Starting phenix.real_space_refine on Fri Mar 6 10:58:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7py7_13715/03_2026/7py7_13715.cif Found real_map, /net/cci-nas-00/data/ceres_data/7py7_13715/03_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_13715/03_2026/7py7_13715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7py7_13715/03_2026/7py7_13715.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7py7_13715/03_2026/7py7_13715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7py7_13715/03_2026/7py7_13715.map" } 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-5986/lib/python3.9/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: 5.80, per 1000 atoms: 0.19 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: 2.52 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: 3.76 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: 6.33 Time building geometry restraints manager: 3.31 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=" N VAL D 357 " pdb=" CA VAL D 357 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.93e+00 bond pdb=" N TYR D 360 " pdb=" CA TYR D 360 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.01e+00 ... (remaining 30548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 41222 2.59 - 5.17: 378 5.17 - 7.76: 50 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=" 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=" C ALA C 910 " pdb=" N SER C 911 " pdb=" CA SER C 911 " ideal model delta sigma weight residual 121.70 128.96 -7.26 1.80e+00 3.09e-01 1.63e+01 angle pdb=" C LEU C 946 " pdb=" N GLU C 947 " pdb=" CA GLU C 947 " ideal model delta sigma weight residual 121.14 114.20 6.94 1.75e+00 3.27e-01 1.57e+01 angle pdb=" C LYS C1035 " pdb=" N ILE C1036 " pdb=" CA ILE C1036 " ideal model delta sigma weight residual 121.97 128.50 -6.53 1.80e+00 3.09e-01 1.32e+01 ... (remaining 41652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 18089 35.44 - 70.89: 466 70.89 - 106.33: 29 106.33 - 141.78: 2 141.78 - 177.22: 2 Dihedral angle restraints: 18588 sinusoidal: 7585 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 18585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3295 0.039 - 0.077: 1077 0.077 - 0.116: 391 0.116 - 0.154: 55 0.154 - 0.193: 10 Chirality restraints: 4828 Sorted by residual: 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 chirality pdb=" CA ASP C 199 " pdb=" N ASP C 199 " pdb=" C ASP C 199 " pdb=" CB ASP C 199 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.75e-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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.870 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 0.053 30558 Z= 0.156 Angle : 0.648 12.928 41663 Z= 0.342 Chirality : 0.044 0.193 4828 Planarity : 0.004 0.049 5268 Dihedral : 15.459 177.220 11494 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 covalent geometry : bond 0.00318 (30553) covalent geometry : angle 0.64640 (41657) hydrogen bonds : bond 0.20040 ( 1179) hydrogen bonds : angle 7.13482 ( 3216) metal coordination : bond 0.01646 ( 5) metal coordination : angle 4.05894 ( 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 : 1.123 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: 0.1636 time to fit residues: 73.2704 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 : 1.038 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 127 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 573 ASN C 628 HIS C 649 GLN C 832 HIS ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN D 700 ASN E 75 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.088652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.059249 restraints weight = 140359.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.061009 restraints weight = 72806.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.062205 restraints weight = 47047.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.062957 restraints weight = 34907.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.063520 restraints weight = 28790.757| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1198 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= 0.219 Angle : 0.622 14.245 41663 Z= 0.331 Chirality : 0.043 0.172 4828 Planarity : 0.004 0.053 5268 Dihedral : 13.538 177.100 4950 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.82 % Favored : 94.10 % Rotamer: Outliers : 0.11 % Allowed : 6.23 % Favored : 93.67 % 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: -1.36 (0.13), residues: 3812 helix: 0.25 (0.15), residues: 1270 sheet: -0.81 (0.23), residues: 452 loop : -1.71 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 275 TYR 0.052 0.002 TYR C1229 PHE 0.017 0.001 PHE C1164 TRP 0.015 0.001 TRP D 580 HIS 0.006 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00467 (30553) covalent geometry : angle 0.61893 (41657) hydrogen bonds : bond 0.04342 ( 1179) hydrogen bonds : angle 5.30831 ( 3216) metal coordination : bond 0.01430 ( 5) metal coordination : angle 5.25871 ( 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 