Starting phenix.real_space_refine on Mon Oct 26 15:07:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s61_24846/10_2026/7s61_24846.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s61_24846/10_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7s61_24846/10_2026/7s61_24846.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s61_24846/10_2026/7s61_24846.cif" model { file = "/net/cci-nas-00/data/ceres_data/7s61_24846/10_2026/7s61_24846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s61_24846/10_2026/7s61_24846.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s61_24846/10_2026/7s61_24846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s61_24846/10_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/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: 4.73, per 1000 atoms: 0.23 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=" 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 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 27 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 816.6 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: 0.65 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: 5.12 Time building geometry restraints manager: 2.21 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: 12266 35.49 - 70.98: 427 70.98 - 106.47: 23 106.47 - 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=" CA GLY E 411 " pdb=" C GLY E 411 " pdb=" N GLU E 412 " pdb=" CA GLU E 412 " ideal model delta harmonic sigma weight residual -180.00 -136.60 -43.40 0 5.00e+00 4.00e-02 7.53e+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: 2.16 - 2.71: 1016 2.71 - 3.26: 18698 3.26 - 3.80: 36469 3.80 - 4.35: 43776 4.35 - 4.90: 72070 Nonbonded interactions: 172029 Sorted by model distance: 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 nonbonded pdb=" OE1 GLN E 775 " pdb="MG MG E1602 " model vdw 2.333 2.170 ... (remaining 172024 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: 4.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.330 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- 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 : 0.010 0.150 21446 Z= 0.466 Angle : 1.582 23.309 29149 Z= 0.871 Chirality : 0.083 0.846 3454 Planarity : 0.013 0.104 3624 Dihedral : 17.635 177.446 7654 Min Nonbonded Distance : 2.160 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 0.01604 / 0.81 ( 5) SS BOND : angle 3.15613 / 2.07 ( 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 : 0.678 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: 0.1343 time to fit residues: 156.9358 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 : 0.749 ------------------------------------------------------------------------------- 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: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] 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 234 HIS ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN B 57 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 HIS ** C 128 GLN ** 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 235 ASN E 265 GLN E 407 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.060210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.050537 restraints weight = 106904.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.052099 restraints weight = 55463.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053155 restraints weight = 35085.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.053884 restraints weight = 25252.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.054405 restraints weight = 19820.196| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21446 Z= 0.146 Angle : 0.756 11.345 29149 Z= 0.388 Chirality : 0.047 0.259 3454 Planarity : 0.006 0.078 3624 Dihedral : 8.440 172.463 2944 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 3.69 % Allowed : 19.66 % Favored : 76.65 % 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: -2.15 (0.14), residues: 2650 helix: -1.10 (0.13), residues: 1280 sheet: -0.48 (0.32), residues: 255 loop : -1.94 (0.16), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1300 TYR 0.021 0.002 TYR D 268 PHE 0.026 0.002 PHE D 86 TRP 0.023 0.002 TRP D 90 HIS 0.006 0.001 HIS E 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (21440) covalent geometry : angle 0.75637 / 0.39 (29139) SS BOND : bond 0.00288 / 0.14 ( 5) SS BOND : angle 1.07478 / 0.66 ( 10) hydrogen bonds : bond 0.04956 / 3.33 ( 1092) hydrogen bonds : angle 5.03178 / 3.50 ( 3246) Misc. bond : bond 0.00058 / 0.03 ( 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 537 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 453 time to evaluate : 0.841 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: 0.8724 (m-40) cc_final: 0.8404 (t0) REVERT: A 47 LYS cc_start: 0.9165 (mmmt) cc_final: 0.8939 (ptpt) REVERT: A 66 LEU cc_start: 0.9329 (mt) cc_final: 0.9059 (mt) REVERT: A 77 MET cc_start: 0.8694 (tpp) cc_final: 0.7607 (tmm) REVERT: A 137 MET cc_start: 0.8374 (ptt) cc_final: 0.8067 (ptp) REVERT: A 170 LYS cc_start: 0.8868 (tptp) cc_final: 0.8532 (tppt) REVERT: A 173 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8624 (pt0) REVERT: A 199 MET cc_start: 0.8747 (mtm) cc_final: 0.8537 (mtt) REVERT: A 209 MET cc_start: 0.8498 (mmp) cc_final: 0.7066 (mmp) REVERT: A 279 GLN cc_start: 0.9178 (tp40) cc_final: 0.8199 (tm-30) REVERT: A 292 GLU cc_start: 0.8058 (pt0) cc_final: 0.7301 (pt0) REVERT: A 332 LYS cc_start: 0.9416 (mttt) cc_final: 0.9128 (mttm) REVERT: B 38 LYS cc_start: 0.9455 (mmmm) cc_final: 0.9187 (mmmm) REVERT: B 43 ASN cc_start: 0.8845 (m110) cc_final: 0.8547 (m-40) REVERT: B 52 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7242 (mm110) REVERT: B 63 LEU cc_start: 0.9647 (tt) cc_final: 0.9229 (pp) REVERT: B 81 CYS cc_start: 0.8111 (t) cc_final: 0.7833 (t) REVERT: B 169 MET cc_start: 0.9246 (mmm) cc_final: 0.8789 (ttm) REVERT: B 170 LYS cc_start: 0.9082 (tptp) cc_final: 0.8663 (tptm) REVERT: B 222 LYS cc_start: 0.9422 (ttpt) cc_final: 0.8859 (ttmm) REVERT: B 237 ASP cc_start: 0.7606 (p0) cc_final: 0.6386 (p0) REVERT: B 288 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8175 (mt-10) REVERT: B 305 LEU cc_start: 0.8900 (mt) cc_final: 0.8518 (mt) REVERT: B 330 TYR cc_start: 0.8665 (m-80) cc_final: 0.8434 (m-80) REVERT: C 39 LYS cc_start: 0.9382 (mmtt) cc_final: 0.9034 (tptt) REVERT: C 86 PHE cc_start: 0.9423 (m-80) cc_final: 0.9152 (m-10) REVERT: C 88 MET cc_start: 0.8848 (ttt) cc_final: 0.7940 (tmm) REVERT: C 152 GLN cc_start: 0.9022 (tt0) cc_final: 0.8422 (tt0) REVERT: C 170 LYS cc_start: 0.9255 (tptp) cc_final: 0.8905 (tptm) REVERT: C 207 LYS cc_start: 0.9221 (mmmm) cc_final: 0.8982 (mmmm) REVERT: C 288 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8281 (mt-10) REVERT: C 293 THR cc_start: 0.9583 (p) cc_final: 0.9303 (t) REVERT: C 296 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8928 (tt) REVERT: C 313 GLN cc_start: 0.8627 (mt0) cc_final: 0.8357 (mt0) REVERT: D 44 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.9015 (t) REVERT: D 47 LYS cc_start: 0.8838 (mmmt) cc_final: 0.8026 (mptt) REVERT: D 77 MET cc_start: 0.8713 (tpp) cc_final: 0.8484 (tmm) REVERT: D 86 PHE cc_start: 0.8867 (m-80) cc_final: 