Starting phenix.real_space_refine on Sat Jul 4 14:31:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s61_24846/07_2026/7s61_24846.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s61_24846/07_2026/7s61_24846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s61_24846/07_2026/7s61_24846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s61_24846/07_2026/7s61_24846.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7s61_24846/07_2026/7s61_24846.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s61_24846/07_2026/7s61_24846.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s61_24846/07_2026/7s61_24846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s61_24846/07_2026/7s61_24846.map" } resolution = 4.0 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= -0.005 sd= 0.074 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 P 5 5.49 5 Mg 2 5.21 5 S 120 5.16 5 C 13564 2.51 5 N 3569 2.21 5 O 3725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20985 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "E" Number of atoms: 10849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1392, 10849 Classifications: {'peptide': 1392} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 43, 'TRANS': 1348} Chain breaks: 8 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 4, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, C, D Time building chain proxies: 4.52, per 1000 atoms: 0.22 Number of scatterers: 20985 At special positions: 0 Unit cell: (133.9, 149.5, 136.5, 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) S 120 16.00 P 5 15.00 Mg 2 11.99 O 3725 8.00 N 3569 7.00 C 13564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.01 Simple disulfide: pdb=" N VAL C 291 " - pdb=" CG2 VAL C 291 " distance=2.75 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.01 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.01 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.01 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 897.4 milliseconds 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 26 sheets defined 48.2% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 67 through 97 Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.619A pdb=" N ALA A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.647A pdb=" N ILE A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 67 through 97 Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.619A pdb=" N ALA B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 129 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 172 removed outlier: 3.647A pdb=" N ILE B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 67 through 97 Processing helix chain 'C' and resid 116 through 129 removed outlier: 3.619A pdb=" N ALA C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 172 removed outlier: 3.648A pdb=" N ILE C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 67 through 97 Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.619A pdb=" N ALA D 120 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 129 " --> pdb=" O ILE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 172 removed outlier: 3.647A pdb=" N ILE D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'D' and resid 305 through 307 No H-bonds generated for 'chain 'D' and resid 305 through 307' Processing helix chain 'E' and resid 21 through 24 Processing helix chain 'E' and resid 25 through 34 Processing helix chain 'E' and resid 34 through 52 removed outlier: 3.959A pdb=" N PHE E 45 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 71 through 98 removed outlier: 3.866A pdb=" N TRP E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 129 Processing helix chain 'E' and resid 137 through 161 removed outlier: 3.594A pdb=" N VAL E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS E 161 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 193 removed outlier: 3.516A pdb=" N GLY E 181 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'E' and resid 234 through 242 removed outlier: 3.921A pdb=" N HIS E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 313 removed outlier: 6.258A pdb=" N ARG E 298 " --> pdb=" O HIS E 294 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU E 300 " --> pdb=" O PHE E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 328 Processing helix chain 'E' and resid 348 through 353 Processing helix chain 'E' and resid 355 through 401 Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 414 through 457 removed outlier: 3.591A pdb=" N VAL E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR E 426 " --> pdb=" O VAL E 422 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASN E 427 " --> pdb=" O ALA E 423 " (cutoff:3.500A) Proline residue: E 437 - end of helix Proline residue: E 443 - end of helix Processing helix chain 'E' and resid 459 through 465 removed outlier: 4.095A pdb=" N ILE E 463 " --> pdb=" O VAL E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 506 removed outlier: 4.410A pdb=" N ALA E 472 " --> pdb=" O ILE E 468 " (cutoff:3.500A) Proline residue: E 473 - end of helix removed outlier: 3.740A pdb=" N GLY E 506 " --> pdb=" O GLU E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 513 removed outlier: 3.729A pdb=" N LEU E 512 " --> pdb=" O LYS E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 565 Proline residue: E 552 - end of helix removed outlier: 4.069A pdb=" N VAL E 564 " --> pdb=" O PHE E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 589 removed outlier: 4.021A pdb=" N ALA E 577 " --> pdb=" O SER E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 593 through 615 Processing helix chain 'E' and resid 721 through 728 Processing helix chain 'E' and resid 783 through 790 Processing helix chain 'E' and resid 795 through 806 Processing helix chain 'E' and resid 832 through 844 removed outlier: 3.911A pdb=" N GLN E 836 " --> pdb=" O GLY E 832 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 871 Processing helix chain 'E' and resid 875 through 880 removed outlier: 3.779A pdb=" N ASP E 879 " --> pdb=" O GLU E 875 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP E 880 " --> pdb=" O LEU E 876 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 875 through 880' Processing helix chain 'E' and resid 913 through 920 Processing helix chain 'E' and resid 921 through 932 removed outlier: 3.545A pdb=" N LEU E 931 " --> pdb=" O HIS E 927 " (cutoff:3.500A) Processing helix chain 'E' and resid 998 through 1009 removed outlier: 3.646A pdb=" N ALA E1002 " --> pdb=" O TRP E 998 " (cutoff:3.500A) Processing helix chain 'E' and resid 1009 through 1039 Processing helix chain 'E' and resid 1062 through 1097 removed outlier: 5.197A pdb=" N PHE E1068 " --> pdb=" O TYR E1064 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E1074 " --> pdb=" O VAL E1070 " (cutoff:3.500A) Processing helix chain 'E' and resid 1100 through 1106 Processing helix chain 'E' and resid 1109 through 1116 removed outlier: 3.657A pdb=" N PHE E1113 " --> pdb=" O PRO E1109 " (cutoff:3.500A) Processing helix chain 'E' and resid 1117 through 1135 removed outlier: 3.762A pdb=" N ILE E1121 " --> pdb=" O PRO E1117 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1135 through 1161 removed outlier: 3.759A pdb=" N THR E1161 " --> pdb=" O ILE E1157 " (cutoff:3.500A) Processing helix chain 'E' and resid 1162 through 1210 removed outlier: 4.377A pdb=" N VAL E1166 " --> pdb=" O PRO E1162 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 4.573A pdb=" N VAL E1184 " --> pdb=" O LYS E1180 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA E1185 " --> pdb=" O TYR E1181 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP E1188 " --> pdb=" O VAL E1184 " (cutoff:3.500A) Proline residue: E1199 - end of helix removed outlier: 3.715A pdb=" N GLU E1209 " --> pdb=" O ALA E1205 " (cutoff:3.500A) Processing helix chain 'E' and resid 1210 through 1218 removed outlier: 3.545A pdb=" N ARG E1218 " --> pdb=" O ILE E1214 " (cutoff:3.500A) Processing helix chain 'E' and resid 1219 through 1274 removed outlier: 3.695A pdb=" N VAL E1259 " --> pdb=" O ILE E1255 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL E1260 " --> pdb=" O GLY E1256 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS E1273 " --> pdb=" O SER E1269 " (cutoff:3.500A) Processing helix chain 'E' and resid 1280 through 1320 removed outlier: 5.627A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP E1297 " --> pdb=" O ASN E1293 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA E1311 " --> pdb=" O LEU E1307 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1384 through 1391 removed outlier: 3.713A pdb=" N SER E1389 " --> pdb=" O LYS E1385 " (cutoff:3.500A) Processing helix chain 'E' and resid 1414 through 1422 removed outlier: 3.791A pdb=" N ARG E1421 " --> pdb=" O THR E1417 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E1422 " --> pdb=" O LEU E1418 " (cutoff:3.500A) Processing helix chain 'E' and resid 1436 through 1441 Processing helix chain 'E' and resid 1447 through 1457 Processing helix chain 'E' and resid 1460 through 1466 Processing helix chain 'E' and resid 1483 through 1498 removed outlier: 4.075A pdb=" N ARG E1498 " --> pdb=" O ARG E1494 " (cutoff:3.500A) Processing helix chain 'E' and resid 1513 through 1528 removed outlier: 3.514A pdb=" N ALA E1527 " --> pdb=" O VAL E1523 " (cutoff:3.500A) Processing helix chain 'E' and resid 1562 through 1570 removed outlier: 4.367A pdb=" N LYS E1570 " --> pdb=" O LEU E1566 " (cutoff:3.500A) Processing helix chain 'E' and resid 1572 through 1582 removed outlier: 3.899A pdb=" N LYS E1582 " --> pdb=" O VAL E1578 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.615A pdb=" N VAL A 202 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 255 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.995A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 230 through 238 removed outlier: 5.273A pdb=" N THR A 223 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 221 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER A 212 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL A 290 " --> pdb=" O