Starting phenix.real_space_refine on Fri Jul 3 07:40:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7a6e_11671/07_2026/7a6e_11671.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a6e_11671/07_2026/7a6e_11671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7a6e_11671/07_2026/7a6e_11671.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7a6e_11671/07_2026/7a6e_11671.cif" model { file = "/net/cci-nas-00/data/ceres_data/7a6e_11671/07_2026/7a6e_11671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a6e_11671/07_2026/7a6e_11671.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7a6e_11671/07_2026/7a6e_11671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a6e_11671/07_2026/7a6e_11671.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 8286 2.51 5 N 2094 2.21 5 O 2327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12757 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9050 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 27, 'TRANS': 1136} Chain breaks: 2 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1656 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CYS%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1647 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PRO%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 404 Unusual residues: {'CLR': 11, 'R1H': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Time building chain proxies: 2.96, per 1000 atoms: 0.23 Number of scatterers: 12757 At special positions: 0 Unit cell: (102.48, 206.64, 100.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2327 8.00 N 2094 7.00 C 8286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.05 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=1.85 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 201 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 646.8 milliseconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 13 sheets defined 53.2% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 35 through 40 removed outlier: 4.111A pdb=" N PHE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 63 removed outlier: 3.543A pdb=" N LYS A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 85 removed outlier: 3.707A pdb=" N ASP A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 157 removed outlier: 3.634A pdb=" N HIS A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 removed outlier: 3.694A pdb=" N VAL A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N HIS A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 211 removed outlier: 3.762A pdb=" N THR A 176 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLY A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.722A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 247 removed outlier: 3.654A pdb=" N LEU A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N THR A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASP A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.768A pdb=" N VAL A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 269 through 324 removed outlier: 3.618A pdb=" N GLU A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 371 removed outlier: 4.066A pdb=" N VAL A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Proline residue: A 350 - end of helix removed outlier: 3.585A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 441 removed outlier: 3.657A pdb=" N GLN A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.973A pdb=" N THR A 460 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.594A pdb=" N LEU A 466 " --> pdb=" O ASN A 462 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 525 through 529 removed outlier: 3.828A pdb=" N GLY A 528 " --> pdb=" O GLY A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 546 Processing helix chain 'A' and resid 562 through 576 removed outlier: 3.566A pdb=" N GLU A 566 " --> pdb=" O ASP A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 619 removed outlier: 3.610A pdb=" N LYS A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 707 through 741 removed outlier: 3.832A pdb=" N PHE A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLN A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Proline residue: A 726 - end of helix removed outlier: 4.114A pdb=" N PHE A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 799 Processing helix chain 'A' and resid 801 through 806 Processing helix chain 'A' and resid 810 through 854 removed outlier: 3.786A pdb=" N THR A 815 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LYS A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY A 846 " --> pdb=" O ASN A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 863 removed outlier: 3.548A pdb=" N THR A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 860 " --> pdb=" O GLN A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 881 Processing helix chain 'A' and resid 884 through 891 removed outlier: 3.516A pdb=" N LYS A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 903 removed outlier: 4.420A pdb=" N ALA A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 910 Processing helix chain 'A' and resid 912 through 966 removed outlier: 4.084A pdb=" N VAL A 926 " --> pdb=" O GLN A 922 " (cutoff:3.500A) Proline residue: A 927 - end of helix removed outlier: 3.589A pdb=" N ASN A 930 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 932 " --> pdb=" O TYR A 928 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG A 933 " --> pdb=" O ARG A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 995 removed outlier: 