248 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 245 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.8686 (mmm) cc_final: 0.8327 (mmm) REVERT: C 239 MET cc_start: 0.9036 (mmm) cc_final: 0.8340 (mmm) REVERT: C 403 MET cc_start: 0.9097 (tmm) cc_final: 0.8721 (tmm) REVERT: C 488 MET cc_start: 0.8990 (tpt) cc_final: 0.8581 (tpt) REVERT: C 632 ASP cc_start: 0.8238 (p0) cc_final: 0.8021 (p0) REVERT: C 681 MET cc_start: 0.8986 (ttp) cc_final: 0.7948 (ptp) REVERT: C 685 MET cc_start: 0.8758 (ptp) cc_final: 0.8337 (ptp) REVERT: C 704 MET cc_start: 0.8775 (mmp) cc_final: 0.8545 (mmp) REVERT: C 760 ASN cc_start: 0.8294 (m110) cc_final: 0.8070 (m110) REVERT: C 764 CYS cc_start: 0.9306 (t) cc_final: 0.9040 (t) REVERT: C 1151 LEU cc_start: 0.8587 (tp) cc_final: 0.8326 (tp) REVERT: C 1230 MET cc_start: 0.8790 (ppp) cc_final: 0.8337 (ppp) REVERT: C 1243 MET cc_start: 0.9384 (tmm) cc_final: 0.9119 (tmm) REVERT: C 1275 VAL cc_start: 0.9386 (t) cc_final: 0.9171 (t) REVERT: C 1290 MET cc_start: 0.9272 (tpp) cc_final: 0.8726 (mmm) REVERT: C 1292 THR cc_start: 0.8874 (m) cc_final: 0.8408 (p) REVERT: C 1319 MET cc_start: 0.8843 (tmm) cc_final: 0.7982 (tmm) REVERT: D 343 LEU cc_start: 0.9459 (mt) cc_final: 0.8973 (mt) REVERT: D 484 MET cc_start: 0.8221 (mpp) cc_final: 0.7729 (mpp) REVERT: D 625 MET cc_start: 0.8766 (ttp) cc_final: 0.8350 (tmm) REVERT: D 644 MET cc_start: 0.8512 (mpp) cc_final: 0.7913 (mpp) REVERT: D 1260 MET cc_start: 0.8711 (mmm) cc_final: 0.8417 (tpp) REVERT: D 1349 GLU cc_start: 0.8182 (pm20) cc_final: 0.7598 (pm20) REVERT: E 43 ASN cc_start: 0.9029 (t0) cc_final: 0.8725 (t0) REVERT: G 29 HIS cc_start: 0.9067 (m90) cc_final: 0.8634 (m90) REVERT: G 35 MET cc_start: 0.6905 (mpp) cc_final: 0.6323 (mpp) REVERT: G 43 MET cc_start: 0.6439 (mmm) cc_final: 0.5939 (mmm) outliers start: 3 outliers final: 1 residues processed: 247 average time/residue: 0.1618 time to fit residues: 68.4916 Evaluate side-chains 193 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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: 3.9990 chunk 85 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 211 optimal weight: 0.3980 chunk 104 optimal weight: 7.9990 chunk 329 optimal weight: 30.0000 chunk 275 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 305 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS B 137 ASN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 649 GLN C1146 GLN D1326 GLN D1367 GLN E 75 GLN G 81 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.090598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.061734 restraints weight = 138564.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.063583 restraints weight = 70669.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.064810 restraints weight = 44990.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.065604 restraints weight = 33103.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.066055 restraints weight = 27017.462| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30558 Z= 0.117 Angle : 0.552 10.916 41663 Z= 0.291 Chirality : 0.042 0.212 4828 Planarity : 0.004 0.049 5268 Dihedral : 13.598 175.597 4950 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.12 % Rotamer: Outliers : 0.07 % Allowed : 4.68 % Favored : 95.25 % 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: -1.18 (0.13), residues: 3812 helix: 0.48 (0.15), residues: 1279 sheet: -0.87 (0.23), residues: 449 loop : -1.62 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 275 TYR 0.027 0.001 TYR C1229 PHE 0.016 0.001 PHE C1164 TRP 0.008 0.001 TRP D 580 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00251 (30553) covalent geometry : angle 0.55080 (41657) hydrogen bonds : bond 0.03468 ( 1179) hydrogen bonds : angle 4.87581 ( 3216) metal coordination : bond 0.00603 ( 5) metal coordination : angle 3.17432 ( 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 279 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 277 time to evaluate : 1.133 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: 0.8037 (p) cc_final: 0.7674 (p) REVERT: C 47 TYR cc_start: 0.2276 (m-80) cc_final: 0.1768 (m-80) REVERT: C 130 MET cc_start: 0.8565 (mmm) cc_final: 0.8139 (mmm) REVERT: C 315 MET cc_start: 0.8535 (ttp) cc_final: 0.8208 (ptm) REVERT: C 403 MET cc_start: 0.9085 (tmm) cc_final: 0.8719 (tmm) REVERT: C 488 MET cc_start: 0.9019 (tpt) cc_final: 0.8536 (tpt) REVERT: C 632 ASP cc_start: 0.8370 (p0) cc_final: 0.8095 (p0) REVERT: C 681 MET cc_start: 0.9006 (ttp) cc_final: 0.7727 (ptp) REVERT: C 685 MET cc_start: 0.8785 (ptp) cc_final: 0.8311 (ptp) REVERT: C 704 MET cc_start: 0.8646 (mmp) cc_final: 0.8434 (mmp) REVERT: C 760 ASN cc_start: 0.8338 (m110) cc_final: 0.7960 (m110) REVERT: C 788 SER cc_start: 0.8781 (m) cc_final: 0.8008 (t) REVERT: C 796 LEU cc_start: 0.9154 (mt) cc_final: 0.8812 (mt) REVERT: C 962 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7921 (tm-30) REVERT: C 1034 ARG cc_start: 0.9059 (tmm160) cc_final: 0.8645 (ttp80) REVERT: C 1151 LEU cc_start: 0.8565 (tp) cc_final: 0.8271 (tp) REVERT: C 1230 MET cc_start: 0.8684 (ppp) cc_final: 0.7629 (ppp) REVERT: C 1243 MET cc_start: 0.9273 (tmm) cc_final: 0.9050 (tmm) REVERT: C 1319 MET cc_start: 0.8715 (tmm) cc_final: 0.8050 (tmm) REVERT: D 298 MET cc_start: 0.9224 (ttp) cc_final: 0.8961 (ttp) REVERT: D 343 LEU cc_start: 0.9446 (mt) cc_final: 0.9165 (mt) REVERT: D 479 GLU cc_start: 0.8582 (pp20) cc_final: 0.8369 (pp20) REVERT: D 484 MET cc_start: 0.8301 (mpp) cc_final: 0.7847 (mpp) REVERT: D 485 MET cc_start: 0.8026 (mtt) cc_final: 0.7786 (mmm) REVERT: D 625 MET cc_start: 0.8752 (ttp) cc_final: 0.8497 (tmm) REVERT: D 644 MET cc_start: 0.8091 (mpp) cc_final: 0.7513 (mpp) REVERT: D 1156 LEU cc_start: 0.9231 (mp) cc_final: 0.8978 (mp) REVERT: D 1260 MET cc_start: 0.8716 (mmm) cc_final: 0.8495 (tpp) REVERT: D 1349 GLU cc_start: 0.8200 (pm20) cc_final: 0.7727 (pm20) REVERT: E 43 ASN cc_start: 0.9097 (t0) cc_final: 0.8798 (t0) REVERT: G 29 HIS cc_start: 0.9081 (m90) cc_final: 0.8634 (m90) REVERT: G 43 MET cc_start: 0.6613 (mmm) cc_final: 0.6102 (mmm) REVERT: G 73 MET cc_start: 0.8424 (pmm) cc_final: 0.8164 (pmm) outliers start: 2 outliers final: 1 residues processed: 277 average time/residue: 0.1573 time to fit residues: 74.6578 Evaluate side-chains 209 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 5.9990 chunk 335 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 253 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 649 GLN D 700 ASN ** 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 = 0.3813 r_free = 0.3813 target = 0.089027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.059848 restraints weight = 137543.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.061647 restraints weight = 70704.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.062828 restraints weight = 45432.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.063591 restraints weight = 33705.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.064139 restraints weight = 27696.217| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30558 Z= 0.172 Angle : 0.577 12.990 41663 Z= 0.305 Chirality : 0.042 0.169 4828 Planarity : 0.004 0.052 5268 Dihedral : 13.654 173.588 4950 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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: 0.59 (0.15), residues: 1262 sheet: -0.87 (0.23), residues: 444 loop : -1.63 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 275 TYR 0.065 0.002 TYR C1229 PHE 0.021 0.001 PHE C1025 TRP 0.008 0.001 TRP D 580 HIS 0.006 0.001 HIS C 554 Details of bonding type rmsd covalent geometry : bond 0.00374 (30553) covalent geometry : angle 0.57584 (41657) hydrogen bonds : bond 0.03571 ( 1179) hydrogen bonds : angle 4.87531 ( 3216) metal coordination : bond 0.00950 ( 5) metal coordination : angle 3.50946 ( 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 253 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.056 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: 0.8063 (p) cc_final: 0.7662 (p) REVERT: C 130 MET cc_start: 0.8609 (mmm) cc_final: 0.8172 (mmm) REVERT: C 403 MET cc_start: 0.9101 (tmm) cc_final: 0.8729 (tmm) REVERT: C 423 ASP cc_start: 0.8714 (p0) cc_final: 0.8510 (p0) REVERT: C 488 MET cc_start: 0.9049 (tpt) cc_final: 0.8698 (tpt) REVERT: C 632 ASP cc_start: 0.8447 (p0) cc_final: 0.8163 (p0) REVERT: C 674 ASP cc_start: 0.9193 (m-30) cc_final: 0.8825 (m-30) REVERT: C 681 MET cc_start: 0.9029 (ttp) cc_final: 0.7830 (ptm) REVERT: C 685 MET cc_start: 0.8806 (ptp) cc_final: 0.8330 (ptp) REVERT: C 704 MET cc_start: 0.8796 (mmp) cc_final: 0.8580 (mmp) REVERT: C 764 CYS cc_start: 0.9356 (t) cc_final: 0.9074 (t) REVERT: C 788 SER cc_start: 0.8798 (m) cc_final: 0.8046 (t) REVERT: C 796 LEU cc_start: 0.9253 (mt) cc_final: 0.8927 (mt) REVERT: C 1034 ARG cc_start: 0.9085 (tmm160) cc_final: 0.8655 (ttp80) REVERT: C 1101 LEU cc_start: 0.9261 (mm) cc_final: 0.9004 (mm) REVERT: C 1107 MET cc_start: 0.8109 (mpp) cc_final: 0.7884 (mmt) REVERT: C 1151 LEU cc_start: 0.8631 (tp) cc_final: 0.8322 (tp) REVERT: C 1230 MET cc_start: 0.9022 (ppp) cc_final: 0.8620 (ppp) REVERT: C 1243 MET cc_start: 0.9231 (tmm) cc_final: 0.8974 (tmm) REVERT: C 1304 MET cc_start: 0.8580 (ttm) cc_final: 0.8230 (mtp) REVERT: C 1319 MET cc_start: 0.8780 (tmm) cc_final: 0.8239 (tmm) REVERT: D 298 MET cc_start: 0.9266 (ttp) cc_final: 0.9064 (ttp) REVERT: D 484 MET cc_start: 0.8170 (mpp) cc_final: 0.7645 (mpp) REVERT: D 625 MET cc_start: 0.8825 (ttp) cc_final: 0.8483 (tmm) REVERT: D 822 MET cc_start: 0.8243 (tpt) cc_final: 0.7980 (tpp) REVERT: D 1349 GLU cc_start: 0.8213 (pm20) cc_final: 0.7960 (pm20) REVERT: E 30 MET cc_start: 0.9126 (tpp) cc_final: 0.8655 (tpp) REVERT: E 43 ASN cc_start: 0.8946 (t0) cc_final: 0.8484 (t0) REVERT: G 29 HIS cc_start: 0.9171 (m90) cc_final: 0.8674 (m90) REVERT: G 73 MET cc_start: 0.8428 (pmm) cc_final: 0.8091 (pmm) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1647 time to fit residues: 71.0512 Evaluate side-chains 190 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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: 50.0000 chunk 359 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 326 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 249 optimal weight: 9.