0.8201 (m-10) REVERT: D 128 GLN cc_start: 0.8894 (tt0) cc_final: 0.8598 (tm-30) REVERT: D 137 MET cc_start: 0.8052 (ptm) cc_final: 0.7747 (ttm) REVERT: D 183 PHE cc_start: 0.9047 (m-80) cc_final: 0.8531 (m-10) REVERT: D 185 LYS cc_start: 0.8878 (ttpp) cc_final: 0.8432 (tptt) REVERT: D 202 VAL cc_start: 0.9289 (OUTLIER) cc_final: 0.9025 (p) REVERT: D 211 ILE cc_start: 0.9364 (mp) cc_final: 0.8226 (mp) REVERT: D 217 MET cc_start: 0.8508 (mtm) cc_final: 0.7897 (mtm) REVERT: D 218 GLN cc_start: 0.9256 (mm-40) cc_final: 0.8888 (mm-40) REVERT: D 235 GLN cc_start: 0.8903 (mt0) cc_final: 0.8522 (pm20) REVERT: D 247 ASN cc_start: 0.8043 (p0) cc_final: 0.7426 (p0) REVERT: D 299 GLN cc_start: 0.9506 (tt0) cc_final: 0.8653 (tm-30) REVERT: E 39 PHE cc_start: 0.9068 (t80) cc_final: 0.8635 (t80) REVERT: E 89 GLU cc_start: 0.9114 (tp30) cc_final: 0.8674 (tm-30) REVERT: E 105 LEU cc_start: 0.9258 (tp) cc_final: 0.9009 (tp) REVERT: E 109 MET cc_start: 0.8132 (tpp) cc_final: 0.7459 (tpp) REVERT: E 113 MET cc_start: 0.9178 (mmt) cc_final: 0.8691 (mmp) REVERT: E 128 ILE cc_start: 0.9630 (tp) cc_final: 0.9357 (tp) REVERT: E 182 MET cc_start: 0.9287 (mmm) cc_final: 0.8737 (mmm) REVERT: E 234 MET cc_start: 0.9158 (mmm) cc_final: 0.8899 (mmm) REVERT: E 369 LEU cc_start: 0.9411 (tp) cc_final: 0.9174 (tp) REVERT: E 430 MET cc_start: 0.9071 (ttp) cc_final: 0.8854 (ttp) REVERT: E 584 PHE cc_start: 0.8609 (m-10) cc_final: 0.8284 (m-80) REVERT: E 711 MET cc_start: 0.8979 (mmm) cc_final: 0.8529 (mpp) REVERT: E 1021 LEU cc_start: 0.9608 (mm) cc_final: 0.9325 (pp) REVERT: E 1140 LEU cc_start: 0.9473 (mt) cc_final: 0.9233 (mt) REVERT: E 1276 LEU cc_start: 0.7901 (mp) cc_final: 0.7248 (tt) REVERT: E 1298 MET cc_start: 0.8958 (ttt) cc_final: 0.8436 (tmm) REVERT: E 1305 MET cc_start: 0.9371 (tpp) cc_final: 0.9140 (tpp) outliers start: 84 outliers final: 36 residues processed: 509 average time/residue: 0.1289 time to fit residues: 105.3438 Evaluate side-chains 412 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 372 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 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 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 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 296 ILE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 125 ILE 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 38 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 359 LEU Chi-restraints excluded: chain E residue 497 LEU 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: [98, 21, 161, 195, 151, 3, 221, 237, 32, 60, 58] chunk 98 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 161 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 HIS A 97 HIS ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS B 128 GLN B 175 HIS ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN D 46 HIS D 97 HIS D 160 ASN D 175 HIS E 72 HIS ** E 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.054463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.044908 restraints weight = 112462.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.046356 restraints weight = 59070.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.047339 restraints weight = 38196.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.048036 restraints weight = 28019.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.048485 restraints weight = 22282.933| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 21446 Z= 0.322 Angle : 0.820 9.930 29149 Z= 0.430 Chirality : 0.048 0.209 3454 Planarity : 0.005 0.066 3624 Dihedral : 6.987 155.027 2884 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.60 % Favored : 95.36 % Rotamer: Outliers : 5.01 % Allowed : 21.77 % Favored : 73.22 % 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: 0.13 (0.14), residues: 1334 sheet: -0.73 (0.29), residues: 307 loop : -1.67 (0.18), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 192 TYR 0.027 0.002 TYR D 268 PHE 0.032 0.002 PHE C 86 TRP 0.020 0.002 TRP E1247 HIS 0.021 0.002 HIS C 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.32 (21440) covalent geometry : angle 0.81966 / 0.43 (29139) SS BOND : bond 0.00285 / 0.14 ( 5) SS BOND : angle 1.93210 / 1.12 ( 10) hydrogen bonds : bond 0.04932 / 3.28 ( 1092) hydrogen bonds : angle 4.90986 / 3.40 ( 3246) Misc. bond : bond 0.00085 / 0.04 ( 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 449 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 335 time to evaluate : 0.720 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 43 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8124 (t0) REVERT: A 66 LEU cc_start: 0.9386 (mt) cc_final: 0.9179 (mt) REVERT: A 77 MET cc_start: 0.8751 (tpp) cc_final: 0.8050 (tmm) REVERT: A 137 MET cc_start: 0.8764 (ptt) cc_final: 0.8374 (ptp) REVERT: A 155 VAL cc_start: 0.9706 (OUTLIER) cc_final: 0.9480 (p) REVERT: A 170 LYS cc_start: 0.8845 (tptp) cc_final: 0.8438 (tppt) REVERT: A 208 SER cc_start: 0.8832 (p) cc_final: 0.8596 (p) REVERT: A 209 MET cc_start: 0.8378 (mmp) cc_final: 0.7416 (mmp) REVERT: A 211 ILE cc_start: 0.9569 (OUTLIER) cc_final: 0.9189 (mp) REVERT: A 234 HIS cc_start: 0.8238 (t-170) cc_final: 0.7895 (t-90) REVERT: A 292 GLU cc_start: 0.8438 (pt0) cc_final: 0.7722 (pt0) REVERT: A 332 LYS cc_start: 0.9431 (mttt) cc_final: 0.9172 (mttp) REVERT: B 38 LYS cc_start: 0.9506 (mmmm) cc_final: 0.9292 (mmmm) REVERT: B 43 ASN cc_start: 0.8728 (m110) cc_final: 0.7542 (p0) REVERT: B 77 MET cc_start: 0.8760 (tmm) cc_final: 0.7557 (tpt) REVERT: B 169 MET cc_start: 0.9170 (mmm) cc_final: 0.8773 (ttm) REVERT: B 170 LYS cc_start: 0.9166 (tptp) cc_final: 0.8648 (tptp) REVERT: B 175 HIS cc_start: 0.8993 (OUTLIER) cc_final: 0.8646 (p90) REVERT: B 288 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8332 (mt-10) REVERT: B 305 LEU cc_start: 0.9108 (mt) cc_final: 0.8547 (mt) REVERT: B 330 TYR cc_start: 0.8896 (m-80) cc_final: 0.8524 (m-80) REVERT: B 332 LYS cc_start: 0.9556 (mttt) cc_final: 0.9201 (mmtt) REVERT: B 339 VAL cc_start: 0.9263 (OUTLIER) cc_final: 0.8804 (m) REVERT: C 39 LYS cc_start: 0.9374 (mmtt) cc_final: 0.9111 (tptt) REVERT: C 170 LYS cc_start: 0.9118 (tptp) cc_final: 0.8888 (tptm) REVERT: C 209 MET cc_start: 0.8578 (tpp) cc_final: 0.8264 (tpt) REVERT: C 296 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9061 (tt) REVERT: C 332 LYS cc_start: 0.9511 (mtpp) cc_final: 0.9263 (ttpp) REVERT: D 77 MET cc_start: 0.8851 (tpp) cc_final: 0.8517 (tmm) REVERT: D 128 GLN cc_start: 0.9035 (tt0) cc_final: 0.8634 (tm-30) REVERT: D 183 PHE cc_start: 0.9156 (m-80) cc_final: 0.8519 (m-10) REVERT: D 202 VAL cc_start: 0.9396 (OUTLIER) cc_final: 0.9032 (p) REVERT: D 218 GLN cc_start: 0.9197 (mm-40) cc_final: 0.8686 (mm-40) REVERT: D 235 GLN cc_start: 0.9038 (mt0) cc_final: 0.8820 (pm20) REVERT: D 240 MET cc_start: 0.8218 (tmm) cc_final: 0.7806 (tmm) REVERT: D 247 ASN cc_start: 0.8230 (p0) cc_final: 0.7950 (p0) REVERT: D 262 ASP cc_start: 0.8944 (t70) cc_final: 0.8313 (t0) REVERT: D 268 TYR cc_start: 0.8281 (t80) cc_final: 0.7992 (t80) REVERT: D 299 GLN cc_start: 0.9627 (tt0) cc_final: 0.8654 (tm-30) REVERT: D 332 LYS cc_start: 0.9473 (mttt) cc_final: 0.8999 (mmmt) REVERT: E 39 PHE cc_start: 0.9227 (t80) cc_final: 0.8603 (t80) REVERT: E 43 ILE cc_start: 0.9525 (tp) cc_final: 0.9265 (pt) REVERT: E 89 GLU cc_start: 0.9160 (tp30) cc_final: 0.8705 (tm-30) REVERT: E 105 LEU cc_start: 0.9330 (tp) cc_final: 0.9034 (tp) REVERT: E 109 MET cc_start: 0.8454 (tpp) cc_final: 0.8021 (tpp) REVERT: E 113 MET cc_start: 0.9264 (mmt) cc_final: 0.8856 (mmp) REVERT: E 182 MET cc_start: 0.9338 (mmm) cc_final: 0.8863 (mmm) REVERT: E 503 MET cc_start: 0.9224 (tpp) cc_final: 0.8914 (tpp) REVERT: E 584 PHE cc_start: 0.8592 (m-10) cc_final: 0.8219 (m-80) REVERT: E 711 MET cc_start: 0.8800 (mmm) cc_final: 0.8549 (mpp) REVERT: E 1016 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9230 (tt) REVERT: E 1136 ILE cc_start: 0.9525 (OUTLIER) cc_final: 0.9253 (mm) REVERT: E 1140 LEU cc_start: 0.9548 (mt) cc_final: 0.9256 (mt) REVERT: E 1164 PHE cc_start: 0.8522 (t80) cc_final: 0.8261 (t80) REVERT: E 1276 LEU cc_start: 0.7903 (mp) cc_final: 0.7192 (tt) REVERT: E 1289 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9152 (tt) REVERT: E 1295 LEU cc_start: 0.9693 (tp) cc_final: 0.9481 (tt) REVERT: E 1298 MET cc_start: 0.9004 (ttt) cc_final: 0.8510 (tmm) outliers start: 114 outliers final: 67 residues processed: 422 average time/residue: 0.1240 time to fit residues: 84.7033 Evaluate side-chains 382 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 305 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 55 PHE Chi-restraints excluded: chain A residue 59 VAL 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 175 HIS 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 63 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 339 VAL 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 162 ILE 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 296 ILE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 76 THR 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 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 337 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 176 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 770 VAL 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 1080 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1130 ASN Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1161 THR Chi-restraints excluded: chain E residue 1227 LEU 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 1368 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: [236, 133, 167, 148, 251, 245, 8, 49, 207, 190, 125] chunk 236 optimal weight: 0.0030 chunk 133 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 251 optimal weight: 0.6980 chunk 245 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 173 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN D 160 ASN E 846 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.057511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.047834 restraints weight = 108526.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.049384 restraints weight = 56037.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.050483 restraints weight = 35751.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.051175 restraints weight = 25773.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.051699 restraints weight = 20353.172| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21446 Z= 0.129 Angle : 0.702 11.857 29149 Z= 0.347 Chirality : 0.046 0.267 3454 Planarity : 0.004 0.058 3624 Dihedral : 6.198 142.457 2874 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 4.00 % Allowed : 23.22 % Favored : 72.78 % 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: -0.42 (0.16), residues: 2650 helix: 0.58 (0.14), residues: 1338 sheet: -0.48 (0.30), residues: 299 loop : -1.29 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1251 TYR 0.017 0.001 TYR D 268 PHE 0.027 0.001 PHE E 364 TRP 0.017 0.001 TRP E1247 HIS 0.016 0.001 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (21440) covalent geometry : angle 0.70186 / 0.35 (29139) SS BOND : bond 0.00091 / 0.04 ( 5) SS BOND : angle 1.18479 / 0.63 ( 10) hydrogen bonds : bond 0.04480 / 3.01 ( 1092) hydrogen bonds : angle 4.43614 / 3.08 ( 3246) Misc. bond : bond 0.00060 / 0.03 ( 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 465 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 374 time to evaluate : 0.831 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: A 43 ASN cc_start: 0.8891 (m-40) cc_final: 0.8099 (t0) REVERT: A 66 LEU cc_start: 0.9387 (mt) cc_final: 0.9124 (mp) REVERT: A 77 MET cc_start: 0.8818 (tpp) cc_final: 0.7842 (tmm) REVERT: A 137 MET cc_start: 0.8442 (ptt) cc_final: 0.8192 (ptp) REVERT: A 170 LYS cc_start: 0.8791 (tptp) cc_final: 0.8469 (tppt) REVERT: A 173 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8605 (pt0) REVERT: A 208 SER cc_start: 0.8985 (p) cc_final: 0.8744 (p) REVERT: A 209 MET cc_start: 0.8165 (mmp) cc_final: 0.7307 (mmp) REVERT: A 234 HIS cc_start: 0.8161 (t-170) cc_final: 0.7779 (t-90) REVERT: A 279 GLN cc_start: 0.8868 (tp40) cc_final: 0.8334 (tm-30) REVERT: A 292 GLU cc_start: 0.8503 (pt0) cc_final: 0.7876 (pt0) REVERT: A 332 LYS cc_start: 0.9394 (mttt) cc_final: 0.9080 (mttp) REVERT: B 43 ASN cc_start: 0.8730 (m110) cc_final: 0.7506 (p0) REVERT: B 63 LEU cc_start: 0.9657 (tt) cc_final: 0.9347 (pp) REVERT: B 77 MET cc_start: 0.8461 (tmm) cc_final: 0.8166 (tpt) REVERT: B 81 CYS cc_start: 0.8761 (m) cc_final: 0.8307 (m) REVERT: B 88 MET cc_start: 0.9027 (ttm) cc_final: 0.8825 (ttm) REVERT: B 129 VAL cc_start: 0.9266 (OUTLIER) cc_final: 0.9035 (t) REVERT: B 169 MET cc_start: 0.9065 (mmm) cc_final: 0.8642 (ttm) REVERT: B 170 LYS cc_start: 0.9082 (tptp) cc_final: 0.8557 (tptm) REVERT: B 175 HIS cc_start: 0.8942 (OUTLIER) cc_final: 0.8520 (p90) REVERT: B 305 LEU cc_start: 0.9073 (mt) cc_final: 0.8639 (mt) REVERT: B 330 TYR cc_start: 0.8736 (m-80) cc_final: 0.8339 (m-80) REVERT: B 332 LYS cc_start: 0.9520 (mttt) cc_final: 0.9092 (mmtt) REVERT: C 39 LYS cc_start: 0.9402 (mmtt) cc_final: 0.9180 (mmmt) REVERT: C 209 MET cc_start: 0.8602 (tpp) cc_final: 0.8294 (tpt) REVERT: C 296 ILE cc_start: 0.9186 (mt) cc_final: 0.8835 (tt) REVERT: C 332 LYS cc_start: 0.9495 (mtpp) cc_final: 0.9220 (ttpp) REVERT: D 77 MET cc_start: 0.8850 (tpp) cc_final: 0.8511 (tmm) REVERT: D 86 PHE cc_start: 0.8990 (m-80) cc_final: 0.8420 (m-10) REVERT: D 183 PHE cc_start: 0.9076 (m-80) cc_final: 0.8443 (m-10) REVERT: D 185 LYS cc_start: 0.9116 (ttpp) cc_final: 0.8721 (tptt) REVERT: D 202 VAL cc_start: 0.9261 (p) cc_final: 0.8855 (p) REVERT: D 209 MET cc_start: 0.6918 (mtm) cc_final: 0.6455 (mmm) REVERT: D 240 MET cc_start: 0.8034 (tmm) cc_final: 0.7458 (tmm) REVERT: D 247 ASN cc_start: 0.8333 (p0) cc_final: 0.7932 (p0) REVERT: D 262 ASP cc_start: 0.8867 (t70) cc_final: 0.8321 (t0) REVERT: D 284 ILE cc_start: 0.9679 (pt) cc_final: 0.9363 (tp) REVERT: D 332 LYS cc_start: 0.9441 (mttt) cc_final: 0.9046 (mmmt) REVERT: E 105 LEU cc_start: 0.9295 (tp) cc_final: 0.9058 (tp) REVERT: E 109 MET cc_start: 0.8394 (tpp) cc_final: 0.7763 (tpp) REVERT: E 113 MET cc_start: 0.9176 (mmt) cc_final: 0.8745 (mmp) REVERT: E 144 TRP cc_start: 0.8925 (m100) cc_final: 0.8513 (m100) REVERT: E 182 MET cc_start: 0.9326 (mmm) cc_final: 0.8915 (mmm) REVERT: E 315 PHE cc_start: 0.8954 (m-10) cc_final: 0.8687 (m-10) REVERT: E 430 MET cc_start: 0.9117 (ttp) cc_final: 0.8899 (ttm) REVERT: E 584 PHE cc_start: 0.8672 (m-10) cc_final: 0.8251 (m-80) REVERT: E 711 MET cc_start: 0.8864 (mmm) cc_final: 0.8568 (mpp) REVERT: E 801 MET cc_start: 0.8934 (ptp) cc_final: 0.8689 (ptp) REVERT: E 886 LEU cc_start: 0.9202 (tp) cc_final: 0.8990 (tp) REVERT: E 1136 ILE cc_start: 0.9557 (OUTLIER) cc_final: 0.9193 (mm) REVERT: E 1140 LEU cc_start: 0.9538 (mt) cc_final: 0.9327 (mt) REVERT: E 1298 MET cc_start: 0.9075 (ttt) cc_final: 0.8540 (tmm) REVERT: E 1301 ASN cc_start: 0.9195 (m-40) cc_final: 0.8768 (m-40) REVERT: E 1305 MET cc_start: 0.9438 (tpp) cc_final: 0.9224 (tpp) REVERT: E 1514 MET cc_start: 0.9001 (mtm) cc_final: 0.8572 (mtm) outliers start: 91 outliers final: 49 residues processed: 440 average time/residue: 0.1286 time to fit residues: 90.8759 Evaluate side-chains 384 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 331 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 63 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 230 VAL Chi-restraints excluded: chain A residue 236 VAL 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 166 SER Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 236 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 115 HIS Chi-restraints excluded: chain D residue 138 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 281 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 48 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 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 1034 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 1136 ILE Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 1368 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: [90, 33, 201, 103, 123, 179, 265, 12, 30, 48, 186] chunk 90 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 HIS ** E 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1427 GLN 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 = 0.054936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.045559 restraints weight = 110126.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.047048 restraints weight = 57140.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.048027 restraints weight = 36408.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.048744 restraints weight = 26520.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.049208 restraints weight = 20918.327| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21446 Z= 0.228 Angle : 0.750 12.866 29149 Z= 0.381 Chirality : 0.047 0.266 3454 Planarity : 0.004 0.053 3624 Dihedral : 5.985 126.776 2869 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.36 % Allowed : 23.39 % Favored : 71.24 % 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: -0.14 (0.16), residues: 2650 helix: 0.80 (0.14), residues: 1338 sheet: -0.54 (0.30), residues: 299 loop : -1.08 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1251 TYR 0.020 0.002 TYR E1064 PHE 0.026 0.002 PHE E1164 TRP 0.048 0.002 TRP E1033 HIS 0.007 0.001 HIS C 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.23 (21440) covalent geometry : angle 0.74931 / 0.38 (29139) SS BOND : bond 0.00257 / 0.13 ( 5) SS BOND : angle 1.61899 / 0.87 ( 10) hydrogen bonds : bond 0.04503 / 3.02 ( 1092) hydrogen bonds : angle 4.57018 / 3.16 ( 3246) Misc. bond : bond 0.00101 / 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 452 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 330 time to evaluate : 0.549 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 43 ASN cc_start: 0.8983 (OUTLIER) cc_final: 0.8109 (t0) REVERT: A 47 LYS cc_start: 0.9423 (mmmt) cc_final: 0.9174 (mmmt) REVERT: A 77 MET cc_start: 0.8750 (tpp) cc_final: 0.7948 (tmm) REVERT: A 137 MET cc_start: 0.8597 (ptt) cc_final: 0.8314 (ptp) REVERT: A 170 LYS cc_start: 0.8758 (tptp) cc_final: 0.8516 (tppt) REVERT: A 209 MET cc_start: 0.8343 (mmp) cc_final: 0.7720 (mmp) REVERT: A 234 HIS cc_start: 0.8393 (t-170) cc_final: 0.8035 (t-90) REVERT: A 279 GLN cc_start: 0.8842 (tp40) cc_final: 0.8359 (tm-30) REVERT: A 313 GLN cc_start: 0.8195 (mt0) cc_final: 0.7954 (mp10) REVERT: A 332 LYS cc_start: 0.9405 (mttt) cc_final: 0.9180 (mttp) REVERT: B 43 ASN cc_start: 0.8668 (m110) cc_final: 0.7358 (p0) REVERT: B 77 MET cc_start: 0.8654 (tmm) cc_final: 0.7973 (tpt) REVERT: B 81 CYS cc_start: 0.8946 (m) cc_final: 0.8424 (m) REVERT: B 88 MET cc_start: 0.9073 (ttm) cc_final: 0.8860 (ttm) REVERT: B 129 VAL cc_start: 0.9300 (OUTLIER) cc_final: 0.9075 (p) REVERT: B 169 MET cc_start: 0.9119 (mmm) cc_final: 0.8641 (ttm) REVERT: B 170 LYS cc_start: 0.9071 (tptp) cc_final: 0.8534 (tptm) REVERT: B 296 ILE cc_start: 0.8727 (mp) cc_final: 0.8362 (pt) REVERT: B 305 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8573 (mt) REVERT: B 330 TYR cc_start: 0.8811 (m-80) cc_final: 0.8325 (m-80) REVERT: B 332 LYS cc_start: 0.9545 (mttt) cc_final: 0.9189 (mmtt) REVERT: C 39 LYS cc_start: 0.9393 (mmtt) cc_final: 0.9186 (mmmt) REVERT: C 296 ILE cc_start: 0.9292 (mt) cc_final: 0.8941 (tt) REVERT: C 332 LYS cc_start: 0.9577 (mtpp) cc_final: 0.9324 (ttpp) REVERT: D 77 MET cc_start: 0.8936 (tpp) cc_final: 0.8483 (tpp) REVERT: D 88 MET cc_start: 0.9064 (tpp) cc_final: 0.8803 (tpt) REVERT: D 183 PHE cc_start: 0.9132 (m-80) cc_final: 0.8500 (m-10) REVERT: D 185 LYS cc_start: 0.9159 (ttpp) cc_final: 0.8791 (tptt) REVERT: D 202 VAL cc_start: 0.9353 (OUTLIER) cc_final: 0.8946 (p) REVERT: D 240 MET cc_start: 0.8067 (tmm) cc_final: 0.7486 (tmm) REVERT: D 247 ASN cc_start: 0.8423 (p0) cc_final: 0.8047 (p0) REVERT: D 268 TYR cc_start: 0.8754 (t80) cc_final: 0.8439 (t80) REVERT: D 284 ILE cc_start: 0.9494 (OUTLIER) cc_final: 0.9157 (tp) REVERT: D 332 LYS cc_start: 0.9512 (mttt) cc_final: 0.9195 (mmmt) REVERT: E 39 PHE cc_start: 0.9281 (t80) cc_final: 0.8804 (t80) REVERT: E 43 ILE cc_start: 0.9566 (tp) cc_final: 0.9281 (pt) REVERT: E 105 LEU cc_start: 0.9359 (tp) cc_final: 0.9034 (tp) REVERT: E 109 MET cc_start: 0.8523 (tpp) cc_final: 0.7892 (tpp) REVERT: E 113 MET cc_start: 0.9222 (mmt) cc_final: 0.8761 (mmp) REVERT: E 128 ILE cc_start: 0.9692 (tp) cc_final: 0.9462 (tp) REVERT: E 144 TRP cc_start: 0.9063 (m100) cc_final: 0.8359 (m100) REVERT: E 182 MET cc_start: 0.9410 (mmm) cc_final: 0.8931 (mmm) REVERT: E 234 MET cc_start: 0.9354 (mmm) cc_final: 0.9065 (mmm) REVERT: E 430 MET cc_start: 0.9182 (ttp) cc_final: 0.8924 (ttm) REVERT: E 584 PHE cc_start: 0.8744 (m-10) cc_final: 0.8318 (m-80) REVERT: E 801 MET cc_start: 0.8987 (ptp) cc_final: 0.8739 (ptp) REVERT: E 1136 ILE cc_start: 0.9548 (OUTLIER) cc_final: 0.9224 (mp) REVERT: E 1289 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9107 (tt) REVERT: E 1298 MET cc_start: 0.9150 (ttt) cc_final: 0.8556 (tmm) REVERT: E 1444 ARG cc_start: 0.7798 (mmp80) cc_final: 0.7286 (mmp80) outliers start: 122 outliers final: 75 residues processed: 418 average time/residue: 0.1238 time to fit residues: 82.8864 Evaluate side-chains 400 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 318 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 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 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 55 PHE 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 166 SER Chi-restraints