Starting phenix.real_space_refine on Sat Sep 12 03:52:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6fuw_4225/09_2026/6fuw_4225_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fuw_4225/09_2026/6fuw_4225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6fuw_4225/09_2026/6fuw_4225_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fuw_4225/09_2026/6fuw_4225_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6fuw_4225/09_2026/6fuw_4225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fuw_4225/09_2026/6fuw_4225.map" } resolution = 3.07 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= 0.014 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 8 5.49 5 S 88 5.16 5 C 8557 2.51 5 N 2337 2.21 5 O 2428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13421 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9367 Classifications: {'peptide': 1181} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 61, 'TRANS': 1115} Chain breaks: 13 Chain: "B" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2978 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 897 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "D" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 7} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12643 SG CYS C 41 66.982 15.464 93.239 1.00 69.83 S ATOM 12707 SG CYS C 49 70.877 14.348 95.412 1.00 80.63 S ATOM 12742 SG CYS C 55 69.827 17.994 93.870 1.00 71.19 S ATOM 12844 SG CYS C 68 60.014 27.114 109.007 1.00 44.18 S ATOM 12914 SG CYS C 76 63.413 27.947 107.651 1.00 41.47 S ATOM 12959 SG CYS C 82 62.478 24.853 109.583 1.00 54.43 S ATOM 13080 SG CYS C 96 46.707 33.360 118.497 1.00 58.21 S ATOM 13160 SG CYS C 105 44.547 36.326 117.376 1.00 66.76 S ATOM 13198 SG CYS C 110 45.728 34.284 114.951 1.00 62.16 S Time building chain proxies: 2.83, per 1000 atoms: 0.21 Number of scatterers: 13421 At special positions: 0 Unit cell: (107.916, 106.858, 136.482, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 88 16.00 P 8 15.00 O 2428 8.00 N 2337 7.00 C 8557 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 524.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" NE2 HIS C 59 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 41 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 55 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 49 " pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 76 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 82 " pdb="ZN ZN C 202 " - pdb=" NE2 HIS C 86 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 68 " pdb=" ZN C 203 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 96 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 105 " pdb="ZN ZN C 203 " - pdb=" NE2 HIS C 114 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 110 " Number of angles added : 9 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3112 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 28 sheets defined 7.1% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 506 through 509 removed outlier: 3.561A pdb=" N ASN A 509 " --> pdb=" O HIS A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 506 through 509' Processing helix chain 'A' and resid 1352 through 1370 removed outlier: 3.515A pdb=" N ARG A1358 " --> pdb=" O LYS A1354 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A1370 " --> pdb=" O LEU A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1376 removed outlier: 3.752A pdb=" N LEU A1376 " --> pdb=" O HIS A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1383 removed outlier: 3.834A pdb=" N MET A1383 " --> pdb=" O ALA A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1410 Processing helix chain 'A' and resid 1411 through 1423 Processing helix chain 'A' and resid 1425 through 1440 removed outlier: 3.760A pdb=" N THR A1440 " --> pdb=" O THR A1436 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 71 removed outlier: 4.243A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.887A pdb=" N ASN B 104 " --> pdb=" O ASN B 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 20 removed outlier: 3.853A pdb=" N GLU C 20 " --> pdb=" O GLU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 96 through 101 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 9 removed outlier: 5.869A pdb=" N ILE A1345 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR A1310 " --> pdb=" O ALA A1339 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.817A pdb=" N PHE A 16 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU A 38 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A 71 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL A 40 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.674A pdb=" N LEU A 103 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU A 120 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 105 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 143 Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 208 removed outlier: 5.800A pdb=" N CYS A 238 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TRP A 256 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER A 244 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL A 254 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 271 removed outlier: 6.574A pdb=" N PHE A 281 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL A 279 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA A 270 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY A 277 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN A 290 " --> pdb=" O PRO A 294 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ARG A 313 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY A 297 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 328 removed outlier: 6.711A pdb=" N VAL A 346 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LYS A 364 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 373 through 376 removed outlier: 6.233A pdb=" N SER A 391 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER A 468 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 393 " --> pdb=" O CYS A 466 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 478 through 481 removed outlier: 6.642A pdb=" N GLY A 510 " --> pdb=" O LEU A1018 " (cutoff:3.500A) removed outlier: 11.946A