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 E 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.088194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.062087 restraints weight = 121427.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.063810 restraints weight = 64323.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.064926 restraints weight = 41406.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.065704 restraints weight = 30611.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.066169 restraints weight = 25013.293| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30558 Z= 0.184 Angle : 0.590 13.032 41663 Z= 0.310 Chirality : 0.043 0.166 4828 Planarity : 0.004 0.053 5268 Dihedral : 13.717 170.771 4950 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.15 % Rotamer: Outliers : 0.04 % Allowed : 3.34 % Favored : 96.62 % 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: 0.60 (0.15), residues: 1266 sheet: -0.88 (0.23), residues: 446 loop : -1.64 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 275 TYR 0.030 0.002 TYR C1229 PHE 0.017 0.001 PHE A 35 TRP 0.010 0.001 TRP C1276 HIS 0.005 0.001 HIS C 554 Details of bonding type rmsd covalent geometry : bond 0.00399 (30553) covalent geometry : angle 0.58813 (41657) hydrogen bonds : bond 0.03553 ( 1179) hydrogen bonds : angle 4.85553 ( 3216) metal coordination : bond 0.00993 ( 5) metal coordination : angle 3.41949 ( 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 250 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 1.116 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 54 CYS cc_start: 0.7777 (p) cc_final: 0.7200 (t) REVERT: C 130 MET cc_start: 0.8667 (mmm) cc_final: 0.8193 (mmm) REVERT: C 403 MET cc_start: 0.8953 (tmm) cc_final: 0.8557 (tmm) REVERT: C 423 ASP cc_start: 0.8620 (p0) cc_final: 0.8344 (p0) REVERT: C 488 MET cc_start: 0.8915 (tpt) cc_final: 0.8581 (tpp) REVERT: C 674 ASP cc_start: 0.9125 (m-30) cc_final: 0.8698 (m-30) REVERT: C 681 MET cc_start: 0.8977 (ttp) cc_final: 0.7882 (ttp) REVERT: C 685 MET cc_start: 0.8658 (ptp) cc_final: 0.8176 (ptp) REVERT: C 704 MET cc_start: 0.8620 (mmp) cc_final: 0.8386 (mmp) REVERT: C 764 CYS cc_start: 0.9233 (t) cc_final: 0.8936 (t) REVERT: C 788 SER cc_start: 0.8683 (m) cc_final: 0.7913 (t) REVERT: C 1066 MET cc_start: 0.8512 (ppp) cc_final: 0.8151 (ppp) REVERT: C 1151 LEU cc_start: 0.8520 (tp) cc_final: 0.8213 (tp) REVERT: C 1243 MET cc_start: 0.9192 (tmm) cc_final: 0.8812 (tmm) REVERT: C 1304 MET cc_start: 0.8440 (ttm) cc_final: 0.8022 (mtp) REVERT: C 1319 MET cc_start: 0.8786 (tmm) cc_final: 0.8357 (tmm) REVERT: D 625 MET cc_start: 0.8750 (ttp) cc_final: 0.8310 (tmm) REVERT: D 822 MET cc_start: 0.8214 (tpt) cc_final: 0.8012 (tpp) REVERT: E 30 MET cc_start: 0.8999 (tpp) cc_final: 0.8541 (tpp) REVERT: E 43 ASN cc_start: 0.8836 (t0) cc_final: 0.8377 (t0) REVERT: G 29 HIS cc_start: 0.9129 (m90) cc_final: 0.8629 (m90) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.1587 time to fit residues: 67.8982 Evaluate side-chains 188 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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: 9.9990 chunk 232 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 chunk 339 optimal weight: 50.0000 chunk 154 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 362 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 377 optimal weight: 0.0980 chunk 108 optimal weight: 0.9980 chunk 350 optimal weight: 50.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 649 GLN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS D 700 ASN E 75 GLN G 81 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.090446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.064682 restraints weight = 118707.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.066483 restraints weight = 62153.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.067698 restraints weight = 39641.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.068452 restraints weight = 28946.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.069003 restraints weight = 23540.528| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30558 Z= 0.106 Angle : 0.553 10.134 41663 Z= 0.288 Chirality : 0.042 0.191 4828 Planarity : 0.004 0.052 5268 Dihedral : 13.662 170.331 4950 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.67 % Favored : 95.25 % Rotamer: Outliers : 0.14 % Allowed : 2.50 % Favored : 97.36 % 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: -1.00 (0.13), residues: 3812 helix: 0.71 (0.15), residues: 1258 sheet: -0.77 (0.24), residues: 446 loop : -1.54 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 150 TYR 0.058 0.001 TYR C1229 PHE 0.023 0.001 PHE C1025 TRP 0.029 0.001 TRP D 115 HIS 0.004 0.001 HIS C 554 Details of bonding type rmsd covalent geometry : bond 0.00229 (30553) covalent geometry : angle 0.55281 (41657) hydrogen bonds : bond 