excluded: chain B residue 186 HIS 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 236 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 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 284 ILE 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 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 219 LEU Chi-restraints excluded: chain E residue 224 ASN 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 884 VAL 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 1136 ILE Chi-restraints excluded: chain E residue 1154 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 1289 LEU Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 1368 LEU 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: [9, 90, 153, 124, 99, 218, 191, 55, 249, 27, 151] chunk 9 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 218 optimal weight: 0.7980 chunk 191 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 249 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS C 277 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.057119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.047533 restraints weight = 108463.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.049084 restraints weight = 56482.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.050119 restraints weight = 36041.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.050871 restraints weight = 26214.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.051377 restraints weight = 20622.950| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21446 Z= 0.130 Angle : 0.721 13.337 29149 Z= 0.351 Chirality : 0.047 0.307 3454 Planarity : 0.004 0.053 3624 Dihedral : 5.853 130.814 2868 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 4.22 % Allowed : 25.37 % 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: 0.10 (0.16), residues: 2650 helix: 1.00 (0.14), residues: 1338 sheet: -0.39 (0.29), residues: 303 loop : -0.99 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 177 TYR 0.012 0.001 TYR E 379 PHE 0.026 0.001 PHE E1164 TRP 0.045 0.001 TRP E 52 HIS 0.007 0.001 HIS D 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (21440) covalent geometry : angle 0.72088 / 0.35 (29139) SS BOND : bond 0.00356 / 0.18 ( 5) SS BOND : angle 1.15155 / 0.61 ( 10) hydrogen bonds : bond 0.04352 / 2.92 ( 1092) hydrogen bonds : angle 4.36081 / 3.03 ( 3246) Misc. bond : bond 0.00066 / 0.03 ( 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 458 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 362 time to evaluate : 0.782 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 43 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8166 (t0) REVERT: A 56 LEU cc_start: 0.9218 (mm) cc_final: 0.8837 (pp) REVERT: A 77 MET cc_start: 0.8750 (tpp) cc_final: 0.7936 (tmm) REVERT: A 170 LYS cc_start: 0.8781 (tptp) cc_final: 0.8377 (tppt) REVERT: A 209 MET cc_start: 0.8315 (mmp) cc_final: 0.7727 (mmp) REVERT: A 234 HIS cc_start: 0.8356 (t-170) cc_final: 0.7991 (t-90) REVERT: A 262 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8368 (m-30) REVERT: A 279 GLN cc_start: 0.8789 (tp40) cc_final: 0.8358 (tm-30) REVERT: A 288 GLU cc_start: 0.8005 (tt0) cc_final: 0.7799 (mm-30) REVERT: A 332 LYS cc_start: 0.9431 (mttt) cc_final: 0.9176 (mttm) REVERT: B 43 ASN cc_start: 0.8674 (m110) cc_final: 0.7350 (p0) REVERT: B 63 LEU cc_start: 0.9691 (tp) cc_final: 0.9393 (pp) REVERT: B 129 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8945 (p) REVERT: B 169 MET cc_start: 0.9054 (mmm) cc_final: 0.8607 (ttm) REVERT: B 170 LYS cc_start: 0.9049 (tptp) cc_final: 0.8490 (tptm) REVERT: B 181 LEU cc_start: 0.9525 (mm) cc_final: 0.9220 (mm) REVERT: B 185 LYS cc_start: 0.9165 (pptt) cc_final: 0.8637 (ttpp) REVERT: B 212 SER cc_start: 0.8816 (p) cc_final: 0.8163 (p) REVERT: B 296 ILE cc_start: 0.8846 (mp) cc_final: 0.8604 (pt) REVERT: B 305 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8546 (mt) REVERT: B 330 TYR cc_start: 0.8729 (m-80) cc_final: 0.8426 (m-80) REVERT: B 332 LYS cc_start: 0.9525 (mttt) cc_final: 0.9129 (mmtt) REVERT: C 39 LYS cc_start: 0.9389 (mmtt) cc_final: 0.8998 (mmmt) REVERT: C 47 LYS cc_start: 0.8883 (tppt) cc_final: 0.8314 (tptp) REVERT: C 163 MET cc_start: 0.9198 (mmm) cc_final: 0.8465 (mmm) REVERT: C 268 TYR cc_start: 0.9183 (t80) cc_final: 0.8640 (t80) REVERT: C 296 ILE cc_start: 0.9275 (mt) cc_final: 0.8896 (tt) REVERT: C 332 LYS cc_start: 0.9542 (mtpp) cc_final: 0.9339 (ttpp) REVERT: D 77 MET cc_start: 0.8854 (tpp) cc_final: 0.8393 (tpp) REVERT: D 185 LYS cc_start: 0.9097 (ttpp) cc_final: 0.8822 (tptt) REVERT: D 202 VAL cc_start: 0.9284 (OUTLIER) cc_final: 0.9013 (p) REVERT: D 240 MET cc_start: 0.8171 (tmm) cc_final: 0.7645 (tmm) REVERT: D 247 ASN cc_start: 0.8371 (p0) cc_final: 0.8105 (p0) REVERT: D 250 PHE cc_start: 0.9117 (t80) cc_final: 0.8461 (t80) REVERT: D 332 LYS cc_start: 0.9479 (mttt) cc_final: 0.9109 (mmmt) REVERT: E 39 PHE cc_start: 0.9209 (t80) cc_final: 0.8777 (t80) REVERT: E 43 ILE cc_start: 0.9539 (tp) cc_final: 0.9169 (pt) REVERT: E 105 LEU cc_start: 0.9284 (tp) cc_final: 0.9074 (tp) REVERT: E 109 MET cc_start: 0.8433 (tpp) cc_final: 0.7733 (tpp) REVERT: E 113 MET cc_start: 0.9194 (mmt) cc_final: 0.8747 (mmp) REVERT: E 144 TRP cc_start: 0.8981 (m100) cc_final: 0.8478 (m100) REVERT: E 182 MET cc_start: 0.9354 (mmm) cc_final: 0.8826 (mmm) REVERT: E 352 PHE cc_start: 0.9405 (t80) cc_final: 0.9147 (t80) REVERT: E 369 LEU cc_start: 0.9392 (tp) cc_final: 0.9085 (tp) REVERT: E 373 PHE cc_start: 0.9246 (m-80) cc_final: 0.8802 (m-10) REVERT: E 430 MET cc_start: 0.9133 (ttp) cc_final: 0.8878 (ttm) REVERT: E 584 PHE cc_start: 0.8696 (m-10) cc_final: 0.8320 (m-80) REVERT: E 711 MET cc_start: 0.8802 (mmm) cc_final: 0.8593 (mpp) REVERT: E 720 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.8814 (mtpp) REVERT: E 1066 MET cc_start: 0.8461 (mmm) cc_final: 0.8244 (mmp) REVERT: E 1110 MET cc_start: 0.8505 (mmm) cc_final: 0.8228 (mmt) REVERT: E 1289 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9099 (tt) REVERT: E 1298 MET cc_start: 0.9136 (ttt) cc_final: 0.8289 (tmm) REVERT: E 1301 ASN cc_start: 0.9141 (m-40) cc_final: 0.8734 (m-40) REVERT: E 1305 MET cc_start: 0.9335 (tpp) cc_final: 0.9085 (tpp) REVERT: E 1313 LYS cc_start: 0.9059 (tppt) cc_final: 0.8832 (tppt) REVERT: E 1444 ARG cc_start: 0.7424 (mmp80) cc_final: 0.7028 (mmp80) outliers start: 96 outliers final: 59 residues processed: 430 average time/residue: 0.1284 time to fit residues: 88.5962 Evaluate side-chains 400 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 334 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 54 ARG Chi-restraints excluded: chain A residue 55 PHE 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 296 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 55 PHE 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 219 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 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 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 138 VAL 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 328 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 222 PHE 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 720 LYS Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL 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 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 1289 LEU Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 1368 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: [233, 124, 157, 17, 6, 187, 253, 248, 109, 144, 36] chunk 233 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 187 optimal weight: 8.9990 chunk 253 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS C 235 GLN D 160 ASN D 175 HIS ** E 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1234 ASN ** E1373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.054893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.045614 restraints weight = 110619.