3.533A pdb=" N VAL A 974 " --> pdb=" O SER A 970 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 984 " --> pdb=" O ALA A 980 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1013 Processing helix chain 'A' and resid 1077 through 1084 Processing helix chain 'A' and resid 1100 through 1104 Processing helix chain 'A' and resid 1105 through 1113 removed outlier: 3.805A pdb=" N LEU A1109 " --> pdb=" O ASN A1105 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A1113 " --> pdb=" O LEU A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1133 Processing helix chain 'A' and resid 1141 through 1152 Processing helix chain 'A' and resid 1154 through 1161 removed outlier: 3.729A pdb=" N LEU A1161 " --> pdb=" O PHE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1174 removed outlier: 3.865A pdb=" N GLY A1173 " --> pdb=" O GLY A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1191 removed outlier: 3.607A pdb=" N VAL A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1222 removed outlier: 3.867A pdb=" N LYS A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A1218 " --> pdb=" O VAL A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1239 removed outlier: 4.281A pdb=" N ASN A1239 " --> pdb=" O SER A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1263 Processing helix chain 'A' and resid 1265 through 1272 removed outlier: 3.732A pdb=" N SER A1269 " --> pdb=" O GLY A1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 132 Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.556A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 206 through 209 Processing sheet with id=AA1, first strand: chain 'A' and resid 415 through 417 removed outlier: 3.844A pdb=" N ARG A 395 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET A 450 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL A 397 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU A 448 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 473 removed outlier: 6.603A pdb=" N GLY A 471 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ASP A 555 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 473 " --> pdb=" O ASP A 555 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 425 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY A 600 " --> pdb=" O VAL A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1056 through 1060 removed outlier: 5.104A pdb=" N LEU A1056 " --> pdb=" O GLU A1039 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL A1040 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA A1091 " --> pdb=" O VAL A1040 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1114 through 1116 removed outlier: 3.766A pdb=" N LEU A1198 " --> pdb=" O GLY A1114 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A1116 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A1200 " --> pdb=" O VAL A1116 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A1068 " --> pdb=" O VAL A1229 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA A1067 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE A1246 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL A1069 " --> pdb=" O PHE A1246 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A1245 " --> pdb=" O LYS A1252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 14 removed outlier: 3.518A pdb=" N GLU B 110 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP B 40 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 14 removed outlier: 3.518A pdb=" N GLU B 110 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN B 95 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR B 102 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.532A pdb=" N ASN B 142 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR B 178 " --> pdb=" O ASN B 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 150 through 155 removed outlier: 3.709A pdb=" N LYS B 154 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR B 197 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.368A pdb=" N GLY C 10 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER C 35 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 50 " --> pdb=" O TYR C 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 126 through 130 removed outlier: 6.024A pdb=" N TYR C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU C 176 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N THR C 182 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA C 174 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER C 184 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 160 removed outlier: 4.312A pdb=" N ILE C 199 " --> pdb=" O ILE C 216 " (cutoff:3.500A) 729 hydrogen bonds defined for protein. 