0.03153 ( 1179) hydrogen bonds : angle 4.63618 ( 3216) metal coordination : bond 0.00311 ( 5) metal coordination : angle 1.97215 ( 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 269 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 265 time to evaluate : 0.812 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: 0.7834 (p) cc_final: 0.7204 (t) REVERT: C 130 MET cc_start: 0.8573 (mmm) cc_final: 0.8088 (mmm) REVERT: C 403 MET cc_start: 0.8938 (tmm) cc_final: 0.8586 (tmm) REVERT: C 419 ILE cc_start: 0.9560 (pt) cc_final: 0.8790 (mm) REVERT: C 423 ASP cc_start: 0.8616 (p0) cc_final: 0.8320 (p0) REVERT: C 488 MET cc_start: 0.8825 (tpt) cc_final: 0.8596 (tpp) REVERT: C 632 ASP cc_start: 0.8164 (p0) cc_final: 0.7814 (p0) REVERT: C 674 ASP cc_start: 0.9071 (m-30) cc_final: 0.8655 (m-30) REVERT: C 681 MET cc_start: 0.8942 (ttp) cc_final: 0.7643 (ptm) REVERT: C 685 MET cc_start: 0.8669 (ptp) cc_final: 0.8226 (ptp) REVERT: C 704 MET cc_start: 0.8539 (mmp) cc_final: 0.8331 (mmp) REVERT: C 760 ASN cc_start: 0.8238 (m110) cc_final: 0.7294 (m110) REVERT: C 788 SER cc_start: 0.8681 (m) cc_final: 0.7939 (t) REVERT: C 1085 MET cc_start: 0.9420 (mmp) cc_final: 0.9199 (mmt) REVERT: C 1107 MET cc_start: 0.7907 (mpp) cc_final: 0.7643 (mmt) REVERT: C 1151 LEU cc_start: 0.8477 (tp) cc_final: 0.8167 (tp) REVERT: C 1230 MET cc_start: 0.8754 (ppp) cc_final: 0.7382 (ppp) REVERT: C 1243 MET cc_start: 0.9276 (tmm) cc_final: 0.9045 (tmm) REVERT: C 1304 MET cc_start: 0.8389 (ttm) cc_final: 0.8151 (mtp) REVERT: C 1319 MET cc_start: 0.8672 (tmm) cc_final: 0.8379 (tmm) REVERT: D 484 MET cc_start: 0.7684 (mpp) cc_final: 0.7413 (mpp) REVERT: D 625 MET cc_start: 0.8812 (tmm) cc_final: 0.8459 (tmm) REVERT: D 743 MET cc_start: 0.8232 (ppp) cc_final: 0.7758 (ppp) REVERT: D 1325 PHE cc_start: 0.8943 (t80) cc_final: 0.8450 (t80) REVERT: D 1349 GLU cc_start: 0.8026 (pm20) cc_final: 0.7259 (pm20) REVERT: E 30 MET cc_start: 0.9014 (tpp) cc_final: 0.8538 (tpp) REVERT: E 43 ASN cc_start: 0.8869 (t0) cc_final: 0.8421 (t0) REVERT: G 29 HIS cc_start: 0.9100 (m90) cc_final: 0.8597 (m90) REVERT: G 31 LYS cc_start: 0.6370 (pttp) cc_final: 0.6090 (pttm) REVERT: G 73 MET cc_start: 0.8457 (pmm) cc_final: 0.8073 (pmm) REVERT: G 77 ASP cc_start: 0.6601 (t70) cc_final: 0.5732 (t0) REVERT: G 81 HIS cc_start: 0.8745 (OUTLIER) cc_final: 0.8168 (m90) outliers start: 4 outliers final: 0 residues processed: 267 average time/residue: 0.1590 time to fit residues: 72.5371 Evaluate side-chains 197 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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: 8.9990 chunk 65 optimal weight: 4.9990 chunk 274 optimal weight: 0.5980 chunk 165 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 chunk 322 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 303 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN ** C 46 GLN ** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.089751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.064261 restraints weight = 118514.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.066049 restraints weight = 62099.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.067236 restraints weight = 39441.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.068035 restraints weight = 28813.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.068500 restraints weight = 23289.496| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30558 Z= 0.122 Angle : 0.560 11.413 41663 Z= 0.292 Chirality : 0.042 0.243 4828 Planarity : 0.004 0.052 5268 Dihedral : 13.631 170.413 4950 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.88 % Rotamer: Outliers : 0.07 % Allowed : 1.58 % Favored : 98.35 % 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: -0.96 (0.14), residues: 3812 helix: 0.76 (0.15), residues: 1258 sheet: -0.83 (0.23), residues: 449 loop : -1.52 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 275 TYR 0.026 0.001 TYR C1231 PHE 0.025 0.001 PHE C1025 TRP 0.021 0.001 TRP D 115 HIS 0.004 0.001 HIS C 554 Details of bonding type rmsd covalent geometry : bond 0.00268 (30553) covalent geometry : angle 0.55923 (41657) hydrogen bonds : bond 0.03193 ( 1179) hydrogen bonds : angle 4.60600 ( 3216) metal coordination : bond 0.00550 ( 5) metal coordination : angle 2.07944 ( 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 262 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 260 time to evaluate : 0.955 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: 0.7941 (p) cc_final: 0.7195 (t) REVERT: A 145 LYS cc_start: 0.9163 (tttt) cc_final: 0.8869 (ttmm) REVERT: C 130 MET cc_start: 0.8584 (mmm) cc_final: 0.8179 (mmm) REVERT: C 403 MET cc_start: 0.8943 (tmm) cc_final: 0.8604 (tmm) REVERT: C 419 ILE cc_start: 0.9571 (pt) cc_final: 0.8833 (mm) REVERT: C 423 ASP cc_start: 0.8628 (p0) cc_final: 0.8324 (p0) REVERT: C 488 MET cc_start: 0.8800 (tpt) cc_final: 0.8565 (tpp) REVERT: C 632 ASP cc_start: 0.8137 (p0) cc_final: 0.7789 (p0) REVERT: C 674 ASP cc_start: 0.9110 (m-30) cc_final: 0.8667 (m-30) REVERT: C 681 MET cc_start: 