SER A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 322 Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.614A pdb=" N VAL B 202 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 255 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.996A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 230 through 238 removed outlier: 5.273A pdb=" N THR B 223 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 221 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER B 212 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL B 290 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AB1, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AB2, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.615A pdb=" N VAL C 202 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 255 " --> pdb=" O VAL C 202 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.996A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 230 through 238 removed outlier: 5.274A pdb=" N THR C 223 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 221 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER C 212 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL C 290 " --> pdb=" O SER C 212 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AB6, first strand: chain 'C' and resid 319 through 322 Processing sheet with id=AB7, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.614A pdb=" N VAL D 202 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 255 " --> pdb=" O VAL D 202 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.996A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 230 through 238 removed outlier: 5.274A pdb=" N THR D 223 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG D 221 " --> pdb=" O HIS D 234 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER D 212 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL D 290 " --> pdb=" O SER D 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 313 through 315 Processing sheet with id=AC2, first strand: chain 'D' and resid 319 through 322 Processing sheet with id=AC3, first strand: chain 'E' and resid 678 through 680 removed outlier: 4.129A pdb=" N VAL E 680 " --> pdb=" O ILE E 704 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 697 through 701 removed outlier: 4.498A pdb=" N ASN E 699 " --> pdb=" O GLY E 685 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLY E 685 " --> pdb=" O ASN E 699 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR E 701 " --> pdb=" O MET E 683 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N MET E 683 " --> pdb=" O THR E 701 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN E 732 " --> pdb=" O THR E 688 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 771 through 773 removed outlier: 6.108A pdb=" N ALA E 771 " --> pdb=" O PHE E 852 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL E 851 " --> pdb=" O VAL E 885 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL E 887 " --> pdb=" O VAL E 851 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU E 853 " --> pdb=" O VAL E 887 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU E 709 " --> pdb=" O TRP E 899 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE E 901 " --> pdb=" O LEU E 709 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N MET E 711 " --> pdb=" O ILE E 901 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N MET E 903 " --> pdb=" O MET E 711 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL E 713 " --> pdb=" O MET E 903 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE E 900 " --> pdb=" O GLU E 911 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU E 911 " --> pdb=" O ILE E 900 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA E 902 " --> pdb=" O GLN E 909 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 1365 through 1369 removed outlier: 5.392A pdb=" N VAL E1365 " --> pdb=" O ASN E1349 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU E1350 " --> pdb=" O GLU E1400 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLU E1400 " --> pdb=" O LEU E1350 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL E1352 " --> pdb=" O THR E1398 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR E1398 " --> pdb=" O VAL E1352 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 1423 through 1425 removed outlier: 6.170A pdb=" N SER E1423 " --> pdb=" O ILE E1504 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS E1374 " --> pdb=" O LEU E1548 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ILE E1550 " --> pdb=" O LYS E1374 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY E1376 " --> pdb=" O ILE E1550 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU E1552 " --> pdb=" O GLY E1376 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYS E1378 " --> pdb=" O LEU E1552 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU E1559 " --> pdb=" O VAL E1551 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS E1553 " --> pdb=" O ILE E1557 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE E1557 " --> pdb=" O LYS E1553 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 1434 through 1435 removed outlier: 3.617A pdb=" N GLY E1434 " --> pdb=" O ILE E1475 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 3246 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.71 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3601 1.32 - 1.45: 5540 1.45 - 1.57: 12097 1.57 - 1.70: 10 1.70 - 1.82: 192 Bond restraints: 21440 Sorted by residual: bond pdb=" C ILE E 551 " pdb=" N PRO E 552 " ideal model delta sigma weight residual 1.335 1.452 -0.116 1.36e-02 5.41e+03 7.32e+01 bond pdb=" C4 ATP E1604 " pdb=" C5 ATP E1604 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.89e+01 bond pdb=" C5 ATP E1604 " pdb=" C6 ATP E1604 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.27e+01 bond pdb=" C TRP E1339 " pdb=" N PRO E1340 " ideal model delta sigma weight residual 1.340 1.490 -0.150 2.76e-02 1.31e+03 2.97e+01 bond pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 1.374 1.325 0.049 1.00e-02 1.00e+04 2.37e+01 ... (remaining 21435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 28559 4.66 - 9.32: 492 9.32 - 13.99: 78 13.99 - 18.65: 5 18.65 - 23.31: 5 Bond angle restraints: 29139 Sorted by residual: angle pdb=" PB ATP E1604 " pdb=" O3B ATP E1604 " pdb=" PG ATP E1604 " ideal model delta sigma weight residual 139.87 120.87 19.00 1.00e+00 1.00e+00 3.61e+02 angle pdb=" PA ATP E1604 " pdb=" O3A ATP E1604 " pdb=" PB ATP E1604 " ideal model delta sigma weight residual 136.83 123.76 13.07 1.00e+00 1.00e+00 1.71e+02 angle pdb=" C LEU E 261 " pdb=" N THR E 262 " pdb=" CA THR E 262 " ideal model delta sigma weight residual 121.54 139.66 -18.12 1.91e+00 2.74e-01 9.00e+01 angle pdb=" N SER E1100 " pdb=" CA SER E1100 " pdb=" C SER E1100 " ideal model delta sigma weight residual 113.43 102.92 10.51 1.26e+00 6.30e-01 6.96e+01 angle pdb=" C ALA E 5 " pdb=" N PHE E 6 " pdb=" CA PHE E 6 " ideal model delta sigma weight residual 121.54 137.37 -15.83 1.91e+00 2.74e-01 6.87e+01 ... (remaining 29134 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 12265 35.49 - 70.98: 427 70.98 - 106.47: 24 106.47 - 141.96: 0 141.96 - 177.45: 1 Dihedral angle restraints: 12717 sinusoidal: 4949 harmonic: 7768 Sorted by residual: dihedral pdb=" CA VAL E 193 " pdb=" C VAL E 193 " pdb=" N ARG E 194 " pdb=" CA ARG E 194 " ideal model delta harmonic sigma weight residual -180.00 -106.53 -73.47 0 5.00e+00 4.00e-02 2.16e+02 dihedral pdb=" CA GLY E 21 " pdb=" C GLY E 21 " pdb=" N VAL E 22 " pdb=" CA VAL E 22 " ideal model delta harmonic sigma weight residual 180.00 -132.58 -47.42 0 5.00e+00 4.00e-02 9.00e+01 dihedral pdb=" CB VAL C 291 " pdb=" N VAL C 291 " pdb=" CG2 VAL C 291 " pdb=" CB VAL C 291 " ideal model delta sinusoidal sigma weight residual -86.00 -0.00 -86.00 1 1.00e+01 1.00e-02 8.93e+01 ... (remaining 12714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 3282 0.169 - 0.338: 156 0.338 - 0.508: 13 0.508 - 0.677: 2 0.677 - 0.846: 1 Chirality restraints: 3454 Sorted by residual: chirality pdb=" CG LEU E1227 " pdb=" CB LEU E1227 " pdb=" CD1 LEU E1227 " pdb=" CD2 LEU E1227 " both_signs ideal model delta sigma weight residual False -2.59 -1.74 -0.85 2.00e-01 2.50e+01 1.79e+01 chirality pdb=" CG LEU E 183 " pdb=" CB LEU E 183 " pdb=" CD1 LEU E 183 " pdb=" CD2 LEU E 183 " both_signs ideal model delta sigma weight residual False -2.59 -1.96 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CB VAL E 556 " pdb=" CA VAL E 556 " pdb=" CG1 VAL E 556 " pdb=" CG2 VAL E 556 " both_signs ideal model delta sigma weight residual False -2.63 -2.09 -0.54 2.00e-01 2.50e+01 7.25e+00 ... (remaining 3451 not shown) Planarity restraints: 3624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 267 " 0.024 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C LEU E 267 " -0.081 2.00e-02 2.50e+03 pdb=" O LEU E 267 " 0.031 2.00e-02 2.50e+03 pdb=" N CYS E 268 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 589 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO E 590 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E1017 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C VAL E1017 " -0.067 2.00e-02 2.50e+03 pdb=" O VAL E1017 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE E1018 " 0.022 2.00e-02 2.50e+03 ... (remaining 3621 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 269 2.60 - 3.18: 15762 3.18 - 3.75: 35089 3.75 - 4.33: 46327 4.33 - 4.90: 74583 Nonbonded interactions: 172030 Sorted by model distance: nonbonded pdb=" SG CYS E 7 " pdb=" SG CYS E 27 " model vdw 2.028 3.760 nonbonded pdb=" O1B ADP E1601 " pdb="MG MG E1603 " model vdw 2.160 2.170 nonbonded pdb="MG MG E1602 " pdb=" O3B ATP E1604 " model vdw 2.162 2.170 nonbonded pdb="MG MG E1602 " pdb=" O2B ATP E1604 " model vdw 2.170 2.170 nonbonded pdb=" NE2 GLN E 775 " pdb="MG MG E1602 " model vdw 2.246 2.250 ... (remaining 172025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.280 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.011 0.717 21446 Z= 0.527 Angle : 1.654 70.859 29149 Z= 0.901 Chirality : 0.083 0.846 3454 Planarity : 