2082 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2015 1.30 - 1.44: 3463 1.44 - 1.57: 7484 1.57 - 1.71: 1 1.71 - 1.84: 83 Bond restraints: 13046 Sorted by residual: bond pdb=" C13 R1H A1302 " pdb=" N08 R1H A1302 " ideal model delta sigma weight residual 1.448 1.292 0.156 2.00e-02 2.50e+03 6.10e+01 bond pdb=" C13 R1H A1301 " pdb=" N08 R1H A1301 " ideal model delta sigma weight residual 1.448 1.296 0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" C31 R1H A1302 " pdb=" N30 R1H A1302 " ideal model delta sigma weight residual 1.357 1.487 -0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" C31 R1H A1301 " pdb=" N30 R1H A1301 " ideal model delta sigma weight residual 1.357 1.480 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C22 R1H A1302 " pdb=" N21 R1H A1302 " ideal model delta sigma weight residual 1.353 1.469 -0.116 2.00e-02 2.50e+03 3.38e+01 ... (remaining 13041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 16990 2.17 - 4.33: 633 4.33 - 6.50: 90 6.50 - 8.67: 16 8.67 - 10.83: 2 Bond angle restraints: 17731 Sorted by residual: angle pdb=" C SER A1126 " pdb=" N ILE A1127 " pdb=" CA ILE A1127 " ideal model delta sigma weight residual 120.46 125.94 -5.48 1.37e+00 5.33e-01 1.60e+01 angle pdb=" N LYS A 808 " pdb=" CA LYS A 808 " pdb=" C LYS A 808 " ideal model delta sigma weight residual 111.36 107.10 4.26 1.09e+00 8.42e-01 1.53e+01 angle pdb=" N ALA C 92 " pdb=" CA ALA C 92 " pdb=" C ALA C 92 " ideal model delta sigma weight residual 107.73 113.97 -6.24 1.61e+00 3.86e-01 1.50e+01 angle pdb=" C09 R1H A1302 " pdb=" N08 R1H A1302 " pdb=" C13 R1H A1302 " ideal model delta sigma weight residual 118.02 107.19 10.83 3.00e+00 1.11e-01 1.30e+01 angle pdb=" N LYS A 380 " pdb=" CA LYS A 380 " pdb=" C LYS A 380 " ideal model delta sigma weight residual 113.23 108.88 4.35 1.24e+00 6.50e-01 1.23e+01 ... (remaining 17726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.10: 7193 21.10 - 42.20: 398 42.20 - 63.30: 61 63.30 - 84.40: 11 84.40 - 105.50: 4 Dihedral angle restraints: 7667 sinusoidal: 3081 harmonic: 4586 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 159.28 -66.28 1 1.00e+01 1.00e-02 5.74e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 93 " pdb=" CB CYS B 93 " ideal model delta sinusoidal sigma weight residual 93.00 46.99 46.01 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" CA ALA C 104 " pdb=" C ALA C 104 " pdb=" N TRP C 105 " pdb=" CA TRP C 105 " ideal model delta harmonic sigma weight residual -180.00 -153.95 -26.05 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 7664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1649 0.064 - 0.127: 324 0.127 - 0.191: 42 0.191 - 0.255: 24 0.255 - 0.318: 7 Chirality restraints: 2046 Sorted by residual: chirality pdb=" CB VAL A 224 " pdb=" CA VAL A 224 " pdb=" CG1 VAL A 224 " pdb=" CG2 VAL A 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C10 CLR A1304 " pdb=" C1 CLR A1304 " pdb=" C5 CLR A1304 " pdb=" C9 CLR A1304 " both_signs ideal model delta sigma weight residual False -2.85 -2.54 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C13 CLR A1311 " pdb=" C12 CLR A1311 " pdb=" C14 CLR A1311 " pdb=" C17 CLR A1311 " both_signs ideal model delta sigma weight residual False -2.93 -2.62 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 2043 not shown) Planarity restraints: 2168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 807 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C PRO A 807 " -0.064 2.00e-02 2.50e+03 pdb=" O PRO A 807 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS A 808 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 380 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C LYS A 380 " -0.060 2.00e-02 2.50e+03 pdb=" O LYS A 380 " 0.023 2.00e-02 2.50e+03 pdb=" N SER A 381 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 224 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C VAL A 224 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL A 224 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 225 " 0.013 2.00e-02 2.50e+03 ... (remaining 2165 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 2 2.07 - 2.77: 2625 2.77 - 3.48: 17788 3.48 - 4.19: 28572 4.19 - 4.90: 50822 Nonbonded interactions: 99809 Sorted by model distance: nonbonded pdb=" O TRP A 803 " pdb=" ND2 ASN A 809 " model vdw 1.357 3.120 nonbonded pdb=" OG SER A 238 " pdb=" NZ LYS A 242 " model vdw 2.033 3.120 nonbonded pdb=" N GLN A 347 " pdb=" OE1 GLN A 347 " model vdw 2.079 3.120 nonbonded pdb=" N ASP B 156 " pdb=" O SER B 196 " model vdw 2.127 3.120 nonbonded pdb=" ND2 ASN A 721 " pdb=" OE1 GLN A 773 " model vdw 2.128 3.120 ... (remaining 99804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.380 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 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 : 0.010 0.181 13051 Z= 0.472 Angle : 0.981 25.395 17741 Z= 0.536 Chirality : 0.057 0.318 2046 Planarity : 0.005 0.047 2168 Dihedral : 13.444 105.502 4712 Min Nonbonded Distance : 1.357 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.72 % Allowed : 5.09 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.18), residues: 1584 helix: -1.62 (0.16), residues: 770 sheet: -1.00 (0.30), residues: 271 loop : -2.67 (0.22), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 749 TYR 0.022 0.002 TYR C 95 PHE 0.020 0.002 PHE B 94 TRP 0.013 0.002 TRP A 232 HIS 0.006 0.001 HIS A1112 Details of bonding type rmsd/Z covalent geometry : bond 0.00965 / 0.47 (13046) covalent geometry : angle 0.94294 / 0.52 (17731) SS BOND : bond 0.08163 / 4.11 ( 5) SS BOND : angle 11.46499 / 6.65 ( 10) hydrogen bonds : bond 0.15563 / 10.34 ( 724) hydrogen bonds : angle 7.30405 / 5.26 ( 2082) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.470 Fit side-chains REVERT: A 156 MET cc_start: 0.7960 (mmm) cc_final: 0.7735 (mmp) REVERT: A 616 MET cc_start: 0.1551 (mmp) cc_final: -0.2230 (ptp) REVERT: A 876 MET cc_start: 0.8021 (mmp) cc_final: 0.7811 (tpp) REVERT: A 953 TYR cc_start: 0.7943 (t80) cc_final: 0.7301 (t80) REVERT: A 1027 MET cc_start: -0.0786 (tpp) cc_final: -0.2537 (mpp) REVERT: B 86 GLU cc_start: 0.7607 (tp30) cc_final: 0.7335 (tt0) REVERT: C 87 ARG cc_start: 0.7837 (ttm170) cc_final: 0.7611 (mtt180) REVERT: C 103 GLU cc_start: 0.7468 (mp0) cc_final: 0.7247 (mt-10) outliers start: 23 outliers final: 13 residues processed: 172 average time/residue: 0.1365 time to fit residues: 32.8546 Evaluate side-chains 106 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 121 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 HIS A 438 GLN A 475 GLN A 537 GLN A 612 HIS A 725 GLN A 824 GLN A 839 ASN A1054 GLN A1105 ASN ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 HIS A1182 GLN ** A1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1248 ASN B 27 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 ASN B 218 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.209949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.157192 restraints weight = 17309.