0.8952 (ttp) cc_final: 0.7700 (ptm) REVERT: C 685 MET cc_start: 0.8675 (ptp) cc_final: 0.8214 (ptp) REVERT: C 704 MET cc_start: 0.8586 (mmp) cc_final: 0.8339 (mmp) REVERT: C 764 CYS cc_start: 0.9200 (t) cc_final: 0.8891 (t) REVERT: C 788 SER cc_start: 0.8694 (m) cc_final: 0.7943 (t) REVERT: C 1107 MET cc_start: 0.7851 (mpp) cc_final: 0.7648 (mmt) REVERT: C 1151 LEU cc_start: 0.8504 (tp) cc_final: 0.8191 (tp) REVERT: C 1230 MET cc_start: 0.8849 (ppp) cc_final: 0.8343 (ppp) REVERT: C 1268 GLN cc_start: 0.8599 (mp10) cc_final: 0.8329 (mp10) REVERT: C 1315 MET cc_start: 0.8092 (mmm) cc_final: 0.7888 (mmm) REVERT: C 1319 MET cc_start: 0.8714 (tmm) cc_final: 0.8442 (tmm) REVERT: D 237 MET cc_start: 0.9466 (mtm) cc_final: 0.9255 (mtm) REVERT: D 625 MET cc_start: 0.8797 (tmm) cc_final: 0.8458 (tmm) REVERT: D 1254 GLU cc_start: 0.8161 (tt0) cc_final: 0.6999 (tp30) REVERT: D 1325 PHE cc_start: 0.9008 (t80) cc_final: 0.8525 (t80) REVERT: D 1349 GLU cc_start: 0.8050 (pm20) cc_final: 0.7358 (pm20) REVERT: E 30 MET cc_start: 0.8992 (tpp) cc_final: 0.8538 (tpp) REVERT: E 43 ASN cc_start: 0.8886 (t0) cc_final: 0.8433 (t0) REVERT: G 29 HIS cc_start: 0.9092 (m90) cc_final: 0.8586 (m90) REVERT: G 31 LYS cc_start: 0.6368 (pttp) cc_final: 0.6083 (pttm) REVERT: G 115 LEU cc_start: 0.7738 (tp) cc_final: 0.7496 (pp) outliers start: 2 outliers final: 1 residues processed: 261 average time/residue: 0.1641 time to fit residues: 73.0692 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 : 1.060 ------------------------------------------------------------------------------- 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: 5.9990 chunk 86 optimal weight: 10.0000 chunk 368 optimal weight: 50.0000 chunk 266 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 316 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 357 optimal weight: 20.0000 chunk 153 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 649 GLN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS D 700 ASN E 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.086928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.057454 restraints weight = 141484.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.059160 restraints weight = 73241.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.060243 restraints weight = 47331.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.061000 restraints weight = 35531.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.061422 restraints weight = 29430.379| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 30558 Z= 0.282 Angle : 0.709 15.129 41663 Z= 0.370 Chirality : 0.045 0.166 4828 Planarity : 0.004 0.055 5268 Dihedral : 13.886 168.142 4950 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.98 % Favored : 92.94 % Rotamer: Outliers : 0.04 % Allowed : 1.55 % Favored : 98.42 % 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: -1.31 (0.13), residues: 3812 helix: 0.47 (0.15), residues: 1262 sheet: -0.98 (0.23), residues: 431 loop : -1.75 (0.13), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 275 TYR 0.022 0.002 TYR D 631 PHE 0.033 0.002 PHE C 464 TRP 0.035 0.002 TRP G 9 HIS 0.008 0.001 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00609 (30553) covalent geometry : angle 0.70699 (41657) hydrogen bonds : bond 0.04140 ( 1179) hydrogen bonds : angle 5.05551 ( 3216) metal coordination : bond 0.01726 ( 5) metal coordination : angle 4.52117 ( 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 234 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.8020 (mtp) cc_final: 0.7789 (mtp) REVERT: C 403 MET cc_start: 0.9080 (tmm) cc_final: 0.8663 (tmm) REVERT: C 419 ILE cc_start: 0.9658 (pt) cc_final: 0.8867 (mm) REVERT: C 423 ASP cc_start: 0.8698 (p0) cc_final: 0.8399 (p0) REVERT: C 488 MET cc_start: 0.8997 (tpt) cc_final: 0.8712 (tpt) REVERT: C 674 ASP cc_start: 0.9175 (m-30) cc_final: 0.8698 (m-30) REVERT: C 681 MET cc_start: 0.9048 (ttp) cc_final: 0.7774 (ptm) REVERT: C 685 MET cc_start: 0.8772 (ptp) cc_final: 0.8288 (ptp) REVERT: C 704 MET cc_start: 0.8833 (mmp) cc_final: 0.8573 (mmp) REVERT: C 764 CYS cc_start: 0.9301 (t) cc_final: 0.8982 (t) REVERT: C 785 ASP cc_start: 0.8794 (p0) cc_final: 0.8532 (p0) REVERT: C 1107 MET cc_start: 0.8044 (mpp) cc_final: 0.7774 (mmt) REVERT: C 1151 LEU cc_start: 0.8649 (tp) cc_final: 0.8301 (tp) REVERT: C 1230 MET cc_start: 0.8941 (ppp) cc_final: 0.8666 (ppp) REVERT: C 1268 GLN cc_start: 0.8605 (mp10) cc_final: 0.8215 (mp10) REVERT: C 1304 MET cc_start: 0.8558 (ttm) cc_final: 0.8251 (mtp) REVERT: C 1319 MET cc_start: 0.8899 (tmm) cc_final: 0.8404 (tmm) REVERT: D 174 ASP cc_start: 0.8034 (p0) cc_final: 0.7798 (p0) REVERT: D 180 MET cc_start: 0.7641 (tmm) cc_final: 0.7228 (ttp) REVERT: D 237 MET cc_start: 0.9564 (mtm) cc_final: 0.8796 (mtm) REVERT: D 625 MET cc_start: 0.8972 (tmm) cc_final: 0.8599 (tmm) REVERT: D 1349 GLU cc_start: 0.8262 (pm20) cc_final: 0.7818 (pm20) REVERT: E 30 MET cc_start: 0.9134 (tpp) cc_final: 0.8706 (tpp) REVERT: E 43 ASN cc_start: 0.8915 (t0) cc_final: 0.8540 (t0) REVERT: G 29 HIS