pdb=" N ARG A1019 " --> pdb=" O ASN A1041 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASN A1041 " --> pdb=" O ARG A1019 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA A1037 " --> pdb=" O HIS A1023 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL A1025 " --> pdb=" O ALA A1035 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA A1035 " --> pdb=" O VAL A1025 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR A1027 " --> pdb=" O VAL A1033 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL A1033 " --> pdb=" O TYR A1027 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 522 through 526 removed outlier: 5.303A pdb=" N VAL A 523 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A1000 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 974 " --> pdb=" O PHE A 990 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 534 through 539 removed outlier: 4.063A pdb=" N ASP A 534 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET A 584 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 608 through 610 removed outlier: 3.689A pdb=" N VAL A 619 " --> pdb=" O GLY A 610 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 627 " --> pdb=" O GLN A 620 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 646 through 652 removed outlier: 3.844A pdb=" N LYS A 671 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 681 " --> pdb=" O LYS A 671 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 695 through 703 removed outlier: 3.703A pdb=" N THR A 697 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 806 " --> pdb=" O ILE A 796 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN A 798 " --> pdb=" O LEU A 804 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 804 " --> pdb=" O GLN A 798 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 817 through 818 removed outlier: 3.773A pdb=" N PHE A 892 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE A 873 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 931 through 935 removed outlier: 4.193A pdb=" N SER A 941 " --> pdb=" O VAL A 955 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 955 " --> pdb=" O SER A 941 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1098 through 1109 removed outlier: 5.190A pdb=" N VAL A1100 " --> pdb=" O CYS A1126 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS A1126 " --> pdb=" O VAL A1100 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS A1102 " --> pdb=" O GLY A1124 " (cutoff:3.500A) removed outlier: 19.832A pdb=" N LEU A1117 " --> pdb=" O GLU A1146 " (cutoff:3.500A) removed outlier: 15.429A pdb=" N GLU A1146 " --> pdb=" O LEU A1117 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N GLY A1119 " --> pdb=" O VAL A1144 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL A1144 " --> pdb=" O GLY A1119 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG A1136 " --> pdb=" O LEU A1127 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLY A1137 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLU A1167 " --> pdb=" O GLY A1137 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A1139 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU A1165 " --> pdb=" O ILE A1139 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A1141 " --> pdb=" O LEU A1163 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A1159 " --> pdb=" O ILE A1145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1172 through 1177 removed outlier: 6.766A pdb=" N ALA A1185 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A1175 " --> pdb=" O VAL A1183 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A1183 " --> pdb=" O LEU A1175 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A1204 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N SER A1194 " --> pdb=" O GLY A1202 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLY A1202 " --> pdb=" O SER A1194 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1212 through 1218 removed outlier: 6.720A pdb=" N ALA A1225 " --> pdb=" O HIS A1213 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET A1215 " --> pdb=" O LEU A1223 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU A1223 " --> pdb=" O MET A1215 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N SER A1217 " --> pdb=" O PHE A1221 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE A1221 " --> pdb=" O SER A1217 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG A1235 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU A1245 " --> pdb=" O ARG A1235 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1255 through 1263 removed outlier: 6.882A pdb=" N SER A1272 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL A1258 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A1270 " --> pdb=" O VAL A1258 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE A1260 " --> pdb=" O GLY A1268 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLY A1268 " --> pdb=" O PHE A1260 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N VAL A1262 " --> pdb=" O GLN A1266 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLN A1266 " --> pdb=" O VAL A1262 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET A1282 " --> pdb=" O ARG A1298 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG A1298 " --> pdb=" O MET A1282 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 109 through 113 removed outlier: 6.801A pdb=" N PHE B 401 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR B 113 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER B 399 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 122 through 127 removed outlier: 3.505A pdb=" N ALA B 138 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE B 143 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE B 156 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU B 145 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 166 through 169 removed outlier: 4.084A pdb=" N LYS B 196 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 205 through 210 removed outlier: 7.076A pdb=" N CYS B 220 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA B 208 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA B 218 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N PHE B 210 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LYS