tmm) REVERT: C 419 ILE cc_start: 0.9637 (pt) cc_final: 0.8916 (mm) REVERT: C 423 ASP cc_start: 0.8634 (p0) cc_final: 0.8368 (p0) REVERT: C 488 MET cc_start: 0.8840 (tpt) cc_final: 0.8593 (tpp) REVERT: C 659 GLN cc_start: 0.9108 (pp30) cc_final: 0.8443 (pp30) REVERT: C 674 ASP cc_start: 0.9061 (m-30) cc_final: 0.8620 (m-30) REVERT: C 681 MET cc_start: 0.8983 (ttp) cc_final: 0.7942 (ttp) REVERT: C 685 MET cc_start: 0.8639 (ptp) cc_final: 0.8150 (ptp) REVERT: C 704 MET cc_start: 0.8762 (mmp) cc_final: 0.8490 (mmp) REVERT: C 764 CYS cc_start: 0.9256 (t) cc_final: 0.8997 (t) REVERT: C 1107 MET cc_start: 0.8161 (mpp) cc_final: 0.7688 (mmt) REVERT: C 1151 LEU cc_start: 0.8560 (tp) cc_final: 0.8254 (tp) REVERT: C 1281 TYR cc_start: 0.7765 (m-10) cc_final: 0.7458 (m-10) REVERT: C 1319 MET cc_start: 0.8851 (tmm) cc_final: 0.8371 (tmm) REVERT: D 484 MET cc_start: 0.7656 (mpp) cc_final: 0.7373 (mpp) REVERT: D 822 MET cc_start: 0.8555 (tpt) cc_final: 0.8323 (tpp) REVERT: D 1349 GLU cc_start: 0.8191 (pm20) cc_final: 0.7447 (pm20) REVERT: E 43 ASN cc_start: 0.8848 (t0) cc_final: 0.8358 (t0) REVERT: G 29 HIS cc_start: 0.9026 (m90) cc_final: 0.8418 (m90) REVERT: G 31 LYS cc_start: 0.6533 (pttp) cc_final: 0.6268 (pttm) outliers start: 2 outliers final: 0 residues processed: 242 average time/residue: 0.1742 time to fit residues: 72.2157 Evaluate side-chains 193 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 174 optimal weight: 7.9990 chunk 360 optimal weight: 40.0000 chunk 37 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 325 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 649 GLN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.089432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.063303 restraints weight = 118547.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.065029 restraints weight = 62397.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.066173 restraints weight = 40056.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.066934 restraints weight = 29471.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.067462 restraints weight = 24059.548| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30558 Z= 0.160 Angle : 0.614 12.486 41663 Z= 0.320 Chirality : 0.044 0.310 4828 Planarity : 0.004 0.053 5268 Dihedral : 13.159 173.218 4896 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.67 % Favored : 94.28 % Rotamer: Outliers : 0.04 % Allowed : 0.42 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % 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: -1.22 (0.13), residues: 3812 helix: 0.50 (0.15), residues: 1266 sheet: -0.99 (0.23), residues: 457 loop : -1.65 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 275 TYR 0.047 0.002 TYR C1229 PHE 0.017 0.001 PHE C1025 TRP 0.009 0.001 TRP C1276 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (30553) covalent geometry : angle 0.61349 / 0.32 (41657) hydrogen bonds : bond 0.03560 / 3.83 ( 1179) hydrogen bonds : angle 4.90444 / 5.30 ( 3216) metal coordination : bond 0.00792 / 0.77 ( 5) metal coordination : angle 2.58902 / 5.22 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 1.235 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: A 145 LYS cc_start: 0.9224 (tttt) cc_final: 0.8934 (ttmm) REVERT: C 130 MET cc_start: 0.8623 (mmm) cc_final: 0.8156 (mmm) REVERT: C 403 MET cc_start: 0.8936 (tmm) cc_final: 0.8584 (tmm) REVERT: C 419 ILE cc_start: 0.9613 (pt) cc_final: 0.8878 (mm) REVERT: C 423 ASP cc_start: 0.8620 (p0) cc_final: 0.8343 (p0) REVERT: C 674 ASP cc_start: 0.9072 (m-30) cc_final: 0.8544 (m-30) REVERT: C 681 MET cc_start: 0.8947 (ttp) cc_final: 0.7932 (ptm) REVERT: C 685 MET cc_start: 0.8675 (ptp) cc_final: 0.8269 (ptt) REVERT: C 704 MET cc_start: 0.8627 (mmp) cc_final: 0.8362 (mmp) REVERT: C 764 CYS cc_start: 0.9227 (t) cc_final: 0.8933 (t) REVERT: C 788 SER cc_start: 0.8702 (m) cc_final: 0.7957 (t) REVERT: C 796 LEU cc_start: 0.9128 (mt) cc_final: 0.8899 (mt) REVERT: C 1101 LEU cc_start: 0.8956 (mm) cc_final: 0.8716 (mp) REVERT: C 1107 MET cc_start: 0.7986 (mpp) cc_final: 0.7758 (mmt) REVERT: C 1151 LEU cc_start: 0.8508 (tp) cc_final: 0.8190 (tp) REVERT: C 1319 MET cc_start: 0.8741 (tmm) cc_final: 0.8372 (tmm) REVERT: D 484 MET cc_start: 0.7654 (mpp) cc_final: 0.7363 (mpp) REVERT: D 725 MET cc_start: 0.9170 (mmt) cc_final: 0.8882 (mmm) REVERT: D 1260 MET cc_start: 0.8468 (tpp) cc_final: 0.8218 (tpp) REVERT: D 1349 GLU cc_start: 0.8100 (pm20) cc_final: 0.7372 (pm20) REVERT: E 43 ASN cc_start: 0.8842 (t0) cc_final: 0.8477 (t0) REVERT: G 29 HIS cc_start: 0.9029 (m90) cc_final: 0.8412 (m90) REVERT: G 31 LYS cc_start: 0.6466 (pttp) cc_final: 0.6206 (pttm) outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.1730 time to fit residues: 73.0284 Evaluate side-chains 196 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 321 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 337 optimal weight: 0.0570 chunk 281 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 55 optimal weight: 7.9990 chunk 193 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 573 ASN C 649 GLN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.089801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.060980 restraints weight = 137353.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.062840 restraints weight = 69777.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.064042 restraints weight = 44276.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.064814 restraints weight = 32685.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.065354 restraints weight = 26779.289| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30558 Z= 0.116 Angle : 0.598 10.747 41663 Z= 0.309 Chirality : 0.044 0.311 4828 Planarity : 0.004 0.054 5268 Dihedral : 13.101 173.739 4896 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.27 % Favored : 94.65 % Rotamer: Outliers : 0.04 % Allowed : 0.53 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % 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: -1.10 (0.13), residues: 3812 helix: 0.60 (0.15), residues: 1265 sheet: -1.00 (0.23), residues: 456 loop : -1.54 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 275 TYR 0.022 0.001 TYR C1231 PHE 0.017 0.001 PHE C1025 TRP 0.008 0.001 TRP D 115 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (30553) covalent geometry : angle 0.59578 / 0.31 (41657) hydrogen bonds : bond 0.03390 / 3.66 ( 1179) hydrogen bonds : angle 4.76112 / 5.10 ( 3216) metal coordination : bond 0.00688 / 0.51 ( 5) metal coordination : angle 4.39707 / 8.07 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5630.38 seconds wall clock time: 98 minutes 3.11 seconds (5883.11 seconds total)