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.047107 restraints weight = 57420.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.048128 restraints weight = 36506.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.048816 restraints weight = 26369.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.049330 restraints weight = 20762.417| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 21446 Z= 0.215 Angle : 0.752 12.099 29149 Z= 0.378 Chirality : 0.047 0.243 3454 Planarity : 0.004 0.051 3624 Dihedral : 5.860 124.159 2868 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.35 % Allowed : 25.55 % Favored : 70.10 % 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: 0.19 (0.16), residues: 2650 helix: 1.07 (0.14), residues: 1333 sheet: -0.57 (0.29), residues: 295 loop : -0.83 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 249 TYR 0.022 0.002 TYR D 268 PHE 0.027 0.002 PHE E1164 TRP 0.039 0.002 TRP E 52 HIS 0.012 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.22 (21440) covalent geometry : angle 0.75116 / 0.38 (29139) SS BOND : bond 0.00213 / 0.11 ( 5) SS BOND : angle 1.46714 / 0.80 ( 10) hydrogen bonds : bond 0.04422 / 2.96 ( 1092) hydrogen bonds : angle 4.55774 / 3.17 ( 3246) Misc. bond : bond 0.00091 / 0.05 ( 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 426 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 327 time to evaluate : 0.772 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: 0.8814 (tpp) cc_final: 0.8041 (tmm) REVERT: A 170 LYS cc_start: 0.8807 (tptp) cc_final: 0.8395 (tppt) REVERT: A 209 MET cc_start: 0.8292 (mmp) cc_final: 0.7738 (mmp) REVERT: A 262 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8575 (m-30) REVERT: A 279 GLN cc_start: 0.8809 (tp40) cc_final: 0.8350 (tm-30) REVERT: A 288 GLU cc_start: 0.8109 (tt0) cc_final: 0.7866 (mm-30) REVERT: A 332 LYS cc_start: 0.9423 (mttt) cc_final: 0.9180 (mttp) REVERT: B 43 ASN cc_start: 0.8672 (m110) cc_final: 0.7365 (p0) REVERT: B 77 MET cc_start: 0.8899 (tpt) cc_final: 0.8665 (tpt) REVERT: B 129 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.9009 (p) REVERT: B 169 MET cc_start: 0.9021 (mmm) cc_final: 0.8602 (ttm) REVERT: B 170 LYS cc_start: 0.9084 (tptp) cc_final: 0.8854 (tptm) REVERT: B 181 LEU cc_start: 0.9558 (mm) cc_final: 0.9272 (mm) REVERT: B 185 LYS cc_start: 0.9326 (pptt) cc_final: 0.9074 (tptt) REVERT: B 296 ILE cc_start: 0.8808 (mp) cc_final: 0.8535 (pt) REVERT: B 305 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8595 (mt) REVERT: B 330 TYR cc_start: 0.8776 (m-80) cc_final: 0.8414 (m-80) REVERT: B 332 LYS cc_start: 0.9531 (mttt) cc_final: 0.9167 (mmtt) REVERT: C 39 LYS cc_start: 0.9380 (mmtt) cc_final: 0.9177 (mmmt) REVERT: C 47 LYS cc_start: 0.8922 (tppt) cc_final: 0.8523 (tppt) REVERT: C 185 LYS cc_start: 0.9494 (tppp) cc_final: 0.9088 (tppp) REVERT: C 268 TYR cc_start: 0.9209 (t80) cc_final: 0.8654 (t80) REVERT: C 296 ILE cc_start: 0.9374 (mt) cc_final: 0.8981 (tt) REVERT: D 77 MET cc_start: 0.8959 (tpp) cc_final: 0.8411 (tpp) REVERT: D 137 MET cc_start: 0.8541 (ttp) cc_final: 0.8225 (ttm) REVERT: D 185 LYS cc_start: 0.9137 (ttpp) cc_final: 0.8820 (tptt) REVERT: D 240 MET cc_start: 0.8098 (tmm) cc_final: 0.7645 (tmm) REVERT: D 247 ASN cc_start: 0.8568 (p0) cc_final: 0.8358 (p0) REVERT: D 250 PHE cc_start: 0.9174 (t80) cc_final: 0.8560 (t80) REVERT: D 332 LYS cc_start: 0.9523 (mttt) cc_final: 0.9197 (mmmt) REVERT: E 43 ILE cc_start: 0.9548 (tp) cc_final: 0.9233 (pt) REVERT: E 105 LEU cc_start: 0.9360 (tp) cc_final: 0.9023 (tp) REVERT: E 109 MET cc_start: 0.8586 (tpp) cc_final: 0.7907 (tpp) REVERT: E 113 MET cc_start: 0.9220 (mmt) cc_final: 0.8729 (mmp) REVERT: E 144 TRP cc_start: 0.9092 (m100) cc_final: 0.8390 (m100) REVERT: E 182 MET cc_start: 0.9362 (mmm) cc_final: 0.8868 (mmm) REVERT: E 183 LEU cc_start: 0.9607 (mm) cc_final: 0.8007 (mm) REVERT: E 234 MET cc_start: 0.9343 (mmm) cc_final: 0.9113 (mmm) REVERT: E 368 LEU cc_start: 0.9488 (tp) cc_final: 0.9269 (tp) REVERT: E 413 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8143 (ptm) REVERT: E 430 MET cc_start: 0.9174 (ttp) cc_final: 0.8954 (ttm) REVERT: E 584 PHE cc_start: 0.8718 (m-10) cc_final: 0.8274 (m-80) REVERT: E 586 ILE cc_start: 0.9505 (pt) cc_final: 0.9297 (pt) REVERT: E 798 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8832 (ttt-90) REVERT: E 1066 MET cc_start: 0.8557 (mmm) cc_final: 0.8344 (mmp) REVERT: E 1298 MET cc_start: 0.9157 (ttt) cc_final: 0.8299 (tmm) REVERT: E 1313 LYS cc_start: 0.9049 (tppt) cc_final: 0.8829 (tppt) REVERT: E 1444 ARG cc_start: 0.7460 (mmp80) cc_final: 0.7184 (mmp80) outliers start: 99 outliers final: 75 residues processed: 401 average time/residue: 0.1297 time to fit residues: 83.6979 Evaluate side-chains 394 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 314 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 155 VAL 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 B residue 55 PHE 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 219 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 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 220 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 294 THR 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 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 175 HIS 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 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 256 ILE 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 38 VAL 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 222 PHE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 413 MET 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 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 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 1368 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: [34, 192, 189, 149, 4, 83, 53, 81, 145, 210, 99] chunk 34 optimal weight: 0.7980 chunk 192 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 210 optimal weight: 0.0040 chunk 99 optimal weight: 2.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN E 836 GLN E 867 HIS ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 933 ASN ** 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 = 0.3132 r_free = 0.3132 target = 0.056711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.047167 restraints weight = 109163.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.048704 restraints weight = 57270.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.049746 restraints weight = 36566.