0.013 0.104 3624 Dihedral : 17.635 177.446 7654 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.57 % Favored : 95.32 % Rotamer: Outliers : 8.22 % Allowed : 10.60 % Favored : 81.18 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -4.86 (0.12), residues: 2650 helix: -4.05 (0.07), residues: 1289 sheet: -1.03 (0.30), residues: 275 loop : -2.51 (0.15), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 314 TYR 0.051 0.004 TYR E1287 PHE 0.047 0.004 PHE E1164 TRP 0.034 0.004 TRP E1247 HIS 0.014 0.003 HIS E1098 Details of bonding type rmsd/Z covalent geometry : bond 0.00968 / 0.47 (21440) covalent geometry : angle 1.58125 / 0.87 (29139) SS BOND : bond 0.32123 / 16.07 ( 5) SS BOND : angle 26.25139 / 12.81 ( 10) hydrogen bonds : bond 0.15559 / 10.00 ( 1092) hydrogen bonds : angle 8.17319 / 5.72 ( 3246) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 619 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8758 (tt) REVERT: A 129 VAL cc_start: 0.9139 (t) cc_final: 0.8589 (t) REVERT: A 130 THR cc_start: 0.9024 (p) cc_final: 0.8659 (t) REVERT: A 137 MET cc_start: 0.8511 (ptt) cc_final: 0.8254 (ptp) REVERT: A 148 ILE cc_start: 0.9469 (tp) cc_final: 0.9256 (tp) REVERT: A 160 ASN cc_start: 0.9323 (m-40) cc_final: 0.8316 (m-40) REVERT: A 170 LYS cc_start: 0.8989 (tptp) cc_final: 0.8700 (tppt) REVERT: A 199 MET cc_start: 0.9026 (mtm) cc_final: 0.8725 (mtt) REVERT: A 211 ILE cc_start: 0.9323 (mp) cc_final: 0.8755 (mp) REVERT: A 265 SER cc_start: 0.9335 (OUTLIER) cc_final: 0.9053 (p) REVERT: A 279 GLN cc_start: 0.9020 (tp40) cc_final: 0.8527 (tm-30) REVERT: A 330 TYR cc_start: 0.8993 (m-80) cc_final: 0.8358 (m-80) REVERT: A 332 LYS cc_start: 0.9425 (mttt) cc_final: 0.8972 (mttm) REVERT: B 43 ASN cc_start: 0.8753 (m110) cc_final: 0.8353 (m-40) REVERT: B 44 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8569 (t) REVERT: B 52 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7571 (mm110) REVERT: B 67 LYS cc_start: 0.7998 (tptt) cc_final: 0.7634 (tptt) REVERT: B 77 MET cc_start: 0.8323 (tpp) cc_final: 0.8014 (tmm) REVERT: B 166 SER cc_start: 0.9296 (OUTLIER) cc_final: 0.9058 (p) REVERT: B 170 LYS cc_start: 0.9053 (tptp) cc_final: 0.8469 (tppt) REVERT: B 191 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8908 (tp) REVERT: B 218 GLN cc_start: 0.8563 (mt0) cc_final: 0.8236 (mt0) REVERT: B 281 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8923 (tt) REVERT: B 288 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8141 (mt-10) REVERT: B 305 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8119 (mt) REVERT: B 343 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8511 (tt) REVERT: C 39 LYS cc_start: 0.9237 (mmtt) cc_final: 0.8939 (tppt) REVERT: C 162 ILE cc_start: 0.9280 (mt) cc_final: 0.9053 (mt) REVERT: C 166 SER cc_start: 0.9564 (OUTLIER) cc_final: 0.9348 (p) REVERT: C 170 LYS cc_start: 0.9247 (tptp) cc_final: 0.8947 (tptm) REVERT: C 237 ASP cc_start: 0.8287 (p0) cc_final: 0.7190 (p0) REVERT: C 258 TYR cc_start: 0.8958 (p90) cc_final: 0.8741 (p90) REVERT: C 287 LEU cc_start: 0.9751 (tp) cc_final: 0.9523 (tt) REVERT: C 288 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8446 (mt-10) REVERT: C 293 THR cc_start: 0.9308 (p) cc_final: 0.9027 (t) REVERT: C 316 VAL cc_start: 0.9646 (OUTLIER) cc_final: 0.9420 (m) REVERT: C 332 LYS cc_start: 0.9563 (mttt) cc_final: 0.9338 (mmmt) REVERT: C 335 ASN cc_start: 0.9266 (m-40) cc_final: 0.8553 (m-40) REVERT: D 44 VAL cc_start: 0.9268 (OUTLIER) cc_final: 0.8931 (t) REVERT: D 66 LEU cc_start: 0.9280 (mt) cc_final: 0.8993 (mt) REVERT: D 77 MET cc_start: 0.8504 (tpp) cc_final: 0.8104 (tmm) REVERT: D 86 PHE cc_start: 0.9019 (m-80) cc_final: 0.8276 (m-80) REVERT: D 91 TRP cc_start: 0.8797 (t60) cc_final: 0.8533 (t60) REVERT: D 130 THR cc_start: 0.8871 (p) cc_final: 0.8657 (t) REVERT: D 147 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9261 (mm) REVERT: D 163 MET cc_start: 0.8962 (mmm) cc_final: 0.8723 (mmm) REVERT: D 166 SER cc_start: 0.9661 (OUTLIER) cc_final: 0.9427 (p) REVERT: D 183 PHE cc_start: 0.9088 (m-80) cc_final: 0.8616 (m-10) REVERT: D 191 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8125 (tp) REVERT: D 202 VAL cc_start: 0.9369 (OUTLIER) cc_final: 0.9017 (p) REVERT: D 209 MET cc_start: 0.7624 (mmp) cc_final: 0.6949 (mmp) REVERT: D 211 ILE cc_start: 0.9493 (mp) cc_final: 0.8370 (mp) REVERT: D 235 GLN cc_start: 0.8748 (mt0) cc_final: 0.8417 (pm20) REVERT: D 240 MET cc_start: 0.7932 (tmm) cc_final: 0.7562 (tmm) REVERT: D 244 VAL cc_start: 0.9195 (OUTLIER) cc_final: 0.8727 (m) REVERT: D 247 ASN cc_start: 0.8445 (p0) cc_final: 0.7780 (p0) REVERT: D 250 PHE cc_start: 0.8846 (t80) cc_final: 0.8635 (t80) REVERT: D 265 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.7928 (p) REVERT: D 305 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9138 (mt) REVERT: D 348 GLN cc_start: 0.8998 (mt0) cc_final: 0.8552 (mt0) REVERT: E 33 ASN cc_start: 0.8895 (t0) cc_final: 0.8647 (t0) REVERT: E 43 ILE cc_start: 0.9643 (tp) cc_final: 0.9394 (pt) REVERT: E 45 PHE cc_start: 0.8604 (t80) cc_final: 0.8272 (t80) REVERT: E 79 THR cc_start: 0.9466 (OUTLIER) cc_final: 0.9265 (m) REVERT: E 113 MET cc_start: 0.8948 (mmt) cc_final: 0.8659 (mmp) REVERT: E 128 ILE cc_start: 0.9642 (tp) cc_final: 0.9354 (tp) REVERT: E 225 LEU cc_start: 0.9279 (tp) cc_final: 0.9051 (tt) REVERT: E 320 CYS cc_start: 0.8993 (m) cc_final: 0.8763 (m) REVERT: E 324 ILE cc_start: 0.9423 (mt) cc_final: 0.9125 (mm) REVERT: E 359 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9043 (tt) REVERT: E 369 LEU cc_start: 0.9383 (tp) cc_final: 0.9115 (tp) REVERT: E 382 ILE cc_start: 0.9659 (mm) cc_final: 0.9440 (mm) REVERT: E 430 MET cc_start: 0.9148 (ttp) cc_final: 0.8920 (ttp) REVERT: E 584 PHE cc_start: 0.8824 (m-10) cc_final: 0.8613 (m-80) REVERT: E 886 LEU cc_start: 0.9208 (tp) cc_final: 0.8447 (tp) REVERT: E 891 LEU cc_start: 0.9073 (mt) cc_final: 0.8815 (mp) REVERT: E 1021 LEU cc_start: 0.9577 (mm) cc_final: 0.9375 (pp) REVERT: E 1031 ASP cc_start: 0.8722 (p0) cc_final: 0.8518 (p0) REVERT: E 1110 MET cc_start: 0.8423 (tpp) cc_final: 0.7989 (tpp) REVERT: E 1130 ASN cc_start: 0.9290 (t0) cc_final: 0.9061 (t0) REVERT: E 1173 ILE cc_start: 0.9058 (tp) cc_final: 0.8842 (tp) REVERT: E 1261 LEU cc_start: 0.9480 (tp) cc_final: 0.9160 (tp) REVERT: E 1276 LEU cc_start: 0.8203 (mp) cc_final: 0.7908 (tt) REVERT: E 1298 MET cc_start: 0.8780 (ttt) cc_final: 0.8483 (ttt) REVERT: E 1305 MET cc_start: 0.9141 (tpp) cc_final: 0.8863 (tpp) REVERT: E 1514 MET cc_start: 0.9066 (mtp) cc_final: 0.8859 (mtm) outliers start: 187 outliers final: 38 residues processed: 742 average time/residue: 0.1450 time to fit residues: 169.3196 Evaluate side-chains 492 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 434 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 359 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN B 57 GLN B 128 GLN B 277 HIS ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS C 277 HIS ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN D 277 HIS ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN E 265 GLN E 407 ASN E 438 ASN E 548 ASN E 563 HIS E 795 ASN E 820 GLN E 836 GLN E 935 GLN E1197 GLN ** E1373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.060242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.050408 restraints weight = 106969.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.052005 restraints weight = 54650.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053119 restraints weight = 34290.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.053838 restraints weight = 24388.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.054380 restraints weight = 19139.173| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.199 21446 Z= 0.150 Angle : 0.842 58.311 29149 Z= 0.427 Chirality : 0.047 0.354 3454 Planarity : 0.006 0.081 3624 Dihedral : 8.245 172.323 2944 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.62 % Favored : 96.34 % Rotamer: Outliers : 3.69 % Allowed : 19.39 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.13 (0.14), residues: 2650 helix: -1.09 (0.13), residues: 1282 sheet: -0.66 (0.30), residues: 283 loop : -1.88 (0.16), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E1300 TYR 0.021 0.002 TYR D 268 PHE 0.027 0.001 PHE D 86 TRP 0.023 0.001 TRP D 90 HIS 0.005 0.001 HIS E1098 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (21440) covalent geometry : angle 0.75291 / 0.39 (29139) SS BOND : bond 0.00629 / 0.31 ( 5) SS BOND : angle 20.40851 / 10.00 ( 10) hydrogen bonds : bond 0.04958 / 3.33 ( 1092) hydrogen bonds : angle 4.96451 / 3.45 ( 3246) Misc. bond : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 456 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8716 (m-40) cc_final: 0.8353 (t0) REVERT: A 47 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8922 (mmmt) REVERT: A 66 LEU cc_start: 0.9323 (mt) cc_final: 0.9012 (mt) REVERT: A 77 MET cc_start: 0.8703 (tpp) cc_final: 0.7602 (tmm) REVERT: A 137 MET cc_start: 0.8280 (ptt) cc_final: 0.7959 (ptp) REVERT: A 170 LYS cc_start: 0.8834 (tptp) cc_final: 0.8486 (tppt) REVERT: A 173 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8621 (pt0) REVERT: A 199 MET cc_start: 0.8797 (mtm) cc_final: 0.8451 (mtt) REVERT: A 209 MET cc_start: 0.8463 (mmp) cc_final: 0.7012 (mmp) REVERT: A 279 GLN cc_start: 0.9178 (tp40) cc_final: 0.8098 (tm-30) REVERT: A 292 GLU cc_start: 0.8135 (pt0) cc_final: 0.7294 (pt0) REVERT: A 330 TYR cc_start: 0.8943 (m-80) cc_final: 0.8518 (m-80) REVERT: A 332 LYS cc_start: 0.9371 (mttt) cc_final: 0.9080 (mttm) REVERT: B 43 ASN cc_start: 0.8823 (m110) cc_final: 0.8509 (m-40) REVERT: B 52 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7363 (mm110) REVERT: B 63 LEU cc_start: 0.9650 (tt) cc_final: 0.9251 (pp) REVERT: B 77 MET cc_start: 0.8617 (tpp) cc_final: 0.8264 (tmm) REVERT: B 81 CYS cc_start: 0.8181 (t) cc_final: 0.7912 (t) REVERT: B 169 MET cc_start: 0.9306 (mmm) cc_final: 0.8785 (ttm) REVERT: B 170 LYS cc_start: 0.9049 (tptp) cc_final: 0.8635 (tptm) REVERT: B 237 ASP cc_start: 0.7605 (p0) cc_final: 0.6396 (p0) REVERT: B 240 MET