B 216 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP B 230 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU B 236 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 247 through 251 removed outlier: 3.608A pdb=" N ILE B 270 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 291 through 296 Processing sheet with id=AD1, first strand: chain 'B' and resid 334 through 339 removed outlier: 6.579A pdb=" N GLY B 350 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL B 337 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 348 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TRP B 339 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU B 346 " --> pdb=" O TRP B 339 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1083 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: 3.00 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4192 1.33 - 1.45: 2398 1.45 - 1.57: 7017 1.57 - 1.69: 15 1.69 - 1.81: 139 Bond restraints: 13761 Sorted by residual: bond pdb=" CA ARG B 308 " pdb=" C ARG B 308 " ideal model delta sigma weight residual 1.522 1.477 0.044 1.72e-02 3.38e+03 6.61e+00 bond pdb=" N7 A D 6 " pdb=" C5 A D 6 " ideal model delta sigma weight residual 1.388 1.374 0.014 6.00e-03 2.78e+04 5.20e+00 bond pdb=" N7 A D 4 " pdb=" C5 A D 4 " ideal model delta sigma weight residual 1.388 1.375 0.013 6.00e-03 2.78e+04 4.48e+00 bond pdb=" CG1 ILE A 585 " pdb=" CD1 ILE A 585 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.12e+00 bond pdb=" N9 A D 6 " pdb=" C4 A D 6 " ideal model delta sigma weight residual 1.374 1.362 0.012 6.00e-03 2.78e+04 4.05e+00 ... (remaining 13756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 18365 3.06 - 6.12: 301 6.12 - 9.18: 19 9.18 - 12.24: 2 12.24 - 15.30: 1 Bond angle restraints: 18688 Sorted by residual: angle pdb=" N VAL A 632 " pdb=" CA VAL A 632 " pdb=" C VAL A 632 " ideal model delta sigma weight residual 113.42 107.91 5.51 1.17e+00 7.31e-01 2.22e+01 angle pdb=" O5' U D 3 " pdb=" C5' U D 3 " pdb=" C4' U D 3 " ideal model delta sigma weight residual 109.40 113.02 -3.62 8.00e-01 1.56e+00 2.05e+01 angle pdb=" C LYS A 99 " pdb=" N ASP A 100 " pdb=" CA ASP A 100 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C PHE B 210 " pdb=" N SER B 211 " pdb=" CA SER B 211 " ideal model delta sigma weight residual 120.49 126.73 -6.24 1.42e+00 4.96e-01 1.93e+01 angle pdb=" O5' A D 6 " pdb=" C5' A D 6 " pdb=" C4' A D 6 " ideal model delta sigma weight residual 109.40 112.70 -3.30 8.00e-01 1.56e+00 1.70e+01 ... (remaining 18683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.94: 8020 23.94 - 47.87: 144 47.87 - 71.81: 16 71.81 - 95.74: 8 95.74 - 119.68: 1 Dihedral angle restraints: 8189 sinusoidal: 3375 harmonic: 4814 Sorted by residual: dihedral pdb=" CA GLY B 183 " pdb=" C GLY B 183 " pdb=" N TYR B 184 " pdb=" CA TYR B 184 " ideal model delta harmonic sigma weight residual 180.00 -150.52 -29.48 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" O4' A D 1 " pdb=" C1' A D 1 " pdb=" N9 A D 1 " pdb=" C4 A D 1 " ideal model delta sinusoidal sigma weight residual 254.00 166.31 87.69 1 1.70e+01 3.46e-03 3.19e+01 dihedral pdb=" CA SER A1290 " pdb=" C SER A1290 " pdb=" N PHE A1291 " pdb=" CA PHE A1291 " ideal model delta harmonic sigma weight residual 180.00 -153.26 -26.74 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 8186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1103 0.041 - 0.082: 628 0.082 - 0.123: 283 0.123 - 0.164: 55 0.164 - 0.205: 12 Chirality restraints: 2081 Sorted by residual: chirality pdb=" CG LEU A 393 " pdb=" CB LEU A 393 " pdb=" CD1 LEU A 393 " pdb=" CD2 LEU A 393 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB THR B 155 " pdb=" CA THR B 155 " pdb=" OG1 THR B 155 " pdb=" CG2 THR B 155 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE A1141 " pdb=" N ILE A1141 " pdb=" C ILE A1141 " pdb=" CB ILE A1141 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2078 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1074 " -0.015 2.00e-02 2.50e+03 2.30e-02 9.29e+00 pdb=" CG PHE A1074 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A1074 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A1074 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A1074 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A1074 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A1074 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 252 " -0.025 2.00e-02 2.50e+03 1.82e-02 8.30e+00 pdb=" CG TRP B 252 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 252 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 252 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 252 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 252 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 252 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 252 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 252 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 252 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 345 " -0.018 2.00e-02 2.50e+03 1.93e-02 7.47e+00 pdb=" CG TYR A 345 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 345 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 345 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 345 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 345 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 345 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 345 " 0.000 2.00e-02 2.50e+03 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1394 2.73 - 3.28: 12019 3.28 - 3.82: 20596 3.82 - 4.36: 26475 4.36 - 4.90: 47067 Nonbonded interactions: 107551 Sorted by model distance: nonbonded pdb=" OD1 ASP A 130 " pdb=" NH2 ARG A 158 " model vdw 2.193 3.120 nonbonded pdb=" O TYR A 19 " pdb=" NH2 ARG A 28 " model vdw 2.198 3.120 nonbonded pdb=" OD1 ASP A1263 " pdb=" N ASN A1264 " model vdw 2.214 3.120 nonbonded pdb=" NE2 GLN B 325 " pdb=" O VAL B 361 " model vdw 2.217 3.120 nonbonded pdb=" OG SER B 162 " pdb=" O HIS B 181 " model vdw 2.218 3.040 ... (remaining 107546 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.950 Find NCS groups from input model: 0.060 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.012 0.459 13773 Z= 0.478 Angle : 1.020 21.732 18697 Z= 0.535 