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 93)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133407 restraints weight = 26108.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.131742 restraints weight = 19435.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.130859 restraints weight = 17857.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.131557 restraints weight = 14664.132| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13051 Z= 0.169 Angle : 0.644 9.345 17741 Z= 0.329 Chirality : 0.043 0.181 2046 Planarity : 0.004 0.036 2168 Dihedral : 8.985 95.574 1905 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.72 % Allowed : 9.89 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.20), residues: 1584 helix: 0.45 (0.18), residues: 778 sheet: -0.31 (0.31), residues: 277 loop : -2.20 (0.23), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 113 TYR 0.021 0.002 TYR B 54 PHE 0.016 0.002 PHE A 732 TRP 0.022 0.002 TRP A 708 HIS 0.004 0.001 HIS A1112 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (13046) covalent geometry : angle 0.64240 / 0.33 (17731) SS BOND : bond 0.00781 / 0.46 ( 5) SS BOND : angle 1.98371 / 1.10 ( 10) hydrogen bonds : bond 0.06118 / 4.10 ( 724) hydrogen bonds : angle 5.03683 / 3.67 ( 2082) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 78 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7692 (mt) REVERT: A 378 TYR cc_start: 0.5731 (OUTLIER) cc_final: 0.3941 (m-80) REVERT: A 708 TRP cc_start: 0.8399 (p-90) cc_final: 0.8188 (p-90) REVERT: A 922 GLN cc_start: 0.8177 (tt0) cc_final: 0.7771 (tt0) REVERT: A 953 TYR cc_start: 0.7674 (t80) cc_final: 0.7004 (t80) REVERT: A 1027 MET cc_start: -0.0245 (tpp) cc_final: -0.1942 (mpp) REVERT: B 17 ASP cc_start: 0.7375 (m-30) cc_final: 0.6107 (t70) REVERT: B 86 GLU cc_start: 0.7907 (tp30) cc_final: 0.7446 (tt0) REVERT: B 110 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6246 (mp0) REVERT: B 195 ASN cc_start: 0.4417 (m-40) cc_final: 0.3851 (t0) REVERT: C 87 ARG cc_start: 0.7975 (ttm170) cc_final: 0.7616 (mtt180) REVERT: C 103 GLU cc_start: 0.7544 (mp0) cc_final: 0.7322 (mt-10) outliers start: 23 outliers final: 13 residues processed: 131 average time/residue: 0.0892 time to fit residues: 18.5853 Evaluate side-chains 110 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 ASN A 912 GLN ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 GLN A1238 GLN C 170 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.206886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.153112 restraints weight = 17205.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.136163 restraints weight = 29576.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128181 restraints weight = 21614.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128188 restraints weight = 22703.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.129024 restraints weight = 16909.010| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13051 Z= 0.206 Angle : 0.662 9.922 17741 Z= 0.337 Chirality : 0.044 0.169 2046 Planarity : 0.004 0.037 2168 Dihedral : 8.620 95.385 1889 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.77 % Allowed : 12.81 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.20), residues: 1584 helix: 0.81 (0.18), residues: 780 sheet: -0.08 (0.32), residues: 277 loop : -2.05 (0.23), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 113 TYR 0.022 0.002 TYR C 95 PHE 0.025 0.002 PHE A 904 TRP 0.026 0.002 TRP B 168 HIS 0.006 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (13046) covalent geometry : angle 0.66063 / 0.34 (17731) SS BOND : bond 0.00762 / 0.50 ( 5) SS BOND : angle 2.05816 / 1.12 ( 10) hydrogen bonds : bond 0.06307 / 4.25 ( 724) hydrogen bonds : angle 4.86171 / 3.57 ( 2082) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 78 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7670 (mt) REVERT: A 450 MET cc_start: 0.3334 (mmt) cc_final: 0.3053 (mmm) REVERT: A 462 ASN cc_start: 0.5266 (t0) cc_final: 0.4669 (m-40) REVERT: A 802 SER cc_start: 0.7363 (p) cc_final: 0.6947 (t) REVERT: A 876 MET cc_start: 0.7952 (tpp) cc_final: 0.7620 (tpt) REVERT: A 922 GLN cc_start: 0.8172 (tt0) cc_final: 0.7778 (tt0) REVERT: A 1027 MET cc_start: -0.0624 (tpp) cc_final: -0.2320 (mpp) REVERT: B 17 ASP cc_start: 0.7250 (m-30) cc_final: 0.6020 (t70) REVERT: B 86 GLU cc_start: 0.7935 (tp30) cc_final: 0.7530 (tt0) REVERT: B 195 ASN cc_start: 0.3831 (m-40) cc_final: 0.3521 (t0) REVERT: C 87 ARG cc_start: 0.7995 (ttm170) cc_final: 0.7725 (mtt180) outliers start: 37 outliers final: 21 residues processed: 121 average time/residue: 0.0898 time to fit residues: 17.1379 Evaluate side-chains 110 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 ASN ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.205374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.152473 restraints weight = 17173.