cc_start: 0.8205 (tmm) cc_final: 0.7730 (tmm) REVERT: B 288 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8240 (mt-10) REVERT: B 305 LEU cc_start: 0.8865 (mt) cc_final: 0.8476 (mt) REVERT: B 330 TYR cc_start: 0.8686 (m-80) cc_final: 0.8432 (m-80) REVERT: C 39 LYS cc_start: 0.9407 (mmtt) cc_final: 0.9044 (tptt) REVERT: C 86 PHE cc_start: 0.9476 (m-80) cc_final: 0.9205 (m-10) REVERT: C 88 MET cc_start: 0.8876 (ttt) cc_final: 0.7958 (tmm) REVERT: C 152 GLN cc_start: 0.9109 (tt0) cc_final: 0.8446 (tt0) REVERT: C 170 LYS cc_start: 0.9223 (tptp) cc_final: 0.8929 (tptm) REVERT: C 207 LYS cc_start: 0.9243 (mmmm) cc_final: 0.8995 (mmmm) REVERT: C 288 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8241 (mt-10) REVERT: C 293 THR cc_start: 0.9573 (p) cc_final: 0.9259 (t) REVERT: C 296 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8872 (tt) REVERT: C 313 GLN cc_start: 0.8789 (mt0) cc_final: 0.8539 (mt0) REVERT: C 335 ASN cc_start: 0.9329 (m-40) cc_final: 0.9079 (m110) REVERT: D 44 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8861 (t) REVERT: D 47 LYS cc_start: 0.8837 (mmmt) cc_final: 0.7835 (mptt) REVERT: D 77 MET cc_start: 0.8773 (tpp) cc_final: 0.8508 (tmm) REVERT: D 86 PHE cc_start: 0.8847 (m-80) cc_final: 0.8358 (m-10) REVERT: D 128 GLN cc_start: 0.8979 (tt0) cc_final: 0.8636 (tm-30) REVERT: D 137 MET cc_start: 0.8164 (ptm) cc_final: 0.7797 (ttm) REVERT: D 183 PHE cc_start: 0.9140 (m-80) cc_final: 0.8627 (m-10) REVERT: D 185 LYS cc_start: 0.8942 (ttpp) cc_final: 0.8467 (tptt) REVERT: D 202 VAL cc_start: 0.9268 (OUTLIER) cc_final: 0.8992 (p) REVERT: D 207 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8001 (tmtt) REVERT: D 211 ILE cc_start: 0.9381 (mp) cc_final: 0.8229 (mp) REVERT: D 212 SER cc_start: 0.9138 (p) cc_final: 0.8934 (p) REVERT: D 217 MET cc_start: 0.8645 (mtm) cc_final: 0.7949 (mtm) REVERT: D 218 GLN cc_start: 0.9271 (mm-40) cc_final: 0.8938 (mm-40) REVERT: D 235 GLN cc_start: 0.8939 (mt0) cc_final: 0.8555 (pm20) REVERT: D 240 MET cc_start: 0.8306 (tmm) cc_final: 0.7522 (tmm) REVERT: D 247 ASN cc_start: 0.7994 (p0) cc_final: 0.7564 (p0) REVERT: D 299 GLN cc_start: 0.9557 (tt0) cc_final: 0.8652 (tm-30) REVERT: E 39 PHE cc_start: 0.9160 (t80) cc_final: 0.8734 (t80) REVERT: E 45 PHE cc_start: 0.8806 (t80) cc_final: 0.8136 (t80) REVERT: E 89 GLU cc_start: 0.9114 (tp30) cc_final: 0.8842 (tm-30) REVERT: E 109 MET cc_start: 0.8201 (tpp) cc_final: 0.7478 (tpp) REVERT: E 113 MET cc_start: 0.9179 (mmt) cc_final: 0.8677 (mmp) REVERT: E 128 ILE cc_start: 0.9651 (tp) cc_final: 0.9375 (tp) REVERT: E 182 MET cc_start: 0.9282 (mmm) cc_final: 0.8720 (mmm) REVERT: E 369 LEU cc_start: 0.9401 (tp) cc_final: 0.9170 (tp) REVERT: E 430 MET cc_start: 0.9079 (ttp) cc_final: 0.8862 (ttp) REVERT: E 584 PHE cc_start: 0.8680 (m-10) cc_final: 0.8324 (m-80) REVERT: E 711 MET cc_start: 0.8929 (mmm) cc_final: 0.8429 (mpp) REVERT: E 903 MET cc_start: 0.7499 (ttm) cc_final: 0.6941 (ttm) REVERT: E 1021 LEU cc_start: 0.9637 (mm) cc_final: 0.9352 (pp) REVERT: E 1261 LEU cc_start: 0.9651 (tp) cc_final: 0.9449 (tp) REVERT: E 1298 MET cc_start: 0.8958 (ttt) cc_final: 0.8436 (tmm) outliers start: 84 outliers final: 37 residues processed: 513 average time/residue: 0.1391 time to fit residues: 114.1487 Evaluate side-chains 414 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 373 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 171 CYS Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1474 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 98 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 161 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 221 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS B 175 HIS B 186 HIS C 48 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN D 97 HIS D 160 ASN D 175 HIS ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 846 GLN ** E1373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.059132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.049348 restraints weight = 109035.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.050897 restraints weight = 57488.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.051947 restraints weight = 36671.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.052675 restraints weight = 26521.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053135 restraints weight = 20936.766| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.191 21446 Z= 0.160 Angle : 0.807 58.528 29149 Z= 0.405 Chirality : 0.046 0.341 3454 Planarity : 0.004 0.065 3624 Dihedral : 6.621 163.452 2880 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.47 % Favored : 96.49 % Rotamer: Outliers : 3.56 % Allowed : 21.50 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.02 (0.15), residues: 2650 helix: 0.06 (0.14), residues: 1331 sheet: -0.58 (0.29), residues: 303 loop : -1.60 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 32 TYR 0.024 0.002 TYR D 268 PHE 0.025 0.001 PHE C 86 TRP 0.018 0.001 TRP E1247 HIS 0.024 0.001 HIS C 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (21440) covalent geometry : angle 0.71285 / 0.36 (29139) SS BOND : bond 0.00506 / 0.25 ( 5) SS BOND : angle 20.47296 / 10.03 ( 10) hydrogen bonds : bond 0.04486 / 2.99 ( 1092) hydrogen bonds : angle 4.54950 / 3.16 ( 3246) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 383 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8824 (m-40) cc_final: 0.8296 (t0) REVERT: A 66 LEU cc_start: 0.9340 (mt) cc_final: 0.9111 (mt) REVERT: A 77 MET cc_start: 0.8771 (tpp) cc_final: 0.7859 (tmm) REVERT: A 84 LEU cc_start: 0.9377 (tp) cc_final: 0.9131 (mp) REVERT: A 137 MET cc_start: 0.8556 (ptt) cc_final: 0.8191 (ptp) REVERT: A 170 LYS cc_start: 0.8878 (tptp) cc_final: 0.8416 (tppt) REVERT: A 173 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8493 (pt0) REVERT: A 209 MET cc_start: 0.8381 (mmp) cc_final: 0.7785 (mmp) REVERT: A 211 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9108 (mp) REVERT: A 234 HIS cc_start: 0.8022 (t-170) cc_final: 0.7691 (t-90) REVERT: A 279 GLN cc_start: 0.8915 (tp40) cc_final: 0.8320 (tm-30) REVERT: A 285 VAL cc_start: 0.9511 (t) cc_final: 0.9306 (t) REVERT: A 332 LYS cc_start: 0.9456 (mttt) cc_final: 0.9132 (mttp) REVERT: A 338 LYS cc_start: 0.8819 (tptt) cc_final: 0.8607 (tppt) REVERT: B 43 ASN cc_start: 0.8832 (m110) cc_final: 0.7704 (p0) REVERT: B 63 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9288 (pp) REVERT: B 169 MET cc_start: 0.9171 (mmm) cc_final: 0.8738 (ttm) REVERT: B 170 LYS cc_start: 0.9097 (tptp) cc_final: 0.8722 (tptm) REVERT: B 288 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8189 (mt-10) REVERT: B 305 LEU cc_start: 0.8968 (mt) cc_final: 0.8527 (mt) REVERT: B 330 TYR cc_start: 0.8771 (m-80) cc_final: 0.8469 (m-80) REVERT: C 39 LYS cc_start: 0.9359 (mmtt) cc_final: 0.9004 (tptt) REVERT: C 170 LYS cc_start: 0.8883 (tptp) cc_final: 0.8608 (tptm) REVERT: C 207 LYS cc_start: 0.9261 (mmmm) cc_final: 0.9046 (mmmm) REVERT: C 209 MET cc_start: 0.8457 (tpp) cc_final: 0.8111 (tpt) REVERT: C 288 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8127 (mt-10) REVERT: C 296 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.9027 (tt) REVERT: C 332 LYS cc_start: 0.9541 (mtpp) cc_final: 0.9221 (ttpp) REVERT: C 335 ASN cc_start: 0.9288 (m-40) cc_final: 0.9031 (m110) REVERT: D 128 GLN cc_start: 0.9091 (tt0) cc_final: 0.8769 (tm-30) REVERT: D 163 MET cc_start: 0.9071 (mmm) cc_final: 0.8780 (mmm) REVERT: D 183 PHE cc_start: 0.9127 (m-80) cc_final: 0.8513 (m-10) REVERT: D 185 LYS cc_start: 0.8919 (ttpp) cc_final: 0.8531 (tptt) REVERT: D 202 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.8872 (p) REVERT: D 207 LYS cc_start: 0.8807 (mmtt) cc_final: 0.8000 (tmtt) REVERT: D 211 ILE cc_start: 0.9308 (mp) cc_final: 0.8290 (mp) REVERT: D 217 MET cc_start: 0.8483 (mtm) cc_final: 0.7962 (mtm) REVERT: D 218 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8905 (mm-40) REVERT: D 240 MET cc_start: 0.8069 (tmm) cc_final: 0.7190 (tmm) REVERT: D 247 ASN cc_start: 0.8130 (p0) cc_final: 0.7816 (p0) REVERT: D 262 ASP cc_start: 0.8947 (t70) cc_final: 0.8191 (t0) REVERT: D 299 GLN cc_start: 0.9616 (tt0) cc_final: 0.8874 (tm-30) REVERT: E 39 PHE cc_start: 0.9107 (t80) cc_final: 0.8763 (t80) REVERT: E 45 PHE cc_start: 0.8801 (t80) cc_final: 0.8564 (t80) REVERT: E 109 MET cc_start: 0.8350 (tpp) cc_final: 0.7780 (tpp) REVERT: E 113 MET cc_start: 0.9224 (mmt) cc_final: 0.8725 (mmp) REVERT: E 182 MET cc_start: 0.9285 (mmm) cc_final: 0.8768 (mmm) REVERT: E 369 LEU cc_start: 0.9451 (tp) cc_final: 0.9208 (tp) REVERT: E 584 PHE cc_start: 0.8612 (m-10) cc_final: 0.8277 (m-80) REVERT: E 711 MET cc_start: 0.8866 (mmm) cc_final: 0.8509 (mpp) REVERT: E 1021 LEU cc_start: 0.9625 (mm) cc_final: 0.9372 (pp) REVERT: E 1261 LEU cc_start: 0.9627 (tp) cc_final: 0.9388 (tp) REVERT: E 1298 MET cc_start: 0.9037 (ttt) cc_final: 0.8471 (tmm) REVERT: E 1301 ASN cc_start: 0.9265 (m-40) cc_final: 0.8826 (m-40) REVERT: E 1525 MET cc_start: 0.9221 (mpp) cc_final: 0.8926 (mmm) outliers start: 81 outliers final: 48 residues processed: 443 average time/residue: 0.1281 time to fit residues: 91.2159 Evaluate side-chains 401 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 348 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1130 ASN Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1474 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 236 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 chunk 245 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 HIS A 97 HIS A 128 GLN ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 160 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS ** E 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.055706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.046050 restraints weight = 111188.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.047551 restraints weight = 57994.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.048580 restraints weight = 37234.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.049306 restraints weight = 27132.