Chirality : 0.058 0.205 2081 Planarity : 0.006 0.065 2352 Dihedral : 10.532 119.677 5077 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.10 (0.17), residues: 1631 helix: -2.78 (0.43), residues: 78 sheet: -2.00 (0.19), residues: 581 loop : -3.33 (0.16), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG A 962 TYR 0.046 0.004 TYR A 345 PHE 0.051 0.004 PHE A1074 TRP 0.049 0.005 TRP B 252 HIS 0.015 0.003 HIS A 979 Details of bonding type rmsd/Z covalent geometry : bond 0.01034 / 0.43 (13761) covalent geometry : angle 0.98399 / 0.53 (18688) hydrogen bonds : bond 0.14951 / 10.38 ( 403) hydrogen bonds : angle 7.95730 / 5.29 ( 1083) metal coordination : bond 0.20472 / 10.74 ( 12) metal coordination : angle 12.34638 / 8.54 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 81 MET cc_start: 0.8894 (ttp) cc_final: 0.8558 (ttm) REVERT: A 213 TYR cc_start: 0.5555 (t80) cc_final: 0.5284 (t80) REVERT: A 328 THR cc_start: 0.8650 (p) cc_final: 0.8387 (t) REVERT: A 580 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6086 (mm-30) REVERT: A 612 ILE cc_start: 0.8030 (mt) cc_final: 0.7775 (mm) REVERT: A 614 ASP cc_start: 0.7915 (m-30) cc_final: 0.7684 (t0) REVERT: A 628 LEU cc_start: 0.7738 (pp) cc_final: 0.7304 (tt) REVERT: A 662 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7162 (mm-30) REVERT: A 809 LYS cc_start: 0.7379 (mtpp) cc_final: 0.7153 (mmtm) REVERT: C 19 VAL cc_start: 0.6658 (t) cc_final: 0.6443 (m) REVERT: C 27 PRO cc_start: 0.8155 (Cg_exo) cc_final: 0.7950 (Cg_endo) REVERT: C 46 LYS cc_start: 0.7705 (mmpt) cc_final: 0.6671 (ptpt) REVERT: C 77 LYS cc_start: 0.8190 (mttp) cc_final: 0.7626 (pttm) REVERT: C 87 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7592 (mt-10) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1365 time to fit residues: 56.0229 Evaluate side-chains 159 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 315 GLN ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 GLN A 648 GLN A1307 HIS B 53 ASN B 60 ASN B 69 ASN B 405 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.146648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.127307 restraints weight = 17352.075| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.70 r_work: 0.3438 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 13773 Z= 0.187 Angle : 0.713 11.316 18697 Z= 0.366 Chirality : 0.048 0.173 2081 Planarity : 0.005 0.062 2352 Dihedral : 8.458 111.384 1908 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.59 % Allowed : 6.28 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.24 (0.18), residues: 1631 helix: -1.66 (0.51), residues: 84 sheet: -1.45 (0.20), residues: 592 loop : -2.77 (0.17), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 962 TYR 0.017 0.002 TYR A1256 PHE 0.022 0.002 PHE A 600 TRP 0.021 0.002 TRP A 952 HIS 0.008 0.001 HIS A 979 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (13761) covalent geometry : angle 0.70830 / 0.37 (18688) hydrogen bonds : bond 0.04501 / 2.98 ( 403) hydrogen bonds : angle 6.55595 / 4.44 ( 1083) metal coordination : bond 0.02707 / 1.37 ( 12) metal coordination : angle 3.88005 / 2.40 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.7657 (mmm-85) cc_final: 0.6494 (mmp80) REVERT: A 213 TYR cc_start: 0.6379 (t80) cc_final: 0.6129 (t80) REVERT: A 260 SER cc_start: 0.7384 (m) cc_final: 0.6991 (p) REVERT: A 328 THR cc_start: 0.8900 (p) cc_final: 0.8569 (t) REVERT: A 612 ILE cc_start: 0.8170 (mt) cc_final: 0.7856 (tt) REVERT: A 614 ASP cc_start: 0.8437 (m-30) cc_final: 0.7838 (t0) REVERT: A 628 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7391 (tt) REVERT: A 662 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7048 (mm-30) REVERT: A 809 LYS cc_start: 0.7580 (mtpp) cc_final: 0.7192 (mmtm) REVERT: B 267 GLN cc_start: 0.8731 (mt0) cc_final: 0.8435 (mm-40) REVERT: C 1 MET cc_start: 0.5639 (ptm) cc_final: 0.4947 (ptm) REVERT: C 19 VAL cc_start: 0.6478 (t) cc_final: 0.6076 (m) REVERT: C 46 LYS cc_start: 0.7552 (mmpt) cc_final: 0.6380 (ptpt) REVERT: C 64 LYS cc_start: 0.6287 (mtmt) cc_final: 0.6003 (mttp) REVERT: C 77 LYS cc_start: 0.8218 (mttp) cc_final: 0.7336 (pttm) REVERT: C 87 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8137 (mt-10) outliers start: 23 outliers final: 15 residues processed: 196 average time/residue: 0.1317 time to fit residues: 36.2740 Evaluate side-chains 172 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 1203 MET Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 66 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 82 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 HIS A 798 GLN A1220 ASN A1373 HIS B 189 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.145000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125875 restraints weight = 17597.182| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.68 r_work: 0.3405 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 13773 Z= 0.227 Angle : 0.712 10.819 18697 Z= 0.364 Chirality : 0.048 0.175 2081 Planarity : 0.005 0.066 2352 Dihedral : 8.350 109.315 1908 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 2.48 % Allowed : 7.73 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.90 (0.19), residues: 1631 helix: -1.30 (0.53), residues: 84 sheet: -1.19 (0.20), residues: 595 loop : -2.58 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1138 TYR 0.019 0.002 TYR A 345 PHE 0.021 0.002 PHE A 708 TRP 0.021 0.002 TRP B 252 HIS 0.010 0.002 HIS A 979 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 (13761) covalent geometry : angle 0.70706 / 0.36 (18688) hydrogen bonds : bond 0.04543 / 2.98 ( 403) hydrogen bonds : angle 6.26008 / 4.21 ( 1083) metal coordination : bond 0.02534 / 1.32 ( 12) metal coordination : angle 3.86790 / 2.40 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7512 (ttm-80) cc_final: 0.7096 (mtm-85) REVERT: A 166 ARG cc_start: 0.7763 (mmm-85) cc_final: 0.6710 (mmp80) REVERT: A 213 TYR cc_start: 0.6495 (t80) cc_final: 0.6214 (t80) REVERT: A 260 SER cc_start: 0.7614 (m) cc_final: 0.7133 (p) REVERT: A 328 THR cc_start: 0.8922 (p) cc_final: 0.8610 (t) REVERT: A 614 ASP cc_start: 0.8412 (m-30) cc_final: 0.7811 (t0) REVERT: A 628 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7264 (pp) REVERT: A 630 GLU cc_start: 0.6764 (tt0) cc_final: 0.5761 (tm-30) REVERT: A 642 LEU cc_start: 0.4210 (OUTLIER) cc_final: 0.3429 (pp) REVERT: A 662 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7038 (mm-30) REVERT: A 809 LYS cc_start: 0.7678 (mtpp) cc_final: 0.7255 (mmtm) REVERT: A 901 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8152 (m-10) REVERT: A 937 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7929 (tt) REVERT: A 1220 ASN cc_start: 0.7390 (t0) cc_final: 0.7095 (t0) REVERT: B 267 GLN cc_start: 0.8718 (mt0) cc_final: 0.8505 (mm-40) REVERT: C 1 MET cc_start: 0.5609 (ptm) cc_final: 0.4883 (ptm) REVERT: C 19 VAL cc_start: 0.6728 (t) cc_final: 0.6354 (m) REVERT: C 46 LYS cc_start: 0.7484 (mmpt) cc_final: 0.6254 (ptpt) REVERT: C 77 LYS cc_start: 0.8273 (mttp) cc_final: 0.7404 (pttm) REVERT: C 87 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8072 (mt-10) outliers start: 36 outliers final: 20 residues processed: 197 average time/residue: 0.1275 time to fit residues: 35.8622 Evaluate side-chains 176 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 66 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 37 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 140 optimal weight: 0.2980 chunk 101 optimal weight: 0.0980 chunk 13 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 GLN A 993 GLN A1307 HIS B 310 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.148047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.129368 restraints weight = 17451.007| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.64 r_work: 0.3443 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13773 Z= 0.133 Angle : 0.604 9.734 18697 Z= 0.312 Chirality : 0.045 0.182 2081 Planarity : 0.005 0.083 2352 Dihedral : 7.990 105.576 1908 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.28 % Allowed : 8.90 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.48 (0.19), residues: 1631 helix: -0.74 (0.56), residues: 84 sheet: -0.82 (0.21), residues: 593 loop : -2.38 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1317 TYR 0.013 0.001 TYR A 533 PHE 0.013 0.001 PHE A 600 TRP 0.014 0.002 TRP A 952 HIS 0.006 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (13761) covalent geometry : angle 0.60189 / 0.31 (18688) hydrogen bonds : bond 0.03682 / 2.40 ( 403) hydrogen bonds : angle 5.96568 / 3.94 ( 1083) metal coordination : bond 0.02020 / 0.99 ( 12) metal coordination : angle 2.50528 / 1.54 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7526 (ttm-80) cc_final: 0.7202 (mtm-85) REVERT: A 166 ARG cc_start: 0.7643 (mmm-85) cc_final: 0.6701 (mmp80) REVERT: A 213 TYR cc_start: 0.6382 (t80) cc_final: 0.6112 (t80) REVERT: A 260 SER cc_start: 0.7433 (m) cc_final: 0.7047 (p) REVERT: A 328 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8697 (t) REVERT: A 593 MET cc_start: 0.7931 (tpt) cc_final: 0.7718 (tpp) REVERT: A 614 ASP cc_start: 0.8370 (m-30) cc_final: 0.7803 (t0) REVERT: A 630 GLU cc_start: 0.6999 (tt0) cc_final: 0.6035 (tm-30) REVERT: A 642 LEU cc_start: 0.4244 (OUTLIER) cc_final: 0.3531 (pp) REVERT: A 662 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7044 (mm-30) REVERT: A 809 LYS cc_start: 0.7624 (mtpp) cc_final: 0.7249 (mmtm) REVERT: A 901 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8072 (m-10) REVERT: A 937 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7918 (tt) REVERT: A 1220 ASN cc_start: 0.7367 (t0) cc_final: 0.6972 (t0) REVERT: A 1348 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8745 (mt) REVERT: A 1432 ASP cc_start: 0.7128 (m-30) cc_final: 0.6815 (m-30) REVERT: B 98 MET cc_start: 0.8569 (ptt) cc_final: 0.8298 (ptm) REVERT: C 1 MET cc_start: 0.5614 (ptm) cc_final: 0.4895 (ptm) REVERT: C 19 VAL cc_start: 0.7028 (t) cc_final: 0.6621 (m) REVERT: C 46 LYS cc_start: 0.7407 (mmpt) cc_final: 0.6166 (ptpt) REVERT: C 77 LYS cc_start: 0.8229 (mttp) cc_final: 0.7429 (pttm) outliers start: 33 outliers final: 20 residues processed: 201 average time/residue: 0.1284 time to fit residues: 37.1203 Evaluate side-chains 186 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1203 MET Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain A residue 1348 LEU Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain C residue 11 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 124 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 685 HIS A1237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.146376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127446 restraints weight = 17461.040| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.68 r_work: 0.3416 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13773 Z= 0.174 Angle : 0.626 10.099 18697 Z= 0.321 Chirality : 0.046 0.163 2081 Planarity : 0.005 0.066 2352 Dihedral : 7.956 104.431 1908 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.04 % Allowed : 9.73 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.34 (0.19), residues: 1631 helix: -0.70 (0.56), residues: 84 sheet: -0.68 (0.21), residues: 599 loop : -2.32 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1317 TYR 0.010 0.002 TYR A 19 PHE 0.014 0.002 PHE A 877 TRP 0.014 0.002 TRP B 252 HIS 0.006 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.17 (13761) covalent geometry : angle 0.62309 / 0.32 (18688) hydrogen bonds : bond 0.03853 / 2.51 ( 403) hydrogen bonds : angle 5.91936 / 3.92 ( 1083) metal coordination : bond 0.02031 / 1.02 ( 12) metal coordination : angle 2.83139 / 1.74 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7485 (ttm-80) cc_final: 0.7134 (mtm-85) REVERT: A 81 MET cc_start: 0.9172 (ttm) cc_final: 0.8901 (ttm) REVERT: A 166 ARG cc_start: 0.7671 (mmm-85) cc_final: 0.6786 (mmp80) REVERT: A 213 TYR cc_start: 0.6499 (t80) cc_final: 0.6191 (t80) REVERT: A 260 SER cc_start: 0.7503 (m) cc_final: 0.7102 (p) REVERT: A 328 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8802 (t) REVERT: A 593 MET cc_start: 0.7950 (tpt) cc_final: 0.7507 (mmt) REVERT: A 614 ASP cc_start: 0.8386 (m-30) cc_final: 0.7742 (t0) REVERT: A 628 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7286 (pp) REVERT: A 630 GLU cc_start: 0.6853 (tt0) cc_final: 0.5927 (tm-30) REVERT: A 642 LEU cc_start: 0.4238 (OUTLIER) cc_final: 0.3488 (pp) REVERT: A 662 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7036 (mm-30) REVERT: A 809 LYS cc_start: 0.7658 (mtpp) cc_final: 0.7250 (mmtm) REVERT: A 901 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8040 (m-10) REVERT: A 937 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.7958 (tt) REVERT: A 1220 ASN cc_start: 0.7374 (t0) cc_final: 0.6983 (t0) REVERT: A 1348 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8793 (mt) REVERT: A 1432 ASP cc_start: 0.7145 (m-30) cc_final: 0.6843 (m-30) REVERT: B 98 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8290 (ptm) REVERT: B 198 PHE cc_start: 0.5044 (t80) cc_final: 0.4329 (t80) REVERT: C 1 MET cc_start: 0.5792 (ptm) cc_final: 0.5091 (ptm) REVERT: C 19 VAL cc_start: 0.6944 (t) cc_final: 0.6533 (m) REVERT: C 46 LYS cc_start: 0.7451 (mmpt) cc_final: 0.6207 (ptpt) REVERT: C 77 LYS cc_start: 0.8192 (mttp) cc_final: 0.7409 (pttm) REVERT: C 90 MET cc_start: 0.8001 (mmp) cc_final: 0.7699 (mmp) outliers start: 44 outliers final: 26 residues processed: 198 average time/residue: 0.1220 time to fit residues: 34.4400 Evaluate side-chains 193 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain A residue 1348 LEU Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 11 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 136 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 ASN B 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.145466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.126553 restraints weight = 17422.022| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.67 r_work: 0.3412 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13773 Z= 0.188 Angle : 0.642 10.279 18697 Z= 0.329 Chirality : 0.046 0.164 2081 Planarity : 0.005 0.065 2352 Dihedral : 7.941 103.932 1908 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.38 % Allowed : 10.21 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.23 (0.19), residues: 1631 helix: -0.62 (0.56), residues: 84 sheet: -0.61 (0.21), residues: 601 loop : -2.25 (0.18), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1317 TYR 0.017 0.002 TYR C 99 PHE 0.014 0.002 PHE A 877 TRP 0.015 0.002 TRP B 252 HIS 0.007 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (13761) covalent geometry : angle 0.63882 / 0.33 (18688) hydrogen bonds : bond 0.03960 / 2.59 ( 403) hydrogen bonds : angle 5.88670 / 3.90 ( 1083) metal coordination : bond 0.01830 / 0.91 ( 12) metal coordination : angle 2.75875 / 1.69 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 162 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7549 (ttm-80) cc_final: 0.7200 (mtm-85) REVERT: A 166 ARG cc_start: 0.7623 (mmm-85) cc_final: 0.6871 (mmp80) REVERT: A 260 SER cc_start: 0.7472 (m) cc_final: 0.7059 (p) REVERT: A 328 THR cc_start: 0.9013 (p) cc_final: 0.8719 (t) REVERT: A 592 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.7052 (mm) REVERT: A 593 MET cc_start: 0.8030 (tpt) cc_final: 0.7569 (mmt) REVERT: A 614 ASP cc_start: 0.8372 (m-30) cc_final: 0.7737 (t0) REVERT: A 628 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7401 (pp) REVERT: A 630 GLU cc_start: 0.6809 (tt0) cc_final: 0.5931 (tm-30) REVERT: A 642 LEU cc_start: 0.4279 (OUTLIER) cc_final: 0.3521 (pp) REVERT: A 662 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7095 (mm-30) REVERT: A 809 LYS cc_start: 0.7662 (mtpp) cc_final: 0.7225 (mmtm) REVERT: A 901 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.7974 (m-10) REVERT: A 937 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7925 (tt) REVERT: A 1220 ASN cc_start: 0.7315 (t0) cc_final: 0.7001 (t0) REVERT: A 1432 ASP cc_start: 0.7169 (m-30) cc_final: 0.6870 (m-30) REVERT: B 98 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8345 (ptm) REVERT: B 198 PHE cc_start: 0.5060 (t80) cc_final: 0.4262 (t80) REVERT: C 1 MET cc_start: 0.5831 (ptm) cc_final: 0.5115 (ptm) REVERT: C 19 VAL cc_start: 0.7259 (t) cc_final: 0.6808 (m) REVERT: C 46 LYS cc_start: 0.7476 (mmpt) cc_final: 0.6248 (ptpt) REVERT: C 77 LYS cc_start: 0.8234 (mttp) cc_final: 0.7355 (pttm) REVERT: C 90 MET cc_start: 0.8017 (mmp) cc_final: 0.7612 (mmp) REVERT: C 102 PHE cc_start: 0.6599 (m-80) cc_final: 0.6341 (m-80) outliers start: 49 outliers final: 34 residues processed: 200 average time/residue: 0.1169 time to fit residues: 33.9543 Evaluate side-chains 197 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1207 ASP Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 11 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 121 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.144296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125378 restraints weight = 17437.409| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.66 r_work: 0.3395 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13773 Z= 0.217 Angle : 0.665 10.569 18697 Z= 0.342 Chirality : 0.047 0.156 2081 Planarity : 0.005 0.064 2352 Dihedral : 8.030 103.584 1908 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.24 % Allowed : 10.90 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.29 (0.19), residues: 1631 helix: -0.87 (0.55), residues: 86 sheet: -0.66 (0.21), residues: 604 loop : -2.26 (0.18), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1235 TYR 0.014 0.002 TYR C 99 PHE 0.015 0.002 PHE A1205 TRP 0.016 0.002 TRP B 252 HIS 0.009 0.002 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.22 (13761) covalent geometry : angle 0.66257 / 0.34 (18688) hydrogen bonds : bond 0.04169 / 2.74 ( 403) hydrogen bonds : angle 5.91474 / 3.92 ( 1083) metal coordination : bond 0.01815 / 0.92 ( 12) metal coordination : angle 2.90463 / 1.