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.050461 restraints weight = 26583.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.050931 restraints weight = 20998.941| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21446 Z= 0.137 Angle : 0.730 14.156 29149 Z= 0.356 Chirality : 0.047 0.237 3454 Planarity : 0.004 0.052 3624 Dihedral : 5.771 128.805 2868 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 3.91 % Allowed : 26.56 % Favored : 69.53 % 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: 0.31 (0.16), residues: 2650 helix: 1.17 (0.14), residues: 1333 sheet: -0.49 (0.30), residues: 295 loop : -0.80 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1251 TYR 0.019 0.001 TYR E1004 PHE 0.024 0.001 PHE E1164 TRP 0.038 0.001 TRP E 52 HIS 0.012 0.001 HIS C 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (21440) covalent geometry : angle 0.72988 / 0.36 (29139) SS BOND : bond 0.00141 / 0.07 ( 5) SS BOND : angle 1.11389 / 0.59 ( 10) hydrogen bonds : bond 0.04324 / 2.90 ( 1092) hydrogen bonds : angle 4.39237 / 3.07 ( 3246) Misc. bond : bond 0.00059 / 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 425 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 336 time to evaluate : 0.729 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: 0.9444 (mmmt) cc_final: 0.9039 (mmmt) REVERT: A 77 MET cc_start: 0.8585 (tpp) cc_final: 0.7864 (tmm) REVERT: A 160 ASN cc_start: 0.9239 (m-40) cc_final: 0.8991 (m-40) REVERT: A 170 LYS cc_start: 0.8748 (tptp) cc_final: 0.8400 (tppt) REVERT: A 209 MET cc_start: 0.8217 (mmp) cc_final: 0.7676 (mmp) REVERT: A 262 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8434 (m-30) REVERT: A 279 GLN cc_start: 0.8728 (tp40) cc_final: 0.8339 (tm-30) REVERT: A 288 GLU cc_start: 0.8042 (tt0) cc_final: 0.7808 (mm-30) REVERT: A 332 LYS cc_start: 0.9420 (mttt) cc_final: 0.9174 (mttp) REVERT: B 43 ASN cc_start: 0.8665 (m110) cc_final: 0.7370 (p0) REVERT: B 63 LEU cc_start: 0.9696 (tt) cc_final: 0.9427 (pp) REVERT: B 77 MET cc_start: 0.8865 (tpt) cc_final: 0.8273 (tmm) REVERT: B 129 VAL cc_start: 0.9085 (OUTLIER) cc_final: 0.8840 (p) REVERT: B 169 MET cc_start: 0.8929 (mmm) cc_final: 0.8557 (ttm) REVERT: B 170 LYS cc_start: 0.9075 (tptp) cc_final: 0.8523 (tptm) REVERT: B 181 LEU cc_start: 0.9500 (mm) cc_final: 0.9200 (mm) REVERT: B 185 LYS cc_start: 0.9239 (pptt) cc_final: 0.9010 (tptt) REVERT: B 296 ILE cc_start: 0.8802 (mp) cc_final: 0.8523 (pt) REVERT: B 305 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8659 (mt) REVERT: B 330 TYR cc_start: 0.8723 (m-80) cc_final: 0.8424 (m-80) REVERT: B 332 LYS cc_start: 0.9540 (mttt) cc_final: 0.9160 (mmtt) REVERT: C 39 LYS cc_start: 0.9364 (mmtt) cc_final: 0.9010 (mmmt) REVERT: C 47 LYS cc_start: 0.8902 (tppt) cc_final: 0.8528 (tppt) REVERT: C 268 TYR cc_start: 0.9158 (t80) cc_final: 0.8642 (t80) REVERT: C 296 ILE cc_start: 0.9332 (mt) cc_final: 0.8946 (tt) REVERT: D 77 MET cc_start: 0.8895 (tpp) cc_final: 0.8541 (tpp) REVERT: D 185 LYS cc_start: 0.9082 (ttpp) cc_final: 0.8879 (tptt) REVERT: D 240 MET cc_start: 0.8163 (tmm) cc_final: 0.7643 (tmm) REVERT: D 250 PHE cc_start: 0.9032 (t80) cc_final: 0.8506 (t80) REVERT: D 268 TYR cc_start: 0.8342 (t80) cc_final: 0.7926 (t80) REVERT: D 332 LYS cc_start: 0.9505 (mttt) cc_final: 0.9176 (mmmt) REVERT: E 43 ILE cc_start: 0.9551 (tp) cc_final: 0.9276 (pt) REVERT: E 105 LEU cc_start: 0.9324 (tp) cc_final: 0.9105 (tp) REVERT: E 109 MET cc_start: 0.8527 (tpp) cc_final: 0.7776 (tpp) REVERT: E 113 MET cc_start: 0.9194 (mmt) cc_final: 0.8692 (mmp) REVERT: E 144 TRP cc_start: 0.8950 (m100) cc_final: 0.8421 (m100) REVERT: E 182 MET cc_start: 0.9343 (mmm) cc_final: 0.8834 (mmm) REVERT: E 183 LEU cc_start: 0.9582 (mm) cc_final: 0.8019 (mm) REVERT: E 234 MET cc_start: 0.9279 (mmm) cc_final: 0.8975 (mmm) REVERT: E 369 LEU cc_start: 0.9360 (tp) cc_final: 0.8966 (tp) REVERT: E 373 PHE cc_start: 0.9242 (m-80) cc_final: 0.8801 (m-10) REVERT: E 413 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8101 (ptm) REVERT: E 430 MET cc_start: 0.9107 (ttp) cc_final: 0.8860 (ttm) REVERT: E 453 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9404 (mm) REVERT: E 584 PHE cc_start: 0.8610 (m-10) cc_final: 0.8329 (m-80) REVERT: E 586 ILE cc_start: 0.9494 (pt) cc_final: 0.9273 (pt) REVERT: E 711 MET cc_start: 0.8816 (mmm) cc_final: 0.8529 (mpp) REVERT: E 798 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8117 (ttt180) REVERT: E 1066 MET cc_start: 0.8412 (mmm) cc_final: 0.8190 (mmp) REVERT: E 1088 TRP cc_start: 0.7905 (OUTLIER) cc_final: 0.7625 (t-100) REVERT: E 1110 MET cc_start: 0.8644 (mmm) cc_final: 0.8341 (mmt) REVERT: E 1228 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9073 (mp) REVERT: E 1261 LEU cc_start: 0.9630 (tp) cc_final: 0.9182 (mt) REVERT: E 1298 MET cc_start: 0.9132 (ttt) cc_final: 0.8263 (tmm) REVERT: E 1313 LYS cc_start: 0.9017 (tppt) cc_final: 0.8764 (tppt) REVERT: E 1444 ARG cc_start: 0.7397 (mmp80) cc_final: 0.7053 (mmp80) outliers start: 89 outliers final: 66 residues processed: 399 average time/residue: 0.1281 time to fit residues: 82.2210 Evaluate side-chains 403 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 329 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 55 PHE 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 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 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 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 175 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 294 THR 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 115 HIS Chi-restraints excluded: chain D residue 138 VAL 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 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 343 LEU Chi-restraints excluded: chain E residue 138 ILE 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 413 MET Chi-restraints excluded: chain E residue 453 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 798 ARG Chi-restraints excluded: chain E residue 884 VAL 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 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 1227 LEU 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 Chi-restraints excluded: chain E residue 1368 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: [106, 35, 264, 21, 55, 143, 261, 240, 12, 4, 76] chunk 106 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 55 optimal weight: 0.0030 chunk 143 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN D 175 HIS E 127 ASN ** E 933 ASN ** 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 = 0.3128 r_free = 0.3128 target = 0.056582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.047049 restraints weight = 109687.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.048571 restraints weight = 57556.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.049596 restraints weight = 36833.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.050323 restraints weight = 26854.