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.049760 restraints weight = 21435.535| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 21446 Z= 0.235 Angle : 0.834 58.550 29149 Z= 0.423 Chirality : 0.047 0.338 3454 Planarity : 0.004 0.055 3624 Dihedral : 6.091 131.297 2874 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 5.10 % Allowed : 21.59 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.16), residues: 2650 helix: 0.63 (0.14), residues: 1340 sheet: -0.46 (0.31), residues: 295 loop : -1.20 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 192 TYR 0.022 0.002 TYR E1004 PHE 0.027 0.002 PHE C 86 TRP 0.018 0.002 TRP E1247 HIS 0.017 0.001 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.24 (21440) covalent geometry : angle 0.74289 / 0.38 (29139) SS BOND : bond 0.00572 / 0.29 ( 5) SS BOND : angle 20.50492 / 10.06 ( 10) hydrogen bonds : bond 0.04536 / 3.03 ( 1092) hydrogen bonds : angle 4.58213 / 3.17 ( 3246) Misc. bond : bond 0.00104 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 337 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8081 (t0) REVERT: A 49 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8294 (pt) REVERT: A 66 LEU cc_start: 0.9402 (mt) cc_final: 0.9169 (mp) REVERT: A 77 MET cc_start: 0.8690 (tpp) cc_final: 0.7844 (tmm) REVERT: A 137 MET cc_start: 0.8638 (ptt) cc_final: 0.8292 (ptp) REVERT: A 170 LYS cc_start: 0.8796 (tptp) cc_final: 0.8432 (tppt) REVERT: A 209 MET cc_start: 0.8197 (mmp) cc_final: 0.7602 (mmp) REVERT: A 211 ILE cc_start: 0.9476 (OUTLIER) cc_final: 0.9220 (mp) REVERT: A 234 HIS cc_start: 0.8306 (t-170) cc_final: 0.7951 (t-90) REVERT: A 279 GLN cc_start: 0.8894 (tp40) cc_final: 0.8265 (tm-30) REVERT: A 288 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7887 (tt0) REVERT: A 332 LYS cc_start: 0.9413 (mttt) cc_final: 0.9166 (mttp) REVERT: B 38 LYS cc_start: 0.9659 (mmmm) cc_final: 0.9406 (mmmm) REVERT: B 43 ASN cc_start: 0.8744 (m110) cc_final: 0.5921 (p0) REVERT: B 88 MET cc_start: 0.9027 (ttm) cc_final: 0.8747 (ttm) REVERT: B 129 VAL cc_start: 0.9347 (OUTLIER) cc_final: 0.9126 (p) REVERT: B 169 MET cc_start: 0.9108 (mmm) cc_final: 0.8666 (ttm) REVERT: B 170 LYS cc_start: 0.9151 (tptp) cc_final: 0.8861 (tptm) REVERT: B 211 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8603 (mp) REVERT: B 288 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8330 (mt-10) REVERT: B 296 ILE cc_start: 0.8804 (mp) cc_final: 0.8488 (pt) REVERT: B 305 LEU cc_start: 0.9064 (mt) cc_final: 0.8561 (mt) REVERT: B 330 TYR cc_start: 0.8747 (m-80) cc_final: 0.8403 (m-80) REVERT: B 332 LYS cc_start: 0.9299 (mppt) cc_final: 0.9089 (mppt) REVERT: C 39 LYS cc_start: 0.9388 (mmtt) cc_final: 0.9009 (mmmt) REVERT: C 170 LYS cc_start: 0.9034 (tptp) cc_final: 0.8822 (tptm) REVERT: C 207 LYS cc_start: 0.9314 (mmmm) cc_final: 0.9094 (mmmm) REVERT: C 296 ILE cc_start: 0.9400 (mt) cc_final: 0.9047 (tt) REVERT: C 326 TYR cc_start: 0.8696 (m-80) cc_final: 0.7516 (m-80) REVERT: C 332 LYS cc_start: 0.9671 (mtpp) cc_final: 0.9393 (ttpp) REVERT: D 86 PHE cc_start: 0.9070 (m-80) cc_final: 0.8656 (m-10) REVERT: D 183 PHE cc_start: 0.9111 (m-80) cc_final: 0.8510 (m-10) REVERT: D 185 LYS cc_start: 0.9108 (ttpp) cc_final: 0.8782 (tptt) REVERT: D 202 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.8909 (p) REVERT: D 209 MET cc_start: 0.7069 (mmp) cc_final: 0.6582 (mmp) REVERT: D 240 MET cc_start: 0.8071 (tmm) cc_final: 0.7196 (tmm) REVERT: D 247 ASN cc_start: 0.8323 (p0) cc_final: 0.7962 (p0) REVERT: D 262 ASP cc_start: 0.8664 (t70) cc_final: 0.8314 (t70) REVERT: D 268 TYR cc_start: 0.8504 (t80) cc_final: 0.8049 (t80) REVERT: E 39 PHE cc_start: 0.9260 (t80) cc_final: 0.8868 (t80) REVERT: E 109 MET cc_start: 0.8541 (tpp) cc_final: 0.8158 (tpp) REVERT: E 113 MET cc_start: 0.9196 (mmt) cc_final: 0.8827 (mmp) REVERT: E 182 MET cc_start: 0.9325 (mmm) cc_final: 0.8922 (mmm) REVERT: E 234 MET cc_start: 0.9286 (mmm) cc_final: 0.9008 (mmm) REVERT: E 369 LEU cc_start: 0.9478 (tp) cc_final: 0.9234 (tp) REVERT: E 584 PHE cc_start: 0.8634 (m-10) cc_final: 0.8201 (m-80) REVERT: E 711 MET cc_start: 0.8815 (mmm) cc_final: 0.8557 (mpp) REVERT: E 801 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8726 (ptp) REVERT: E 1016 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9150 (tt) REVERT: E 1021 LEU cc_start: 0.9651 (mm) cc_final: 0.9363 (pp) REVERT: E 1289 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9159 (tt) REVERT: E 1295 LEU cc_start: 0.9687 (tp) cc_final: 0.9480 (tt) REVERT: E 1298 MET cc_start: 0.9079 (ttt) cc_final: 0.8595 (tmm) REVERT: E 1301 ASN cc_start: 0.9263 (m-40) cc_final: 0.8859 (m-40) outliers start: 116 outliers final: 69 residues processed: 419 average time/residue: 0.1377 time to fit residues: 93.0291 Evaluate side-chains 381 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 303 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 801 MET Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 907 THR Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1039 ASP Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1130 ASN Chi-restraints excluded: chain E residue 1161 THR Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1289 LEU Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 1435 THR Chi-restraints excluded: chain E residue 1474 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 90 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 186 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 HIS C 175 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.055079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.045364 restraints weight = 111364.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.046869 restraints weight = 58941.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.047898 restraints weight = 37789.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.048615 restraints weight = 27607.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.049118 restraints weight = 21775.902| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 21446 Z= 0.238 Angle : 0.851 58.518 29149 Z= 0.427 Chirality : 0.048 0.339 3454 Planarity : 0.004 0.051 3624 Dihedral : 6.051 127.114 2870 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Rotamer: Outliers : 5.72 % Allowed : 22.03 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.16), residues: 2650 helix: 0.82 (0.14), residues: 1340 sheet: -0.57 (0.30), residues: 299 loop : -0.98 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1251 TYR 0.019 0.002 TYR E1004 PHE 0.023 0.002 PHE C 86 TRP 0.030 0.002 TRP E 52 HIS 0.007 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.24 (21440) covalent geometry : angle 0.76202 / 0.39 (29139) SS BOND : bond 0.00562 / 0.28 ( 5) SS BOND : angle 20.49074 / 10.05 ( 10) hydrogen bonds : bond 0.04536 / 3.04 ( 1092) hydrogen bonds : angle 4.56486 / 3.16 ( 3246) Misc. bond : bond 0.00096 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 315 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.9420 (mmmt) cc_final: 0.9165 (mmmt) REVERT: A 77 MET cc_start: 0.8759 (tpp) cc_final: 0.7997 (tmm) REVERT: A 137 MET cc_start: 0.8726 (ptt) cc_final: 0.8406 (ptp) REVERT: A 170 LYS cc_start: 0.8840 (tptp) cc_final: 0.8628 (tppt) REVERT: A 175 HIS cc_start: 0.8482 (OUTLIER) cc_final: 0.8235 (p-80) REVERT: A 209 MET cc_start: 0.8364 (mmp) cc_final: 0.7725 (mmp) REVERT: A 234 HIS cc_start: 0.8367 (t-170) cc_final: 0.7984 (t-90) REVERT: A 279 GLN cc_start: 0.8822 (tp40) cc_final: 0.8330 (tm-30) REVERT: A 288 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7975 (mt-10) REVERT: A 313 GLN cc_start: 0.8191 (mt0) cc_final: 0.7929 (mp10) REVERT: A 332 LYS cc_start: 0.9417 (mttt) cc_final: 0.9190 (mttp) REVERT: B 38 LYS cc_start: 0.9664 (mmmm) cc_final: 0.9311 (mmmm) REVERT: B 63 LEU cc_start: 0.9729 (OUTLIER) cc_final: 0.9474 (pp) REVERT: B 88 MET cc_start: 0.9018 (ttm) cc_final: 0.8751 (ttm) REVERT: B 129 VAL cc_start: 0.9300 (OUTLIER) cc_final: 0.9073 (p) REVERT: B 146 ILE cc_start: 0.9751 (mt) cc_final: 0.9545 (mp) REVERT: B 169 MET cc_start: 0.9067 (mmm) cc_final: 0.8656 (ttm) REVERT: B 170 LYS cc_start: 0.9194 (tptp) cc_final: 0.8909 (tptm) REVERT: B 305 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8546 (mt) REVERT: B 330 TYR cc_start: 0.8772 (m-80) cc_final: 0.8393 (m-80) REVERT: C 38 LYS cc_start: 0.9490 (mmmm) cc_final: 0.9149 (mmmm) REVERT: C 39 LYS cc_start: 0.9402 (mmtt) cc_final: 0.9151 (mppt) REVERT: C 207 LYS cc_start: 0.9300 (mmmm) cc_final: 0.9075 (mmmm) REVERT: C 209 MET cc_start: 0.8545 (tpp) cc_final: 0.8091 (tpt) REVERT: C 296 ILE cc_start: 0.9443 (mt) cc_final: 0.9117 (tt) REVERT: D 183 PHE cc_start: 0.9144 (m-80) cc_final: 0.8485 (m-10) REVERT: D 185 LYS cc_start: 0.9133 (ttpp) cc_final: 0.8817 (tptt) REVERT: D 202 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.8939 (p) REVERT: D 207 LYS cc_start: 0.9076 (mmtt) cc_final: 0.8835 (mmtt) REVERT: D 240 MET cc_start: 0.8161 (tmm) cc_final: 0.7306 (tmm) REVERT: D 247 ASN cc_start: 0.8424 (p0) cc_final: 0.7733 (p0) REVERT: D 262 ASP cc_start: 0.8729 (t70) cc_final: 0.8329 (t70) REVERT: D 268 TYR cc_start: 0.8670 (t80) cc_final: 0.8294 (t80) REVERT: E 43 ILE cc_start: 0.9631 (tp) cc_final: 0.9338 (pt) REVERT: E 109 MET cc_start: 0.8564 (tpp) cc_final: 0.8001 (tpp) REVERT: E 113 MET cc_start: 0.9187 (mmt) cc_final: 0.8685 (mmp) REVERT: E 128 ILE cc_start: 0.9673 (tp) cc_final: 0.9427 (tp) REVERT: E 144 TRP cc_start: 0.9113 (m100) cc_final: 0.8258 (m100) REVERT: E 182 MET cc_start: 0.9395 (mmm) cc_final: 0.8932 (mmm) REVERT: E 364 PHE cc_start: 0.9054 (t80) cc_final: 0.8798 (t80) REVERT: E 369 LEU cc_start: 0.9439 (tp) cc_final: 0.9157 (tp) REVERT: E 584 PHE cc_start: 0.8619 (m-10) cc_final: 0.8199 (m-80) REVERT: E 801 MET cc_start: 0.8931 (ptp) cc_final: 0.8719 (ptp) REVERT: E 1021 LEU cc_start: 0.9646 (mm) cc_final: 0.9403 (pp) REVERT: E 1289 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9097 (tt) REVERT: E 1295 LEU cc_start: 0.9681 (tp) cc_final: 0.9477 (tt) REVERT: E 1298 MET cc_start: 0.9100 (ttt) cc_final: 0.8597 (tmm) REVERT: E 1301 ASN cc_start: 0.9176 (m-40) cc_final: 0.8751 (m110) REVERT: E 1318 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9221 (tt) outliers start: 130 outliers final: 81 residues processed: 414 average time/residue: 0.1365 time to fit residues: 91.1949 Evaluate side-chains 387 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 299 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 907 THR Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1039 ASP Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1130 ASN Chi-restraints excluded: chain E residue 1161 THR Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1289 LEU Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 1318 LEU Chi-restraints excluded: chain E residue 1424 ILE Chi-restraints excluded: chain E residue 1435 THR Chi-restraints excluded: chain E residue 1474 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 9 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 218 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS C 235 GLN D 160 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.055044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.045500 restraints weight = 110208.