cc_start: 0.9183 (m90) cc_final: 0.8698 (m90) REVERT: G 70 LEU cc_start: 0.9449 (mt) cc_final: 0.9016 (tt) REVERT: G 72 GLN cc_start: 0.6968 (tp40) cc_final: 0.5937 (tp-100) REVERT: G 73 MET cc_start: 0.8060 (pmm) cc_final: 0.7610 (pmm) outliers start: 1 outliers final: 0 residues processed: 233 average time/residue: 0.1610 time to fit residues: 64.1573 Evaluate side-chains 187 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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: 2.9990 chunk 127 optimal weight: 5.9990 chunk 232 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 353 optimal weight: 40.0000 chunk 145 optimal weight: 5.9990 chunk 261 optimal weight: 0.0870 chunk 189 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 383 optimal weight: 40.0000 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN C 69 GLN C 573 ASN C 649 GLN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.086944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.060510 restraints weight = 124825.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.062226 restraints weight = 66783.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.063341 restraints weight = 43272.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.064125 restraints weight = 32255.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.064566 restraints weight = 26440.069| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30558 Z= 0.121 Angle : 0.585 10.659 41663 Z= 0.303 Chirality : 0.043 0.190 4828 Planarity : 0.004 0.055 5268 Dihedral : 13.794 166.905 4950 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.85 % Favored : 95.09 % 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: -1.01 (0.14), residues: 3812 helix: 0.73 (0.15), residues: 1257 sheet: -0.93 (0.24), residues: 427 loop : -1.53 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 275 TYR 0.041 0.001 TYR C1229 PHE 0.014 0.001 PHE C 464 TRP 0.019 0.001 TRP G 9 HIS 0.004 0.001 HIS C 554 Details of bonding type rmsd covalent geometry : bond 0.00266 (30553) covalent geometry : angle 0.58419 (41657) hydrogen bonds : bond 0.03297 ( 1179) hydrogen bonds : angle 4.67171 ( 3216) metal coordination : bond 0.00439 ( 5) metal coordination : angle 1.82657 ( 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 254 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 1.077 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: 0.7922 (p) cc_final: 0.7171 (t) REVERT: C 130 MET cc_start: 0.8646 (mmm) cc_final: 0.8093 (mmm) REVERT: C 403 MET cc_start: 0.8940 (tmm) cc_final: 0.8585 (tmm) REVERT: C 419 ILE cc_start: 0.9571 (pt) cc_final: 0.8892 (mm) REVERT: C 423 ASP cc_start: 0.8637 (p0) cc_final: 0.8326 (p0) REVERT: C 488 MET cc_start: 0.8844 (tpt) cc_final: 0.8591 (tpp) REVERT: C 632 ASP cc_start: 0.8221 (p0) cc_final: 0.7865 (p0) REVERT: C 674 ASP cc_start: 0.9096 (m-30) cc_final: 0.8612 (m-30) REVERT: C 681 MET cc_start: 0.8965 (ttp) cc_final: 0.7904 (ptm) REVERT: C 685 MET cc_start: 0.8620 (ptp) cc_final: 0.8225 (ptt) REVERT: C 704 MET cc_start: 0.8550 (mmp) cc_final: 0.8328 (mmp) REVERT: C 741 MET cc_start: 0.8165 (tpt) cc_final: 0.7878 (tpp) REVERT: C 764 CYS cc_start: 0.9215 (t) cc_final: 0.8913 (t) REVERT: C 788 SER cc_start: 0.8656 (m) cc_final: 0.7978 (t) REVERT: C 1151 LEU cc_start: 0.8484 (tp) cc_final: 0.8151 (tp) REVERT: C 1278 LEU cc_start: 0.9409 (tp) cc_final: 0.9093 (tp) REVERT: C 1319 MET cc_start: 0.8691 (tmm) cc_final: 0.8369 (tmm) REVERT: D 237 MET cc_start: 0.9476 (mtm) cc_final: 0.9243 (mtm) REVERT: D 625 MET cc_start: 0.8836 (tmm) cc_final: 0.8505 (tmm) REVERT: D 743 MET cc_start: 0.8231 (ppp) cc_final: 0.7545 (ppp) REVERT: D 1260 MET cc_start: 0.8518 (tpp) cc_final: 0.8216 (tpp) REVERT: D 1349 GLU cc_start: 0.8083 (pm20) cc_final: 0.7431 (pm20) REVERT: E 30 MET cc_start: 0.9022 (tpp) cc_final: 0.8566 (tpp) REVERT: E 43 ASN cc_start: 0.8844 (t0) cc_final: 0.8348 (t0) REVERT: G 29 HIS cc_start: 0.9093 (m90) cc_final: 0.8671 (m90) REVERT: G 70 LEU cc_start: 0.9448 (mt) cc_final: 0.9004 (tt) REVERT: G 72 GLN cc_start: 0.6941 (tp40) cc_final: 0.5919 (tp-100) REVERT: G 73 MET cc_start: 0.8253 (pmm) cc_final: 0.7656 (pmm) REVERT: G 77 ASP cc_start: 0.6051 (t70) cc_final: 0.5827 (t0) outliers start: 1 outliers final: 0 residues processed: 253 average time/residue: 0.1630 time to fit residues: 71.0548 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 : 1.054 ------------------------------------------------------------------------------- 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: 6.9990 chunk 360 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 179 optimal weight: 0.1980 chunk 195 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN C 69 GLN C 573 ASN C 649 GLN D 700 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.088535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.059755 restraints weight = 137872.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.061544 restraints weight = 70275.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.062704 restraints weight = 44928.