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.144143 restraints weight = 26408.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.137483 restraints weight = 27817.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.137038 restraints weight = 26278.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.136754 restraints weight = 17618.017| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13051 Z= 0.215 Angle : 0.662 10.206 17741 Z= 0.339 Chirality : 0.044 0.159 2046 Planarity : 0.004 0.039 2168 Dihedral : 8.585 94.677 1886 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.22 % Allowed : 15.21 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.21), residues: 1584 helix: 0.89 (0.18), residues: 788 sheet: 0.02 (0.32), residues: 275 loop : -1.94 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1110 TYR 0.020 0.002 TYR C 95 PHE 0.019 0.002 PHE B 67 TRP 0.030 0.002 TRP B 168 HIS 0.006 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (13046) covalent geometry : angle 0.66123 / 0.34 (17731) SS BOND : bond 0.00708 / 0.47 ( 5) SS BOND : angle 1.57534 / 0.90 ( 10) hydrogen bonds : bond 0.06289 / 4.25 ( 724) hydrogen bonds : angle 4.79708 / 3.52 ( 2082) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 94 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 78 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7691 (mt) REVERT: A 105 MET cc_start: 0.6388 (mpp) cc_final: 0.4886 (tpt) REVERT: A 242 LYS cc_start: 0.6973 (mmtm) cc_final: 0.5982 (tptm) REVERT: A 440 MET cc_start: 0.4322 (ppp) cc_final: 0.3376 (pmm) REVERT: A 450 MET cc_start: 0.3019 (mmt) cc_final: 0.2727 (mmm) REVERT: A 628 MET cc_start: 0.0150 (tpt) cc_final: -0.0059 (tpt) REVERT: A 818 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7874 (mp) REVERT: A 876 MET cc_start: 0.8008 (tpp) cc_final: 0.7689 (tpt) REVERT: A 953 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7558 (t80) REVERT: A 1027 MET cc_start: -0.1012 (tpp) cc_final: -0.2829 (mpp) REVERT: B 54 TYR cc_start: 0.8505 (p90) cc_final: 0.8278 (p90) REVERT: B 86 GLU cc_start: 0.7959 (tp30) cc_final: 0.7637 (tt0) REVERT: B 110 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.5934 (mp0) REVERT: B 170 ASP cc_start: 0.7064 (p0) cc_final: 0.6416 (t70) REVERT: C 87 ARG cc_start: 0.7912 (ttm170) cc_final: 0.7671 (mtt180) outliers start: 43 outliers final: 27 residues processed: 123 average time/residue: 0.1032 time to fit residues: 19.5196 Evaluate side-chains 121 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 106 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 912 GLN ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1232 HIS A1239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.204494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.152353 restraints weight = 17142.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145766 restraints weight = 26100.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.140950 restraints weight = 24993.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.139950 restraints weight = 22892.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.138275 restraints weight = 17767.988| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13051 Z= 0.228 Angle : 0.677 10.559 17741 Z= 0.347 Chirality : 0.044 0.153 2046 Planarity : 0.005 0.051 2168 Dihedral : 8.591 94.236 1885 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.19 % Allowed : 16.33 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.21), residues: 1584 helix: 0.94 (0.18), residues: 777 sheet: 0.28 (0.32), residues: 269 loop : -2.03 (0.24), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 113 TYR 0.021 0.002 TYR C 95 PHE 0.020 0.002 PHE A 314 TRP 0.031 0.002 TRP B 168 HIS 0.007 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 (13046) covalent geometry : angle 0.67565 / 0.35 (17731) SS BOND : bond 0.00728 / 0.48 ( 5) SS BOND : angle 1.66337 / 0.94 ( 10) hydrogen bonds : bond 0.06446 / 4.35 ( 724) hydrogen bonds : angle 4.81592 / 3.53 ( 2082) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 92 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 78 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7690 (mt) REVERT: A 105 MET cc_start: 0.6316 (mpp) cc_final: 0.4874 (tpp) REVERT: A 235 ILE cc_start: 0.7820 (mm) cc_final: 0.7541 (mm) REVERT: A 242 LYS cc_start: 0.6872 (mmtm) cc_final: 0.5988 (tptp) REVERT: A 293 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7558 (mt) REVERT: A 380 LYS cc_start: 0.6635 (OUTLIER) cc_final: 0.6317 (mtpp) REVERT: A 450 MET cc_start: 0.2910 (mmt) cc_final: 0.2638 (mmm) REVERT: A 628 MET cc_start: 0.0147 (tpt) cc_final: -0.0198 (tpt) REVERT: A 707 GLU cc_start: 0.7752 (tt0) cc_final: 0.7394 (pt0) REVERT: A 818 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7848 (mp) REVERT: A 876 MET cc_start: 0.7994 (tpp) cc_final: 0.7672 (tpt) REVERT: A 953 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7594 (t80) REVERT: A 1027 MET cc_start: -0.0669 (tpp) cc_final: -0.2784 (mpp) REVERT: B 86 GLU cc_start: 0.7953 (tp30) cc_final: 0.7647 (tt0) REVERT: B 110 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.5842 (mp0) REVERT: B 170 ASP cc_start: 0.7119 (p0) cc_final: 0.6659 (t70) REVERT: B 215 PHE cc_start: 0.3137 (OUTLIER) cc_final: 0.1581 (m-80) outliers start: 56 outliers final: 38 residues processed: 136 average time/residue: 0.1092 time to fit residues: 22.2586 Evaluate side-chains 134 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 89 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1191 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 92 optimal weight: 0.0470 chunk 157 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 90 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 110 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1130 ASN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.208621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.157936 restraints weight = 16886.