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.046994 restraints weight = 57894.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.048055 restraints weight = 37133.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.048770 restraints weight = 26899.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.049250 restraints weight = 21264.499| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 21446 Z= 0.202 Angle : 0.831 58.441 29149 Z= 0.413 Chirality : 0.047 0.348 3454 Planarity : 0.004 0.051 3624 Dihedral : 5.934 127.592 2870 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 5.36 % Allowed : 23.31 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.16), residues: 2650 helix: 0.98 (0.14), residues: 1344 sheet: -0.53 (0.29), residues: 307 loop : -0.85 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1251 TYR 0.019 0.001 TYR E1004 PHE 0.024 0.002 PHE E1164 TRP 0.044 0.002 TRP E 52 HIS 0.012 0.001 HIS C 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (21440) covalent geometry : angle 0.73949 / 0.37 (29139) SS BOND : bond 0.00770 / 0.38 ( 5) SS BOND : angle 20.47960 / 10.05 ( 10) hydrogen bonds : bond 0.04435 / 2.97 ( 1092) hydrogen bonds : angle 4.47260 / 3.09 ( 3246) Misc. bond : bond 0.00087 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 315 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8763 (tpp) cc_final: 0.7982 (tmm) REVERT: A 137 MET cc_start: 0.8716 (ptt) cc_final: 0.8389 (ptp) REVERT: A 170 LYS cc_start: 0.8863 (tptp) cc_final: 0.8519 (tppt) REVERT: A 209 MET cc_start: 0.8308 (mmp) cc_final: 0.7748 (mmp) REVERT: A 262 ASP cc_start: 0.9186 (OUTLIER) cc_final: 0.8531 (m-30) REVERT: A 279 GLN cc_start: 0.8757 (tp40) cc_final: 0.8293 (tm-30) REVERT: A 288 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7854 (mt-10) REVERT: A 332 LYS cc_start: 0.9418 (mttt) cc_final: 0.9177 (mttp) REVERT: B 38 LYS cc_start: 0.9668 (mmmm) cc_final: 0.9131 (mmmm) REVERT: B 63 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9437 (pp) REVERT: B 88 MET cc_start: 0.9014 (ttm) cc_final: 0.8777 (ttm) REVERT: B 129 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.9041 (p) REVERT: B 141 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: B 169 MET cc_start: 0.9063 (mmm) cc_final: 0.8640 (ttm) REVERT: B 170 LYS cc_start: 0.9152 (tptp) cc_final: 0.8895 (tptm) REVERT: B 181 LEU cc_start: 0.9570 (mm) cc_final: 0.9262 (mm) REVERT: B 211 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8662 (mp) REVERT: B 296 ILE cc_start: 0.8822 (mp) cc_final: 0.8506 (pt) REVERT: B 305 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8630 (mt) REVERT: B 330 TYR cc_start: 0.8795 (m-80) cc_final: 0.8418 (m-80) REVERT: B 332 LYS cc_start: 0.9333 (mppt) cc_final: 0.8927 (mptt) REVERT: C 39 LYS cc_start: 0.9406 (mmtt) cc_final: 0.9158 (mppt) REVERT: C 47 LYS cc_start: 0.8888 (tppt) cc_final: 0.8287 (tptp) REVERT: C 207 LYS cc_start: 0.9329 (mmmm) cc_final: 0.9119 (mmmm) REVERT: C 296 ILE cc_start: 0.9432 (mt) cc_final: 0.9125 (tt) REVERT: D 114 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.9023 (tp) REVERT: D 137 MET cc_start: 0.8318 (ttp) cc_final: 0.7917 (ttp) REVERT: D 183 PHE cc_start: 0.9161 (m-80) cc_final: 0.8500 (m-10) REVERT: D 185 LYS cc_start: 0.9143 (ttpp) cc_final: 0.8840 (tptt) REVERT: D 202 VAL cc_start: 0.9290 (OUTLIER) cc_final: 0.8950 (p) REVERT: D 207 LYS cc_start: 0.9096 (mmtt) cc_final: 0.8883 (mmtt) REVERT: D 240 MET cc_start: 0.8182 (tmm) cc_final: 0.7320 (tmm) REVERT: D 247 ASN cc_start: 0.8558 (p0) cc_final: 0.7731 (p0) REVERT: E 43 ILE cc_start: 0.9552 (tp) cc_final: 0.9295 (pt) REVERT: E 109 MET cc_start: 0.8590 (tpp) cc_final: 0.8023 (tpp) REVERT: E 113 MET cc_start: 0.9178 (mmt) cc_final: 0.8664 (mmp) REVERT: E 128 ILE cc_start: 0.9672 (tp) cc_final: 0.9448 (tp) REVERT: E 144 TRP cc_start: 0.9096 (m100) cc_final: 0.8319 (m100) REVERT: E 182 MET cc_start: 0.9394 (mmm) cc_final: 0.8914 (mmm) REVERT: E 183 LEU cc_start: 0.9604 (mm) cc_final: 0.8095 (mm) REVERT: E 234 MET cc_start: 0.9302 (mmm) cc_final: 0.8925 (mmm) REVERT: E 369 LEU cc_start: 0.9415 (tp) cc_final: 0.9137 (tp) REVERT: E 584 PHE cc_start: 0.8629 (m-10) cc_final: 0.8193 (m-80) REVERT: E 798 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8634 (ttt-90) REVERT: E 1021 LEU cc_start: 0.9637 (mm) cc_final: 0.9399 (pp) REVERT: E 1298 MET cc_start: 0.9110 (ttt) cc_final: 0.8612 (tmm) REVERT: E 1301 ASN cc_start: 0.9166 (m-40) cc_final: 0.8738 (m-40) outliers start: 122 outliers final: 82 residues processed: 404 average time/residue: 0.1392 time to fit residues: 90.1594 Evaluate side-chains 390 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 299 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 556 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 798 ARG Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 907 THR Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1039 ASP Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1161 THR Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 1435 THR Chi-restraints excluded: chain E residue 1474 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 233 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 187 optimal weight: 9.9990 chunk 253 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.055825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.046358 restraints weight = 110169.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.047841 restraints weight = 58378.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.048857 restraints weight = 37586.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.049579 restraints weight = 27487.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.050082 restraints weight = 21758.851| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.194 21446 Z= 0.168 Angle : 0.822 58.413 29149 Z= 0.403 Chirality : 0.047 0.350 3454 Planarity : 0.004 0.052 3624 Dihedral : 5.846 127.974 2869 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Rotamer: Outliers : 4.44 % Allowed : 24.63 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.16), residues: 2650 helix: 1.12 (0.14), residues: 1336 sheet: -0.47 (0.29), residues: 303 loop : -0.78 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1251 TYR 0.014 0.001 TYR E1064 PHE 0.027 0.001 PHE E1164 TRP 0.040 0.002 TRP E 52 HIS 0.007 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (21440) covalent geometry : angle 0.72925 / 0.36 (29139) SS BOND : bond 0.00542 / 0.27 ( 5) SS BOND : angle 20.45254 / 10.01 ( 10) hydrogen bonds : bond 0.04344 / 2.90 ( 1092) hydrogen bonds : angle 4.41709 / 3.06 ( 3246) Misc. bond : bond 0.00078 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 323 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8760 (tpp) cc_final: 0.7926 (tmm) REVERT: A 160 ASN cc_start: 0.9298 (m-40) cc_final: 0.9037 (m-40) REVERT: A 170 LYS cc_start: 0.8908 (tptp) cc_final: 0.8468 (tppt) REVERT: A 209 MET cc_start: 0.8285 (mmp) cc_final: 0.7759 (mmp) REVERT: A 262 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8465 (m-30) REVERT: A 279 GLN cc_start: 0.8746 (tp40) cc_final: 0.8292 (tm-30) REVERT: A 288 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 332 LYS cc_start: 0.9432 (mttt) cc_final: 0.9184 (mttp) REVERT: B 38 LYS cc_start: 0.9654 (mmmm) cc_final: 0.9408 (mmmm) REVERT: B 63 LEU cc_start: 0.9684 (OUTLIER) cc_final: 0.9446 (pp) REVERT: B 129 VAL cc_start: 0.9193 (OUTLIER) cc_final: 0.8980 (p) REVERT: B 141 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: B 169 MET cc_start: 0.8971 (mmm) cc_final: 0.8606 (ttm) REVERT: B 170 LYS cc_start: 0.9189 (tptp) cc_final: 0.8694 (tptm) REVERT: B 181 LEU cc_start: 0.9572 (mm) cc_final: 0.9256 (mm) REVERT: B 211 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8658 (mp) REVERT: B 305 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8731 (mt) REVERT: B 330 TYR cc_start: 0.8719 (m-80) cc_final: 0.8481 (m-80) REVERT: B 332 LYS cc_start: 0.9328 (mppt) cc_final: 0.8903 (mptt) REVERT: C 39 LYS cc_start: 0.9388 (mmtt) cc_final: 0.9091 (mppt) REVERT: C 47 LYS cc_start: 0.8875 (tppt) cc_final: 0.8482 (tppt) REVERT: C 185 LYS cc_start: 0.9468 (tppp) cc_final: 0.9038 (tppp) REVERT: C 207 LYS cc_start: 0.9309 (mmmm) cc_final: 0.9031 (mmmm) REVERT: C 268 TYR cc_start: 0.9170 (t80) cc_final: 0.8632 (t80) REVERT: C 296 ILE cc_start: 0.9390 (mt) cc_final: 0.9080 (tt) REVERT: D 77 MET cc_start: 0.8727 (tpp) cc_final: 0.8379 (tpp) REVERT: D 185 LYS cc_start: 0.9111 (ttpp) cc_final: 0.8880 (tptt) REVERT: D 202 VAL cc_start: 0.9221 (p) cc_final: 0.8950 (p) REVERT: D 240 MET cc_start: 0.8179 (tmm) cc_final: 0.7398 (tmm) REVERT: D 247 ASN cc_start: 0.8464 (p0) cc_final: 0.8211 (p0) REVERT: D 250 PHE cc_start: 0.9029 (t80) cc_final: 0.8376 (t80) REVERT: E 39 PHE cc_start: 0.9150 (t80) cc_final: 0.8788 (t80) REVERT: E 109 MET cc_start: 0.8583 (tpp) cc_final: 0.8016 (tpp) REVERT: E 113 MET cc_start: 0.9184 (mmt) cc_final: 0.8657 (mmp) REVERT: E 144 TRP cc_start: 0.9037 (m100) cc_final: 0.8349 (m100) REVERT: E 182 MET cc_start: 0.9324 (mmm) cc_final: 0.8801 (mmm) REVERT: E 183 LEU cc_start: 0.9604 (mm) cc_final: 0.7909 (mm) REVERT: E 369 LEU cc_start: 0.9412 (tp) cc_final: 0.9077 (tp) REVERT: E 584 PHE cc_start: 0.8678 (m-10) cc_final: 0.8223 (m-80) REVERT: E 586 ILE cc_start: 0.9472 (pt) cc_final: 0.9244 (pt) REVERT: E 1021 LEU cc_start: 0.9625 (mm) cc_final: 0.9411 (pp) REVERT: E 1088 TRP cc_start: 0.7960 (OUTLIER) cc_final: 0.7708 (t-100) REVERT: E 1110 MET cc_start: 0.8678 (mmm) cc_final: 0.8343 (mmt) REVERT: E 1298 MET cc_start: 0.9127 (ttt) cc_final: 0.8292 (tmm) REVERT: E 1301 ASN cc_start: 0.9134 (m-40) cc_final: 0.8741 (m-40) REVERT: E 1305 MET cc_start: 0.9361 (tpp) cc_final: 0.9140 (tpp) outliers start: 101 outliers final: 74 residues processed: 399 average time/residue: 0.1359 time to fit residues: 87.5706 Evaluate side-chains 389 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 308 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 1039 ASP Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1088 TRP Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1171 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 1435 THR Chi-restraints excluded: chain E residue 1474 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 34 optimal weight: 0.0370 chunk 192 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 210 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 overall best weight: 0.