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.063461 restraints weight = 33239.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.063895 restraints weight = 27329.672| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2723 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= 0.175 Angle : 0.614 12.685 41663 Z= 0.319 Chirality : 0.043 0.191 4828 Planarity : 0.004 0.054 5268 Dihedral : 13.807 168.433 4950 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.30 % Favored : 93.65 % Rotamer: Outliers : 0.07 % Allowed : 0.49 % 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: 0.63 (0.15), residues: 1272 sheet: -0.88 (0.23), residues: 443 loop : -1.61 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 275 TYR 0.024 0.002 TYR C1231 PHE 0.013 0.001 PHE D 629 TRP 0.021 0.002 TRP G 9 HIS 0.006 0.001 HIS D 419 Details of bonding type rmsd covalent geometry : bond 0.00384 (30553) covalent geometry : angle 0.61297 (41657) hydrogen bonds : bond 0.03497 ( 1179) hydrogen bonds : angle 4.73867 ( 3216) metal coordination : bond 0.00972 ( 5) metal coordination : angle 2.57693 ( 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 238 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 236 time to evaluate : 1.214 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: 0.8096 (p) cc_final: 0.7209 (t) REVERT: C 130 MET cc_start: 0.8687 (mmm) cc_final: 0.8123 (mmm) REVERT: C 340 ASP cc_start: 0.8184 (m-30) cc_final: 0.7979 (p0) REVERT: C 403 MET cc_start: 0.9086 (tmm) cc_final: 0.8695 (tmm) REVERT: C 419 ILE cc_start: 0.9607 (pt) cc_final: 0.8853 (mm) REVERT: C 423 ASP cc_start: 0.8725 (p0) cc_final: 0.8440 (p0) REVERT: C 488 MET cc_start: 0.8959 (tpt) cc_final: 0.8685 (tpt) REVERT: C 632 ASP cc_start: 0.8464 (p0) cc_final: 0.8141 (p0) REVERT: C 674 ASP cc_start: 0.9165 (m-30) cc_final: 0.8719 (m-30) REVERT: C 681 MET cc_start: 0.9015 (ttp) cc_final: 0.7904 (ptm) REVERT: C 685 MET cc_start: 0.8731 (ptp) cc_final: 0.8327 (ptt) REVERT: C 704 MET cc_start: 0.8756 (mmp) cc_final: 0.8513 (mmp) REVERT: C 741 MET cc_start: 0.8154 (tpt) cc_final: 0.7883 (tpp) REVERT: C 764 CYS cc_start: 0.9318 (t) cc_final: 0.9026 (t) REVERT: C 788 SER cc_start: 0.8749 (m) cc_final: 0.8036 (t) REVERT: C 1107 MET cc_start: 0.7972 (mpp) cc_final: 0.7622 (mmt) REVERT: C 1151 LEU cc_start: 0.8573 (tp) cc_final: 0.8256 (tp) REVERT: C 1319 MET cc_start: 0.8765 (tmm) cc_final: 0.8399 (tmm) REVERT: D 237 MET cc_start: 0.9575 (mtm) cc_final: 0.9335 (mtm) REVERT: D 625 MET cc_start: 0.8839 (tmm) cc_final: 0.8487 (tmm) REVERT: D 1349 GLU cc_start: 0.8154 (pm20) cc_final: 0.7739 (pm20) REVERT: E 30 MET cc_start: 0.9124 (tpp) cc_final: 0.8698 (tpp) REVERT: E 43 ASN cc_start: 0.8913 (t0) cc_final: 0.8400 (t0) REVERT: G 29 HIS cc_start: 0.9154 (m90) cc_final: 0.8722 (m90) REVERT: G 70 LEU cc_start: 0.9444 (mt) cc_final: 0.8993 (tt) REVERT: G 72 GLN cc_start: 0.6941 (tp40) cc_final: 0.6206 (tp-100) REVERT: G 73 MET cc_start: 0.8172 (pmm) cc_final: 0.7673 (pmm) outliers start: 2 outliers final: 0 residues processed: 236 average time/residue: 0.1542 time to fit residues: 62.9149 Evaluate side-chains 187 residues out of total 3251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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: 4.9990 chunk 185 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 337 optimal weight: 30.0000 chunk 281 optimal weight: 0.0010 chunk 61 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 193 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN C 69 GLN C 573 ASN C 622 ASN C 649 GLN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.090708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.062220 restraints weight = 137334.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.064084 restraints weight = 69227.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.065253 restraints weight = 43878.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.066100 restraints weight = 32332.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.066510 restraints weight = 26341.831| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30558 Z= 0.107 Angle : 0.582 10.749 41663 Z= 0.301 Chirality : 0.043 0.186 4828 Planarity : 0.004 0.053 5268 Dihedral : 13.714 169.756 4950 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.59 % Rotamer: Outliers : 0.07 % Allowed : 0.39 % 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: -0.91 (0.14), residues: 3812 helix: 0.77 (0.15), residues: 1261 sheet: -0.84 (0.24), residues: 429 loop : -1.45 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 275 TYR 0.018 0.001 TYR C1231 PHE 0.011 0.001 PHE G 65 TRP 0.032 0.002 TRP G 9 HIS 0.004 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00235 (30553) covalent geometry : angle 0.58160 (41657) hydrogen bonds : bond 0.03153 ( 1179) hydrogen bonds : angle 4.58135 ( 3216) metal coordination : bond 0.00281 ( 5) metal coordination : angle 1.72302 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5212.23 seconds wall clock time: 90 minutes 33.21 seconds (5433.21 seconds total)