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7505 (ttm-80) cc_final: 0.7151 (mtm-85) REVERT: A 166 ARG cc_start: 0.7648 (mmm-85) cc_final: 0.6831 (mmp80) REVERT: A 260 SER cc_start: 0.7381 (m) cc_final: 0.6962 (p) REVERT: A 328 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8728 (t) REVERT: A 592 ILE cc_start: 0.7351 (OUTLIER) cc_final: 0.7073 (mm) REVERT: A 593 MET cc_start: 0.8065 (tpt) cc_final: 0.7592 (mmt) REVERT: A 614 ASP cc_start: 0.8328 (m-30) cc_final: 0.7737 (t0) REVERT: A 628 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7245 (pp) REVERT: A 630 GLU cc_start: 0.6823 (tt0) cc_final: 0.5965 (tm-30) REVERT: A 642 LEU cc_start: 0.4338 (OUTLIER) cc_final: 0.3516 (pp) REVERT: A 662 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7112 (mm-30) REVERT: A 809 LYS cc_start: 0.7689 (mtpp) cc_final: 0.7239 (mmtm) REVERT: A 901 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8003 (m-10) REVERT: A 937 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.7955 (tt) REVERT: A 1220 ASN cc_start: 0.7336 (t0) cc_final: 0.7013 (t0) REVERT: A 1348 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8727 (mt) REVERT: A 1432 ASP cc_start: 0.7189 (m-30) cc_final: 0.6888 (m-30) REVERT: B 98 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8335 (ptm) REVERT: B 198 PHE cc_start: 0.5131 (t80) cc_final: 0.4223 (t80) REVERT: C 1 MET cc_start: 0.5845 (ptm) cc_final: 0.5121 (ptm) REVERT: C 19 VAL cc_start: 0.7240 (t) cc_final: 0.6789 (m) REVERT: C 46 LYS cc_start: 0.7484 (mmpt) cc_final: 0.6248 (ptpt) REVERT: C 90 MET cc_start: 0.8010 (mmp) cc_final: 0.7608 (mmp) REVERT: C 102 PHE cc_start: 0.6586 (m-80) cc_final: 0.6351 (m-80) outliers start: 47 outliers final: 35 residues processed: 199 average time/residue: 0.1141 time to fit residues: 32.7378 Evaluate side-chains 199 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 156 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1207 ASP Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain A residue 1348 LEU Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 11 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 5 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.126413 restraints weight = 17340.295| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.66 r_work: 0.3403 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13773 Z= 0.175 Angle : 0.630 10.211 18697 Z= 0.324 Chirality : 0.046 0.161 2081 Planarity : 0.005 0.065 2352 Dihedral : 7.920 102.715 1908 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.17 % Allowed : 11.32 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.17 (0.20), residues: 1631 helix: -0.82 (0.55), residues: 87 sheet: -0.63 (0.20), residues: 618 loop : -2.15 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1317 TYR 0.016 0.002 TYR C 99 PHE 0.013 0.002 PHE A 877 TRP 0.014 0.002 TRP B 383 HIS 0.007 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (13761) covalent geometry : angle 0.62752 / 0.32 (18688) hydrogen bonds : bond 0.03876 / 2.55 ( 403) hydrogen bonds : angle 5.84088 / 3.87 ( 1083) metal coordination : bond 0.01668 / 0.83 ( 12) metal coordination : angle 2.57797 / 1.57 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7495 (ttm-80) cc_final: 0.7153 (mtm-85) REVERT: A 166 ARG cc_start: 0.7663 (mmm-85) cc_final: 0.6907 (mmp80) REVERT: A 260 SER cc_start: 0.7349 (m) cc_final: 0.6934 (p) REVERT: A 328 THR cc_start: 0.9072 (p) cc_final: 0.8735 (t) REVERT: A 592 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.7061 (mm) REVERT: A 593 MET cc_start: 0.8042 (tpt) cc_final: 0.7579 (mmt) REVERT: A 614 ASP cc_start: 0.8333 (m-30) cc_final: 0.7734 (t0) REVERT: A 628 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7345 (pp) REVERT: A 630 GLU cc_start: 0.6715 (tt0) cc_final: 0.5884 (tm-30) REVERT: A 642 LEU cc_start: 0.4264 (OUTLIER) cc_final: 0.3506 (pp) REVERT: A 662 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7092 (mm-30) REVERT: A 809 LYS cc_start: 0.7669 (mtpp) cc_final: 0.7217 (mmtm) REVERT: A 901 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.7985 (m-10) REVERT: A 937 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7897 (tt) REVERT: A 1056 GLU cc_start: 0.7874 (mp0) cc_final: 0.6730 (pt0) REVERT: A 1220 ASN cc_start: 0.7260 (t0) cc_final: 0.6975 (t0) REVERT: A 1348 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8718 (mt) REVERT: A 1432 ASP cc_start: 0.7158 (m-30) cc_final: 0.6857 (m-30) REVERT: B 49 ARG cc_start: 0.7303 (ppt90) cc_final: 0.6992 (ttp80) REVERT: B 98 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8355 (ptm) REVERT: B 198 PHE cc_start: 0.5176 (t80) cc_final: 0.4232 (t80) REVERT: C 1 MET cc_start: 0.5812 (ptm) cc_final: 0.5101 (ptm) REVERT: C 19 VAL cc_start: 0.7249 (t) cc_final: 0.6786 (m) REVERT: C 46 LYS cc_start: 0.7479 (mmpt) cc_final: 0.6262 (ptpt) REVERT: C 90 MET cc_start: 0.7930 (mmp) cc_final: 0.7435 (mmp) outliers start: 46 outliers final: 37 residues processed: 199 average time/residue: 0.1217 time to fit residues: 35.1693 Evaluate side-chains 204 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1203 MET Chi-restraints excluded: chain A residue 1207 ASP Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain A residue 1348 LEU Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 11 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 103 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 84 optimal weight: 0.0000 chunk 18 optimal weight: 0.0370 chunk 90 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 overall best weight: 1.0466 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.147748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.128959 restraints weight = 17410.431| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.66 r_work: 0.3440 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13773 Z= 0.109 Angle : 0.576 9.355 18697 Z= 0.298 Chirality : 0.044 0.166 2081 Planarity : 0.004 0.068 2352 Dihedral : 7.703 100.306 1908 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.42 % Allowed : 12.42 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.20), residues: 1631 helix: -0.51 (0.57), residues: 87 sheet: -0.47 (0.21), residues: 623 loop : -2.04 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 328 TYR 0.013 0.001 TYR C 99 PHE 0.010 0.001 PHE A 877 TRP 0.013 0.001 TRP B 359 HIS 0.021 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (13761) covalent geometry : angle 0.57411 / 0.30 (18688) hydrogen bonds : bond 0.03362 / 2.19 ( 403) hydrogen bonds : angle 5.69535 / 3.77 ( 1083) metal coordination : bond 0.01749 / 0.86 ( 12) metal coordination : angle 1.98614 / 1.