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN E 867 HIS E 933 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.056936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.047316 restraints weight = 109096.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.048879 restraints weight = 57373.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.049926 restraints weight = 36646.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.050680 restraints weight = 26633.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.051213 restraints weight = 20866.852| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.196 21446 Z= 0.139 Angle : 0.820 58.380 29149 Z= 0.398 Chirality : 0.047 0.353 3454 Planarity : 0.003 0.053 3624 Dihedral : 5.721 129.164 2868 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 4.00 % Allowed : 25.59 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.16), residues: 2650 helix: 1.19 (0.14), residues: 1340 sheet: -0.42 (0.30), residues: 291 loop : -0.66 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1251 TYR 0.012 0.001 TYR E 379 PHE 0.021 0.001 PHE E 364 TRP 0.037 0.001 TRP E 52 HIS 0.007 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (21440) covalent geometry : angle 0.72782 / 0.35 (29139) SS BOND : bond 0.00520 / 0.26 ( 5) SS BOND : angle 20.43702 / 10.00 ( 10) hydrogen bonds : bond 0.04243 / 2.83 ( 1092) hydrogen bonds : angle 4.31026 / 3.00 ( 3246) Misc. bond : bond 0.00063 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 341 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8649 (tpp) cc_final: 0.7865 (tmm) REVERT: A 160 ASN cc_start: 0.9281 (m-40) cc_final: 0.9006 (m-40) REVERT: A 209 MET cc_start: 0.8267 (mmp) cc_final: 0.7708 (mmp) REVERT: A 262 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8424 (m-30) REVERT: A 279 GLN cc_start: 0.8660 (tp40) cc_final: 0.8295 (tm-30) REVERT: A 288 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7560 (mp0) REVERT: A 332 LYS cc_start: 0.9427 (mttt) cc_final: 0.9185 (mttp) REVERT: B 38 LYS cc_start: 0.9604 (mmmm) cc_final: 0.9158 (mmmm) REVERT: B 63 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9421 (pp) REVERT: B 169 MET cc_start: 0.8909 (mmm) cc_final: 0.8529 (ttm) REVERT: B 170 LYS cc_start: 0.9144 (tptp) cc_final: 0.8624 (tptm) REVERT: B 181 LEU cc_start: 0.9532 (mm) cc_final: 0.9191 (mm) REVERT: B 288 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7957 (mt-10) REVERT: B 305 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8748 (mt) REVERT: B 330 TYR cc_start: 0.8690 (m-80) cc_final: 0.8473 (m-80) REVERT: B 332 LYS cc_start: 0.9345 (mppt) cc_final: 0.8979 (mptt) REVERT: B 351 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8565 (pm20) REVERT: C 39 LYS cc_start: 0.9441 (mmtt) cc_final: 0.9099 (mppt) REVERT: C 47 LYS cc_start: 0.8880 (tppt) cc_final: 0.8537 (tppt) REVERT: C 185 LYS cc_start: 0.9486 (tppp) cc_final: 0.9036 (tppp) REVERT: C 247 ASN cc_start: 0.8988 (p0) cc_final: 0.8074 (p0) REVERT: C 268 TYR cc_start: 0.9159 (t80) cc_final: 0.8647 (t80) REVERT: C 296 ILE cc_start: 0.9324 (mt) cc_final: 0.8947 (tt) REVERT: D 77 MET cc_start: 0.8679 (tpp) cc_final: 0.8251 (tpp) REVERT: D 185 LYS cc_start: 0.9153 (ttpp) cc_final: 0.8891 (tptt) REVERT: D 217 MET cc_start: 0.8660 (mtm) cc_final: 0.8183 (mtm) REVERT: D 240 MET cc_start: 0.8094 (tmm) cc_final: 0.7683 (tmm) REVERT: D 247 ASN cc_start: 0.8543 (p0) cc_final: 0.8326 (p0) REVERT: D 250 PHE cc_start: 0.9046 (t80) cc_final: 0.8446 (t80) REVERT: D 257 ILE cc_start: 0.9381 (mt) cc_final: 0.9121 (mp) REVERT: E 39 PHE cc_start: 0.9205 (t80) cc_final: 0.8698 (t80) REVERT: E 43 ILE cc_start: 0.9601 (tp) cc_final: 0.9220 (pt) REVERT: E 109 MET cc_start: 0.8574 (tpp) cc_final: 0.7966 (tpp) REVERT: E 113 MET cc_start: 0.9150 (mmt) cc_final: 0.8623 (mmp) REVERT: E 144 TRP cc_start: 0.9009 (m100) cc_final: 0.8364 (m100) REVERT: E 182 MET cc_start: 0.9280 (mmm) cc_final: 0.8761 (mmm) REVERT: E 183 LEU cc_start: 0.9580 (mm) cc_final: 0.7713 (mm) REVERT: E 234 MET cc_start: 0.9278 (mmm) cc_final: 0.8930 (mmm) REVERT: E 369 LEU cc_start: 0.9392 (tp) cc_final: 0.9057 (tp) REVERT: E 430 MET cc_start: 0.9071 (ttp) cc_final: 0.8683 (ptm) REVERT: E 584 PHE cc_start: 0.8612 (m-10) cc_final: 0.8294 (m-80) REVERT: E 586 ILE cc_start: 0.9503 (pt) cc_final: 0.9259 (pt) REVERT: E 720 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9118 (mtmm) REVERT: E 1021 LEU cc_start: 0.9580 (mm) cc_final: 0.9313 (pp) REVERT: E 1066 MET cc_start: 0.8481 (mmm) cc_final: 0.8263 (mmp) REVERT: E 1110 MET cc_start: 0.8589 (mmm) cc_final: 0.8312 (mmt) REVERT: E 1298 MET cc_start: 0.9179 (ttt) cc_final: 0.8364 (tmm) REVERT: E 1301 ASN cc_start: 0.9076 (m-40) cc_final: 0.8642 (m-40) REVERT: E 1313 LYS cc_start: 0.9051 (tppt) cc_final: 0.8775 (tppt) outliers start: 91 outliers final: 69 residues processed: 409 average time/residue: 0.1367 time to fit residues: 90.0153 Evaluate side-chains 393 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 319 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 556 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 720 LYS Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 1039 ASP Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1171 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1280 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 1435 THR Chi-restraints excluded: chain E residue 1474 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 106 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 264 optimal weight: 0.0010 chunk 21 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 261 optimal weight: 0.0470 chunk 240 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 ASN ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 797 GLN E 836 GLN E1427 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.057576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.048042 restraints weight = 109101.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.049580 restraints weight = 58021.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.050615 restraints weight = 37362.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.051350 restraints weight = 27281.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.051830 restraints weight = 21552.896| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.196 21446 Z= 0.136 Angle : 0.837 58.364 29149 Z= 0.402 Chirality : 0.047 0.361 3454 Planarity : 0.003 0.053 3624 Dihedral : 5.653 128.398 2868 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 3.91 % Allowed : 25.95 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.16), residues: 2650 helix: 1.22 (0.14), residues: 1333 sheet: -0.32 (0.30), residues: 291 loop : -0.61 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 798 TYR 0.011 0.001 TYR E 379 PHE 0.027 0.001 PHE D 183 TRP 0.030 0.001 TRP E 52 HIS 0.007 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (21440) covalent geometry : angle 0.74651 / 0.36 (29139) SS BOND : bond 0.00523 / 0.26 ( 5) SS BOND : angle 20.43212 / 10.00 ( 10) hydrogen bonds : bond 0.04182 / 2.79 ( 1092) hydrogen bonds : angle 4.28489 / 2.99 ( 3246) Misc. bond : bond 0.00062 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 342 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.9460 (mmmt) cc_final: 0.9231 (mmmt) REVERT: A 77 MET cc_start: 0.8527 (tpp) cc_final: 0.7789 (tmm) REVERT: A 169 MET cc_start: 0.8739 (ttt) cc_final: 0.8337 (tpp) REVERT: A 175 HIS cc_start: 0.8427 (OUTLIER) cc_final: 0.8187 (p-80) REVERT: A 209 MET cc_start: 0.8370 (mmp) cc_final: 0.7786 (mmp) REVERT: A 262 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8468 (m-30) REVERT: A 279 GLN cc_start: 0.8674 (tp40) cc_final: 0.8331 (tm-30) REVERT: A 288 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7713 (mt-10) REVERT: A 332 LYS cc_start: 0.9434 (mttt) cc_final: 0.9189 (mttp) REVERT: B 38 LYS cc_start: 0.9640 (mmmm) cc_final: 0.9191 (mmmm) REVERT: B 63 LEU cc_start: 0.9640 (tt) cc_final: 0.9412 (pp) REVERT: B 169 MET cc_start: 0.8880 (mmm) cc_final: 0.8480 (ttm) REVERT: B 170 LYS cc_start: 0.9159 (tptp) cc_final: 0.8605 (tptm) REVERT: B 181 LEU cc_start: 0.9526 (mm) cc_final: 0.9172 (mm) REVERT: B 211 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8765 (mp) REVERT: B 305 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8752 (mt) REVERT: B 330 TYR cc_start: 0.8664 (m-80) cc_final: 0.8463 (m-80) REVERT: B 332 LYS cc_start: 0.9317 (mppt) cc_final: 0.8939 (mptt) REVERT: C 39 LYS cc_start: 0.9376 (mmtt) cc_final: 0.9042 (mppt) REVERT: C 47 LYS cc_start: 0.8875 (tppt) cc_final: 0.8475 (tppt) REVERT: C 147 LEU cc_start: 0.9589 (tt) cc_final: 0.9259 (mm) REVERT: C 185 LYS cc_start: 0.9466 (tppp) cc_final: 