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.158222 restraints weight = 44891.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.159288 restraints weight = 27644.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.158170 restraints weight = 19700.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.158985 restraints weight = 14937.228| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13051 Z= 0.118 Angle : 0.544 8.695 17741 Z= 0.277 Chirality : 0.040 0.148 2046 Planarity : 0.004 0.041 2168 Dihedral : 8.021 95.844 1883 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.55 % Allowed : 18.35 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.21), residues: 1584 helix: 1.54 (0.19), residues: 780 sheet: 0.30 (0.32), residues: 272 loop : -1.80 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 464 TYR 0.015 0.001 TYR A 953 PHE 0.012 0.001 PHE A 983 TRP 0.027 0.002 TRP B 168 HIS 0.002 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 (13046) covalent geometry : angle 0.54333 / 0.28 (17731) SS BOND : bond 0.00447 / 0.29 ( 5) SS BOND : angle 0.86177 / 0.51 ( 10) hydrogen bonds : bond 0.05134 / 3.45 ( 724) hydrogen bonds : angle 4.42777 / 3.25 ( 2082) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.451 Fit side-chains REVERT: A 69 MET cc_start: 0.8039 (mmp) cc_final: 0.7431 (mmp) REVERT: A 78 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7519 (mt) REVERT: A 105 MET cc_start: 0.6286 (mpp) cc_final: 0.4834 (tpp) REVERT: A 166 HIS cc_start: 0.5124 (t70) cc_final: 0.4483 (t70) REVERT: A 242 LYS cc_start: 0.6852 (mmtm) cc_final: 0.5872 (tptt) REVERT: A 380 LYS cc_start: 0.6621 (OUTLIER) cc_final: 0.6298 (mtpp) REVERT: A 450 MET cc_start: 0.2869 (mmt) cc_final: 0.2586 (mmm) REVERT: A 464 ARG cc_start: 0.5620 (tpt170) cc_final: 0.5393 (tpt170) REVERT: A 628 MET cc_start: 0.0104 (tpt) cc_final: -0.0170 (tpt) REVERT: A 708 TRP cc_start: 0.8105 (p-90) cc_final: 0.7743 (p90) REVERT: A 876 MET cc_start: 0.7914 (tpp) cc_final: 0.7635 (tpt) REVERT: A 1027 MET cc_start: -0.0677 (tpp) cc_final: -0.2812 (mpp) REVERT: B 170 ASP cc_start: 0.6975 (p0) cc_final: 0.6594 (t70) REVERT: B 195 ASN cc_start: 0.4805 (t0) cc_final: 0.4588 (t0) REVERT: B 215 PHE cc_start: 0.3032 (OUTLIER) cc_final: 0.1491 (m-80) REVERT: C 105 TRP cc_start: 0.7527 (m100) cc_final: 0.6860 (m100) REVERT: C 160 TRP cc_start: 0.2216 (m100) cc_final: 0.1952 (m100) outliers start: 34 outliers final: 22 residues processed: 126 average time/residue: 0.1139 time to fit residues: 21.4038 Evaluate side-chains 116 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 994 PHE Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 121 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 34 optimal weight: 30.0000 chunk 71 optimal weight: 0.5980 chunk 32 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.208472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.153972 restraints weight = 16878.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.135580 restraints weight = 27486.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.130566 restraints weight = 20331.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129928 restraints weight = 18646.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.130820 restraints weight = 14688.956| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13051 Z= 0.121 Angle : 0.540 8.412 17741 Z= 0.275 Chirality : 0.040 0.145 2046 Planarity : 0.004 0.041 2168 Dihedral : 7.739 94.988 1882 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.85 % Allowed : 18.58 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.21), residues: 1584 helix: 1.76 (0.19), residues: 773 sheet: 0.34 (0.31), residues: 280 loop : -1.77 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 492 TYR 0.016 0.001 TYR C 95 PHE 0.049 0.001 PHE A 904 TRP 0.030 0.002 TRP B 168 HIS 0.006 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (13046) covalent geometry : angle 0.53857 / 0.27 (17731) SS BOND : bond 0.00588 / 0.36 ( 5) SS BOND : angle 1.74655 / 1.07 ( 10) hydrogen bonds : bond 0.04962 / 3.33 ( 724) hydrogen bonds : angle 4.35392 / 3.17 ( 2082) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.477 Fit side-chains REVERT: A 78 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7506 (mt) REVERT: A 105 MET cc_start: 0.6092 (mpp) cc_final: 0.4783 (tpp) REVERT: A 152 PHE cc_start: 0.8117 (t80) cc_final: 0.7897 (t80) REVERT: A 174 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.5752 (ptt90) REVERT: A 242 LYS cc_start: 0.6553 (mmtm) cc_final: 0.5583 (tptt) REVERT: A 380 LYS cc_start: 0.6292 (OUTLIER) cc_final: 0.6030 (mtpp) REVERT: A 440 MET cc_start: 0.4656 (ppp) cc_final: 0.3872 (pmm) REVERT: A 450 MET cc_start: 0.3085 (mmt) cc_final: 0.2770 (mmm) REVERT: A 628 MET cc_start: 0.0153 (tpt) cc_final: -0.0052 (tpt) REVERT: A 708 TRP cc_start: 0.8290 (p-90) cc_final: 0.7852 (p90) REVERT: A 876 MET cc_start: 0.7994 (tpp) cc_final: 0.7704 (tpt) REVERT: A 922 GLN cc_start: 0.8090 (tt0) cc_final: 0.7730 (mt0) REVERT: A 1027 MET cc_start: -0.0443 (tpp) cc_final: -0.1235 (mmm) REVERT: B 170 ASP cc_start: 0.7416 (p0) cc_final: 0.6666 (t70) REVERT: B 180 MET cc_start: 0.5741 (ttt) cc_final: 0.5212 (tpt) REVERT: B 195 ASN cc_start: 0.5544 (t0) cc_final: 0.5088 (t0) REVERT: B 215 PHE cc_start: 0.3098 (OUTLIER) cc_final: 0.1355 (m-80) REVERT: C 105 TRP cc_start: 0.7576 (m100) cc_final: 0.6979 (m100) REVERT: C 121 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7567 (mttm) outliers start: 38 outliers final: 24 residues processed: 130 average time/residue: 0.1112 time to fit residues: 21.5369 Evaluate side-chains 125 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 108 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 912 GLN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.204919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.157084 restraints weight = 16891.