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.7141 (mtm-85) REVERT: A 166 ARG cc_start: 0.7612 (mmm-85) cc_final: 0.6947 (mmp80) REVERT: A 260 SER cc_start: 0.7392 (m) cc_final: 0.6981 (p) REVERT: A 328 THR cc_start: 0.9073 (p) cc_final: 0.8737 (t) REVERT: A 592 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.7073 (mm) REVERT: A 593 MET cc_start: 0.7942 (tpt) cc_final: 0.7462 (mmt) REVERT: A 614 ASP cc_start: 0.8271 (m-30) cc_final: 0.7664 (t0) REVERT: A 628 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7214 (pp) REVERT: A 630 GLU cc_start: 0.6682 (tt0) cc_final: 0.5886 (tm-30) REVERT: A 642 LEU cc_start: 0.4408 (OUTLIER) cc_final: 0.3653 (mt) REVERT: A 662 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7050 (mm-30) REVERT: A 809 LYS cc_start: 0.7628 (mtpp) cc_final: 0.7183 (mmtm) REVERT: A 901 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.7938 (m-10) REVERT: A 937 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7906 (tt) REVERT: A 1056 GLU cc_start: 0.7846 (mp0) cc_final: 0.6726 (pt0) REVERT: A 1220 ASN cc_start: 0.7237 (t0) cc_final: 0.6997 (t0) REVERT: A 1348 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8703 (mt) REVERT: A 1432 ASP cc_start: 0.6974 (m-30) cc_final: 0.6710 (m-30) REVERT: B 89 TYR cc_start: 0.8802 (p90) cc_final: 0.8520 (p90) REVERT: B 98 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8398 (ptm) REVERT: B 198 PHE cc_start: 0.5282 (t80) cc_final: 0.4250 (t80) REVERT: C 1 MET cc_start: 0.5675 (ptm) cc_final: 0.5042 (ptm) REVERT: C 19 VAL cc_start: 0.7272 (t) cc_final: 0.6818 (m) REVERT: C 46 LYS cc_start: 0.7475 (mmpt) cc_final: 0.6255 (ptpt) REVERT: C 90 MET cc_start: 0.7856 (mmp) cc_final: 0.7244 (mmp) outliers start: 35 outliers final: 24 residues processed: 200 average time/residue: 0.1190 time to fit residues: 34.6612 Evaluate side-chains 194 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1203 MET Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain A residue 1348 LEU Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 11 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 62 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1220 ASN B 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.148065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.129244 restraints weight = 17308.838| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.67 r_work: 0.3442 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13773 Z= 0.117 Angle : 0.573 9.354 18697 Z= 0.294 Chirality : 0.044 0.191 2081 Planarity : 0.004 0.068 2352 Dihedral : 7.593 97.978 1908 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.21 % Allowed : 13.39 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.20), residues: 1631 helix: -0.41 (0.57), residues: 87 sheet: -0.39 (0.21), residues: 625 loop : -1.96 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1317 TYR 0.014 0.001 TYR C 99 PHE 0.011 0.001 PHE A 877 TRP 0.012 0.001 TRP B 339 HIS 0.005 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (13761) covalent geometry : angle 0.57104 / 0.29 (18688) hydrogen bonds : bond 0.03359 / 2.19 ( 403) hydrogen bonds : angle 5.63687 / 3.74 ( 1083) metal coordination : bond 0.01738 / 0.85 ( 12) metal coordination : angle 2.00506 / 1.22 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7555 (ttm-80) cc_final: 0.7214 (mtm-85) REVERT: A 166 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.6973 (mmp80) REVERT: A 260 SER cc_start: 0.7380 (m) cc_final: 0.6993 (p) REVERT: A 328 THR cc_start: 0.9082 (p) cc_final: 0.8756 (t) REVERT: A 592 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.7099 (mm) REVERT: A 593 MET cc_start: 0.7913 (tpt) cc_final: 0.7444 (mmt) REVERT: A 614 ASP cc_start: 0.8256 (m-30) cc_final: 0.7635 (t0) REVERT: A 628 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7162 (pp) REVERT: A 630 GLU cc_start: 0.6793 (tt0) cc_final: 0.5881 (tm-30) REVERT: A 642 LEU cc_start: 0.4385 (OUTLIER) cc_final: 0.3623 (mt) REVERT: A 662 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7026 (mm-30) REVERT: A 809 LYS cc_start: 0.7598 (mtpp) cc_final: 0.7138 (mmtm) REVERT: A 901 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7838 (m-10) REVERT: A 937 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7916 (tt) REVERT: A 1056 GLU cc_start: 0.7835 (mp0) cc_final: 0.6746 (pt0) REVERT: A 1348 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8720 (mt) REVERT: A 1432 ASP cc_start: 0.7090 (m-30) cc_final: 0.6848 (m-30) REVERT: B 89 TYR cc_start: 0.8795 (p90) cc_final: 0.8517 (p90) REVERT: C 1 MET cc_start: 0.5680 (ptm) cc_final: 0.5079 (ptm) REVERT: C 19 VAL cc_start: 0.7258 (t) cc_final: 0.6799 (m) REVERT: C 46 LYS cc_start: 0.7473 (mmpt) cc_final: 0.6259 (ptpt) REVERT: C 90 MET cc_start: 0.7839 (mmp) cc_final: 0.7230 (mmp) outliers start: 32 outliers final: 23 residues processed: 189 average time/residue: 0.1258 time to fit residues: 34.3982 Evaluate side-chains 189 residues out of total 1449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 636 HIS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 901 PHE Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1316 CYS Chi-restraints excluded: chain A residue 1348 LEU Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 11 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 89 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 151 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.148712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.129865 restraints weight = 17331.153| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.68 r_work: 0.3452 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 13773 Z= 0.106 Angle : 0.566 9.265 18697 Z= 0.292 Chirality : 0.044 0.205 2081 Planarity : 0.004 0.068 2352 Dihedral : 7.500 96.503 1908 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.21 % Allowed : 13.87 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.20), residues: 1631 helix: -0.15 (0.57), residues: 84 sheet: -0.34 (0.21), residues: 620 loop : -1.92 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 616 TYR 0.015 0.001 TYR C 99 PHE 0.010 0.001 PHE A 877 TRP 0.011 0.001 TRP B 339 HIS 0.012 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (13761) covalent geometry : angle 0.56439 / 0.29 (18688) hydrogen bonds : bond 0.03279 / 2.14 ( 403) hydrogen bonds : angle 5.57444 / 3.71 ( 1083) metal coordination : bond 0.01731 / 0.85 ( 12) metal coordination : angle 1.84797 / 1.11 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3252.44 seconds wall clock time: 56 minutes 22.24 seconds (3382.24 seconds total)