0.9012 (tppp) REVERT: C 247 ASN cc_start: 0.8884 (p0) cc_final: 0.8084 (p0) REVERT: C 268 TYR cc_start: 0.9124 (t80) cc_final: 0.8643 (t80) REVERT: C 296 ILE cc_start: 0.9340 (mt) cc_final: 0.8927 (tt) REVERT: C 332 LYS cc_start: 0.9527 (mtpp) cc_final: 0.9190 (mtmm) REVERT: D 77 MET cc_start: 0.8638 (tpp) cc_final: 0.8297 (tpp) REVERT: D 126 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8511 (mt-10) REVERT: D 137 MET cc_start: 0.8388 (ttp) cc_final: 0.8022 (ttm) REVERT: D 185 LYS cc_start: 0.9101 (ttpp) cc_final: 0.8884 (tptt) REVERT: D 217 MET cc_start: 0.8545 (mtm) cc_final: 0.8119 (mtm) REVERT: D 240 MET cc_start: 0.8004 (tmm) cc_final: 0.7659 (tmm) REVERT: D 247 ASN cc_start: 0.8640 (p0) cc_final: 0.7965 (p0) REVERT: D 250 PHE cc_start: 0.9086 (t80) cc_final: 0.8502 (t80) REVERT: D 257 ILE cc_start: 0.9414 (mt) cc_final: 0.9165 (mp) REVERT: E 39 PHE cc_start: 0.9202 (t80) cc_final: 0.8826 (t80) REVERT: E 42 PHE cc_start: 0.8813 (m-80) cc_final: 0.8500 (t80) REVERT: E 109 MET cc_start: 0.8564 (tpp) cc_final: 0.7995 (tpp) REVERT: E 113 MET cc_start: 0.9150 (mmt) cc_final: 0.8628 (mmp) REVERT: E 144 TRP cc_start: 0.9014 (m100) cc_final: 0.8411 (m100) REVERT: E 182 MET cc_start: 0.9011 (mmm) cc_final: 0.8598 (mmm) REVERT: E 183 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.7676 (mm) REVERT: E 234 MET cc_start: 0.9222 (mmm) cc_final: 0.8822 (mmm) REVERT: E 369 LEU cc_start: 0.9377 (tp) cc_final: 0.8903 (tt) REVERT: E 430 MET cc_start: 0.8996 (ttp) cc_final: 0.8618 (ptm) REVERT: E 584 PHE cc_start: 0.8545 (m-10) cc_final: 0.8196 (m-80) REVERT: E 586 ILE cc_start: 0.9478 (pt) cc_final: 0.9242 (pt) REVERT: E 720 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9144 (mtmm) REVERT: E 1066 MET cc_start: 0.8449 (mmm) cc_final: 0.8226 (mmp) REVERT: E 1088 TRP cc_start: 0.7884 (OUTLIER) cc_final: 0.7611 (t-100) REVERT: E 1110 MET cc_start: 0.8562 (mmm) cc_final: 0.8288 (mmt) REVERT: E 1228 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9104 (mp) REVERT: E 1254 TYR cc_start: 0.9015 (m-80) cc_final: 0.8812 (m-80) REVERT: E 1261 LEU cc_start: 0.9589 (tp) cc_final: 0.9138 (mt) REVERT: E 1298 MET cc_start: 0.9142 (ttt) cc_final: 0.8330 (tmm) REVERT: E 1301 ASN cc_start: 0.9087 (m-40) cc_final: 0.8666 (m-40) REVERT: E 1313 LYS cc_start: 0.8979 (tppt) cc_final: 0.8721 (tppt) outliers start: 89 outliers final: 65 residues processed: 408 average time/residue: 0.1383 time to fit residues: 90.6844 Evaluate side-chains 397 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 324 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 720 LYS Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 1039 ASP Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1088 TRP Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1157 ILE Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1171 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1307 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 2 optimal weight: 7.9990 chunk 191 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN D 216 HIS ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.054845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.045539 restraints weight = 111638.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.047019 restraints weight = 58640.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.048025 restraints weight = 37498.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.048736 restraints weight = 27216.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.049194 restraints weight = 21481.321| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 21446 Z= 0.227 Angle : 0.883 58.452 29149 Z= 0.435 Chirality : 0.049 0.344 3454 Planarity : 0.004 0.051 3624 Dihedral : 5.749 124.024 2868 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.47 % Rotamer: Outliers : 3.74 % Allowed : 26.56 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.16), residues: 2650 helix: 1.13 (0.14), residues: 1348 sheet: -0.51 (0.29), residues: 295 loop : -0.57 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1444 TYR 0.016 0.001 TYR E1287 PHE 0.024 0.002 PHE C 86 TRP 0.026 0.002 TRP E 52 HIS 0.006 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.23 (21440) covalent geometry : angle 0.79797 / 0.40 (29139) SS BOND : bond 0.00588 / 0.29 ( 5) SS BOND : angle 20.47258 / 10.03 ( 10) hydrogen bonds : bond 0.04376 / 2.90 ( 1092) hydrogen bonds : angle 4.52274 / 3.15 ( 3246) Misc. bond : bond 0.00090 / 0.05 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 309 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8691 (tpp) cc_final: 0.7907 (tmm) REVERT: A 160 ASN cc_start: 0.9285 (m-40) cc_final: 0.9022 (m-40) REVERT: A 209 MET cc_start: 0.8271 (mmp) cc_final: 0.7709 (mmp) REVERT: A 262 ASP cc_start: 0.9160 (OUTLIER) cc_final: 0.8568 (m-30) REVERT: A 279 GLN cc_start: 0.8792 (tp40) cc_final: 0.8361 (tm-30) REVERT: A 288 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7822 (mt-10) REVERT: A 332 LYS cc_start: 0.9444 (mttt) cc_final: 0.9213 (mttp) REVERT: B 38 LYS cc_start: 0.9543 (mmmm) cc_final: 0.9072 (mmmm) REVERT: B 63 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9440 (pp) REVERT: B 146 ILE cc_start: 0.9787 (mt) cc_final: 0.9573 (mp) REVERT: B 169 MET cc_start: 0.8986 (mmm) cc_final: 0.8589 (ttm) REVERT: B 170 LYS cc_start: 0.9163 (tptp) cc_final: 0.8904 (tptm) REVERT: B 181 LEU cc_start: 0.9552 (mm) cc_final: 0.9253 (mm) REVERT: B 211 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8781 (mp) REVERT: B 218 GLN cc_start: 0.8731 (mt0) cc_final: 0.7806 (tt0) REVERT: B 305 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8731 (mt) REVERT: B 330 TYR cc_start: 0.8757 (m-80) cc_final: 0.8424 (m-80) REVERT: C 39 LYS cc_start: 0.9436 (mmtt) cc_final: 0.9155 (mppt) REVERT: C 47 LYS cc_start: 0.8862 (tppt) cc_final: 0.8402 (tppt) REVERT: C 163 MET cc_start: 0.9153 (mmm) cc_final: 0.8641 (mmm) REVERT: C 185 LYS cc_start: 0.9507 (tppp) cc_final: 0.9087 (tppp) REVERT: C 268 TYR cc_start: 0.9194 (t80) cc_final: 0.8648 (t80) REVERT: C 296 ILE cc_start: 0.9423 (mt) cc_final: 0.9053 (tt) REVERT: C 332 LYS cc_start: 0.9623 (mtpp) cc_final: 0.9309 (mtmm) REVERT: D 77 MET cc_start: 0.8779 (tpp) cc_final: 0.8413 (tpp) REVERT: D 137 MET cc_start: 0.8504 (ttp) cc_final: 0.8160 (ttm) REVERT: D 185 LYS cc_start: 0.9156 (ttpp) cc_final: 0.8887 (tptt) REVERT: D 216 HIS cc_start: 0.8277 (m170) cc_final: 0.7851 (m-70) REVERT: D 240 MET cc_start: 0.8007 (tmm) cc_final: 0.7311 (tmm) REVERT: D 247 ASN cc_start: 0.8762 (p0) cc_final: 0.8476 (p0) REVERT: E 39 PHE cc_start: 0.9292 (t80) cc_final: 0.8936 (t80) REVERT: E 42 PHE cc_start: 0.8905 (m-80) cc_final: 0.8559 (t80) REVERT: E 109 MET cc_start: 0.8676 (tpp) cc_final: 0.8111 (tpp) REVERT: E 113 MET cc_start: 0.9157 (mmt) cc_final: 0.8745 (mmp) REVERT: E 144 TRP cc_start: 0.9133 (m100) cc_final: 0.8386 (m100) REVERT: E 182 MET cc_start: 0.9074 (mmm) cc_final: 0.8657 (mmm) REVERT: E 183 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.8015 (mm) REVERT: E 234 MET cc_start: 0.9309 (mmm) cc_final: 0.8925 (mmm) REVERT: E 369 LEU cc_start: 0.9403 (tp) cc_final: 0.9086 (tp) REVERT: E 584 PHE cc_start: 0.8604 (m-10) cc_final: 0.8222 (m-80) REVERT: E 586 ILE cc_start: 0.9524 (pt) cc_final: 0.9295 (pt) REVERT: E 1066 MET cc_start: 0.8495 (mmm) cc_final: 0.8275 (mmp) REVERT: E 1088 TRP cc_start: 0.8017 (OUTLIER) cc_final: 0.7711 (t-100) REVERT: E 1110 MET cc_start: 0.8595 (mmm) cc_final: 0.8311 (mmt) REVERT: E 1298 MET cc_start: 0.9145 (ttt) cc_final: 0.8374 (tmm) REVERT: E 1301 ASN cc_start: 0.9115 (m-40) cc_final: 0.8746 (m110) REVERT: E 1304 ASP cc_start: 0.9170 (m-30) cc_final: 0.8903 (m-30) REVERT: E 1313 LYS cc_start: 0.9029 (tppt) cc_final: 0.8739 (tppt) outliers start: 85 outliers final: 66 residues processed: 372 average time/residue: 0.1493 time to fit residues: 88.7143 Evaluate side-chains 374 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 302 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 1039 ASP Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1088 TRP Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1157 ILE Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1171 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1307 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 64 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 215 optimal weight: 10.0000 chunk 231 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 218 optimal weight: 0.0010 chunk 221 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN D 216 HIS ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 797 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.057202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.047914 restraints weight = 108494.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.049449 restraints weight = 56843.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.050507 restraints weight = 36103.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.051236 restraints weight = 25969.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.051707 restraints weight = 20343.993| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.196 21446 Z= 0.139 Angle : 0.863 58.387 29149 Z= 0.411 Chirality : 0.048 0.360 3454 Planarity : 0.003 0.052 3624 Dihedral : 5.653 129.387 2868 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 3.08 % Allowed : 27.00 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.16), residues: 2650 helix: 1.24 (0.14), residues: 1334 sheet: -0.40 (0.30), residues: 291 loop : -0.58 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1444 TYR 0.013 0.001 TYR E 379 PHE 0.019 0.001 PHE C 86 TRP 0.034 0.001 TRP E 52 HIS 0.007 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (21440) covalent geometry : angle 0.77593 / 0.37 (29139) SS BOND : bond 0.00504 / 0.25 ( 5) SS BOND : angle 20.43535 / 10.00 ( 10) hydrogen bonds : bond 0.04215 / 2.82 ( 1092) hydrogen bonds : angle 4.36792 / 3.04 ( 3246) Misc. bond : bond 0.00065 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3450.14 seconds wall clock time: 60 minutes 56.35 seconds (3656.35 seconds total)