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.151262 restraints weight = 31883.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.146422 restraints weight = 34239.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.145996 restraints weight = 34009.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.144810 restraints weight = 26398.674| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13051 Z= 0.190 Angle : 0.631 10.005 17741 Z= 0.321 Chirality : 0.042 0.141 2046 Planarity : 0.004 0.047 2168 Dihedral : 8.047 92.685 1882 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.30 % Allowed : 18.73 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.21), residues: 1584 helix: 1.43 (0.18), residues: 776 sheet: 0.37 (0.32), residues: 275 loop : -1.74 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 464 TYR 0.021 0.002 TYR C 95 PHE 0.018 0.002 PHE B 94 TRP 0.033 0.002 TRP B 168 HIS 0.005 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (13046) covalent geometry : angle 0.62994 / 0.32 (17731) SS BOND : bond 0.00658 / 0.44 ( 5) SS BOND : angle 1.83560 / 1.07 ( 10) hydrogen bonds : bond 0.05898 / 3.99 ( 724) hydrogen bonds : angle 4.56113 / 3.33 ( 2082) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 95 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 78 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7715 (mt) REVERT: A 105 MET cc_start: 0.6232 (mpp) cc_final: 0.4832 (tpp) REVERT: A 167 ASP cc_start: 0.6360 (t0) cc_final: 0.6003 (t0) REVERT: A 235 ILE cc_start: 0.7827 (mm) cc_final: 0.7558 (mm) REVERT: A 242 LYS cc_start: 0.6740 (mmtm) cc_final: 0.5818 (tptt) REVERT: A 380 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6422 (mtpp) REVERT: A 440 MET cc_start: 0.4449 (ppp) cc_final: 0.3635 (pmm) REVERT: A 450 MET cc_start: 0.2937 (mmt) cc_final: 0.2643 (mmm) REVERT: A 464 ARG cc_start: 0.5822 (tpt170) cc_final: 0.5595 (tpt170) REVERT: A 708 TRP cc_start: 0.8296 (p-90) cc_final: 0.7886 (p90) REVERT: A 876 MET cc_start: 0.8035 (tpp) cc_final: 0.7729 (tpt) REVERT: A 953 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7524 (t80) REVERT: A 1027 MET cc_start: -0.0659 (tpp) cc_final: -0.1501 (mmm) REVERT: B 109 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7405 (mp) REVERT: B 170 ASP cc_start: 0.7063 (p0) cc_final: 0.6812 (t70) REVERT: B 195 ASN cc_start: 0.4972 (t0) cc_final: 0.4316 (t0) REVERT: B 215 PHE cc_start: 0.2991 (OUTLIER) cc_final: 0.1327 (m-80) REVERT: C 105 TRP cc_start: 0.7684 (m100) cc_final: 0.7056 (m100) REVERT: C 121 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7481 (mttm) outliers start: 44 outliers final: 32 residues processed: 130 average time/residue: 0.0919 time to fit residues: 18.3154 Evaluate side-chains 128 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 90 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 35 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 131 optimal weight: 0.0070 chunk 68 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 149 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.207531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.162858 restraints weight = 17125.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.157918 restraints weight = 28450.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.152892 restraints weight = 29684.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.150874 restraints weight = 30662.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.149035 restraints weight = 24420.439| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13051 Z= 0.142 Angle : 0.572 9.248 17741 Z= 0.291 Chirality : 0.040 0.142 2046 Planarity : 0.004 0.040 2168 Dihedral : 7.861 93.960 1882 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.92 % Allowed : 19.18 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.21), residues: 1584 helix: 1.61 (0.19), residues: 777 sheet: 0.43 (0.32), residues: 273 loop : -1.68 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1192 TYR 0.017 0.001 TYR C 95 PHE 0.013 0.001 PHE A 942 TRP 0.030 0.002 TRP B 168 HIS 0.003 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (13046) covalent geometry : angle 0.57130 / 0.29 (17731) SS BOND : bond 0.00516 / 0.34 ( 5) SS BOND : angle 1.38065 / 0.80 ( 10) hydrogen bonds : bond 0.05336 / 3.59 ( 724) hydrogen bonds : angle 4.40500 / 3.21 ( 2082) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 69 MET cc_start: 0.8257 (mmp) cc_final: 0.7901 (mmp) REVERT: A 78 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7666 (mt) REVERT: A 105 MET cc_start: 0.6292 (mpp) cc_final: 0.4882 (tpp) REVERT: A 235 ILE cc_start: 0.7811 (mm) cc_final: 0.7536 (mm) REVERT: A 242 LYS cc_start: 0.6610 (mmtm) cc_final: 0.5779 (tptt) REVERT: A 380 LYS cc_start: 0.6634 (OUTLIER) cc_final: 0.6305 (mtpp) REVERT: A 450 MET cc_start: 0.2877 (mmt) cc_final: 0.2580 (mmm) REVERT: A 464 ARG cc_start: 0.5858 (tpt170) cc_final: 0.5631 (tpt170) REVERT: A 628 MET cc_start: 0.0075 (tpt) cc_final: -0.0174 (tpt) REVERT: A 708 TRP cc_start: 0.8188 (p-90) cc_final: 0.7867 (p90) REVERT: A 876 MET cc_start: 0.8014 (tpp) cc_final: 0.7713 (tpt) REVERT: A 1027 MET cc_start: -0.0702 (tpp) cc_final: -0.1524 (mmm) REVERT: B 109 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7411 (mp) REVERT: B 195 ASN cc_start: 0.4865 (t0) cc_final: 0.4218 (t0) REVERT: B 215 PHE cc_start: 0.2948 (OUTLIER) cc_final: 0.1332 (m-80) REVERT: C 73 ASP cc_start: 0.7423 (t70) cc_final: 0.7102 (t70) REVERT: C 105 TRP cc_start: 0.7631 (m100) cc_final: 0.6971 (m100) REVERT: C 121 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7429 (mttm) outliers start: 39 outliers final: 30 residues processed: 133 average time/residue: 0.1034 time to fit residues: 20.9791 Evaluate side-chains 130 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 0.0170 chunk 114 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 119 optimal weight: 0.0870 chunk 137 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1153 ASN B 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.210657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.168172 restraints weight = 16965.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.167699 restraints weight = 44253.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.163535 restraints weight = 23777.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.161291 restraints weight = 26239.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.162410 restraints weight = 16173.142| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13051 Z= 0.109 Angle : 0.532 9.333 17741 Z= 0.271 Chirality : 0.039 0.143 2046 Planarity : 0.003 0.040 2168 Dihedral : 7.510 94.292 1882 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.25 % Allowed : 20.00 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.22), residues: 1584 helix: 1.92 (0.19), residues: 770 sheet: 0.52 (0.32), residues: 273 loop : -1.56 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1192 TYR 0.013 0.001 TYR C 95 PHE 0.013 0.001 PHE A1086 TRP 0.029 0.001 TRP B 168 HIS 0.002 0.000 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (13046) covalent geometry : angle 0.53179 / 0.27 (17731) SS BOND : bond 0.00383 / 0.25 ( 5) SS BOND : angle 1.05257 / 0.64 ( 10) hydrogen bonds : bond 0.04535 / 3.04 ( 724) hydrogen bonds : angle 4.20742 / 3.06 ( 2082) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 69 MET cc_start: 0.8053 (mmp) cc_final: 0.7688 (mmp) REVERT: A 78 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7433 (mt) REVERT: A 105 MET cc_start: 0.6183 (mpp) cc_final: 0.4960 (tpp) REVERT: A 174 ARG cc_start: 0.6034 (OUTLIER) cc_final: 0.5342 (ptt90) REVERT: A 242 LYS cc_start: 0.6472 (mmtm) cc_final: 0.5653 (tptt) REVERT: A 380 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.6285 (mtpp) REVERT: A 450 MET cc_start: 0.2864 (mmt) cc_final: 0.2565 (mmm) REVERT: A 708 TRP cc_start: 0.8072 (p-90) cc_final: 0.7861 (p90) REVERT: A 879 LEU cc_start: 0.7249 (tp) cc_final: 0.7000 (tt) REVERT: A 1027 MET cc_start: -0.0913 (tpp) cc_final: -0.1631 (mmm) REVERT: A 1080 VAL cc_start: 0.6261 (t) cc_final: 0.5867 (p) REVERT: B 195 ASN cc_start: 0.4868 (t0) cc_final: 0.4311 (t0) REVERT: B 215 PHE cc_start: 0.2937 (OUTLIER) cc_final: 0.1244 (m-80) REVERT: C 73 ASP cc_start: 0.7286 (t70) cc_final: 0.6993 (t70) REVERT: C 105 TRP cc_start: 0.7445 (m100) cc_final: 0.6714 (m100) REVERT: C 121 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7502 (mttm) outliers start: 30 outliers final: 22 residues processed: 129 average time/residue: 0.0993 time to fit residues: 19.5459 Evaluate side-chains 122 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 24 optimal weight: 1.9990 chunk 154 optimal weight: 0.4980 chunk 94 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.205965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.152609 restraints weight = 16905.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 97)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.129969 restraints weight = 24169.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.129412 restraints weight = 18752.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.127183 restraints weight = 18086.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.128399 restraints weight = 14458.710| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13051 Z= 0.175 Angle : 0.606 9.290 17741 Z= 0.307 Chirality : 0.041 0.139 2046 Planarity : 0.004 0.043 2168 Dihedral : 7.746 92.942 1882 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.77 % Allowed : 19.63 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.21), residues: 1584 helix: 1.65 (0.19), residues: 777 sheet: 0.46 (0.32), residues: 275 loop : -1.62 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 492 TYR 0.019 0.002 TYR C 95 PHE 0.019 0.002 PHE A 152 TRP 0.033 0.002 TRP B 168 HIS 0.004 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (13046) covalent geometry : angle 0.60487 / 0.31 (17731) SS BOND : bond 0.00584 / 0.39 ( 5) SS BOND : angle 1.69725 / 0.92 ( 10) hydrogen bonds : bond 0.05480 / 3.70 ( 724) hydrogen bonds : angle 4.38548 / 3.19 ( 2082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2222.74 seconds wall clock time: 39 minutes 17.40 seconds (2357.40 seconds total)