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.050834 restraints weight = 21222.065| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21446 Z= 0.152 Angle : 0.736 13.517 29149 Z= 0.358 Chirality : 0.047 0.273 3454 Planarity : 0.004 0.051 3624 Dihedral : 5.676 126.316 2868 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.30 % Favored : 95.66 % Rotamer: Outliers : 3.61 % Allowed : 26.96 % Favored : 69.44 % 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: 0.38 (0.16), residues: 2650 helix: 1.21 (0.14), residues: 1327 sheet: -0.56 (0.31), residues: 283 loop : -0.68 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1251 TYR 0.019 0.001 TYR E1004 PHE 0.022 0.001 PHE C 86 TRP 0.039 0.001 TRP E 52 HIS 0.009 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (21440) covalent geometry : angle 0.73530 / 0.36 (29139) SS BOND : bond 0.00197 / 0.10 ( 5) SS BOND : angle 1.24542 / 0.65 ( 10) hydrogen bonds : bond 0.04288 / 2.88 ( 1092) hydrogen bonds : angle 4.38547 / 3.06 ( 3246) Misc. bond : bond 0.00071 / 0.04 ( 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 424 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 342 time to evaluate : 0.745 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 47 LYS cc_start: 0.9448 (mmmt) cc_final: 0.9085 (mmmt) REVERT: A 77 MET cc_start: 0.8624 (tpp) cc_final: 0.7908 (tmm) REVERT: A 170 LYS cc_start: 0.8676 (tptp) cc_final: 0.8387 (tppt) REVERT: A 209 MET cc_start: 0.8225 (mmp) cc_final: 0.7681 (mmp) REVERT: A 262 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8469 (m-30) REVERT: A 279 GLN cc_start: 0.8744 (tp40) cc_final: 0.8384 (tm-30) REVERT: A 288 GLU cc_start: 0.8068 (tt0) cc_final: 0.7813 (mm-30) REVERT: A 332 LYS cc_start: 0.9442 (mttt) cc_final: 0.9201 (mttp) REVERT: B 43 ASN cc_start: 0.8670 (m110) cc_final: 0.7373 (p0) REVERT: B 63 LEU cc_start: 0.9677 (tt) cc_final: 0.9418 (pp) REVERT: B 77 MET cc_start: 0.8844 (tpt) cc_final: 0.8256 (tmm) REVERT: B 129 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8866 (p) REVERT: B 169 MET cc_start: 0.8970 (mmm) cc_final: 0.8577 (ttm) REVERT: B 170 LYS cc_start: 0.9085 (tptp) cc_final: 0.8534 (tptm) REVERT: B 296 ILE cc_start: 0.8780 (mp) cc_final: 0.8449 (pt) REVERT: B 305 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8666 (mt) REVERT: B 330 TYR cc_start: 0.8685 (m-80) cc_final: 0.8422 (m-80) REVERT: B 332 LYS cc_start: 0.9542 (mttt) cc_final: 0.9178 (mmtt) REVERT: C 39 LYS cc_start: 0.9358 (mmtt) cc_final: 0.9011 (mmmt) REVERT: C 47 LYS cc_start: 0.8839 (tppt) cc_final: 0.8416 (tppt) REVERT: C 235 GLN cc_start: 0.8890 (mt0) cc_final: 0.8293 (mt0) REVERT: C 268 TYR cc_start: 0.9143 (t80) cc_final: 0.8645 (t80) REVERT: C 296 ILE cc_start: 0.9348 (mt) cc_final: 0.8956 (tt) REVERT: C 332 LYS cc_start: 0.9474 (ttpp) cc_final: 0.9218 (ttpp) REVERT: D 77 MET cc_start: 0.8915 (tpp) cc_final: 0.8428 (tpp) REVERT: D 163 MET cc_start: 0.9121 (mmm) cc_final: 0.8542 (mmt) REVERT: D 185 LYS cc_start: 0.9119 (ttpp) cc_final: 0.8875 (tptt) REVERT: D 240 MET cc_start: 0.8186 (tmm) cc_final: 0.7641 (tmm) REVERT: D 250 PHE cc_start: 0.9187 (t80) cc_final: 0.7914 (t80) REVERT: D 257 ILE cc_start: 0.9428 (mt) cc_final: 0.9171 (mp) REVERT: D 268 TYR cc_start: 0.8569 (t80) cc_final: 0.8148 (t80) REVERT: D 332 LYS cc_start: 0.9521 (mttt) cc_final: 0.9216 (mmmt) REVERT: E 43 ILE cc_start: 0.9571 (tp) cc_final: 0.9334 (pt) REVERT: E 105 LEU cc_start: 0.9321 (tp) cc_final: 0.9118 (tp) REVERT: E 109 MET cc_start: 0.8551 (tpp) cc_final: 0.7898 (tpp) REVERT: E 113 MET cc_start: 0.9208 (mmt) cc_final: 0.8801 (mmp) REVERT: E 144 TRP cc_start: 0.9019 (m100) cc_final: 0.8445 (m100) REVERT: E 182 MET cc_start: 0.9310 (mmm) cc_final: 0.8779 (mmm) REVERT: E 183 LEU cc_start: 0.9591 (mm) cc_final: 0.7973 (mm) REVERT: E 234 MET cc_start: 0.9284 (mmm) cc_final: 0.8949 (mmm) REVERT: E 369 LEU cc_start: 0.9295 (tp) cc_final: 0.8977 (tp) REVERT: E 373 PHE cc_start: 0.9250 (m-80) cc_final: 0.8803 (m-10) REVERT: E 430 MET cc_start: 0.9099 (ttp) cc_final: 0.8878 (ttm) REVERT: E 503 MET cc_start: 0.9320 (tpp) cc_final: 0.9069 (mmm) REVERT: E 584 PHE cc_start: 0.8548 (m-10) cc_final: 0.8243 (m-80) REVERT: E 586 ILE cc_start: 0.9597 (pt) cc_final: 0.9370 (pt) REVERT: E 798 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.7916 (ttt180) REVERT: E 801 MET cc_start: 0.8710 (ptt) cc_final: 0.8351 (ptp) REVERT: E 1066 MET cc_start: 0.8493 (mmm) cc_final: 0.8275 (mmp) REVERT: E 1088 TRP cc_start: 0.7906 (OUTLIER) cc_final: 0.7656 (t-100) REVERT: E 1110 MET cc_start: 0.8625 (mmm) cc_final: 0.8337 (mmt) REVERT: E 1228 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9085 (mp) REVERT: E 1261 LEU cc_start: 0.9601 (tp) cc_final: 0.9134 (mt) REVERT: E 1298 MET cc_start: 0.9150 (ttt) cc_final: 0.8348 (tmm) REVERT: E 1301 ASN cc_start: 0.9166 (m-40) cc_final: 0.8752 (m110) REVERT: E 1313 LYS cc_start: 0.9002 (tppt) cc_final: 0.8788 (tppt) outliers start: 82 outliers final: 66 residues processed: 404 average time/residue: 0.1339 time to fit residues: 86.1827 Evaluate side-chains 403 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 331 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 55 PHE 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 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 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 144 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 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 220 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 55 PHE 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 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 328 VAL Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 176 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 534 LEU 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 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 1140 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 1227 LEU 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 Chi-restraints excluded: chain E residue 1368 LEU Chi-restraints excluded: chain E residue 1435 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: [2, 191, 138, 164, 240, 88, 155, 50, 130, 134, 257] chunk 2 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 240 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 257 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN D 175 HIS E 933 ASN E1190 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.057386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.047762 restraints weight = 109732.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.049308 restraints weight = 57774.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.050371 restraints weight = 37030.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.051068 restraints weight = 26804.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.051592 restraints weight = 21308.803| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21446 Z= 0.133 Angle : 0.754 14.883 29149 Z= 0.360 Chirality : 0.047 0.316 3454 Planarity : 0.004 0.060 3624 Dihedral : 5.660 128.366 2868 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 3.25 % Allowed : 27.57 % Favored : 69.17 % 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: 0.45 (0.16), residues: 2650 helix: 1.25 (0.14), residues: 1331 sheet: -0.50 (0.31), residues: 283 loop : -0.66 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1444 TYR 0.027 0.001 TYR E1004 PHE 0.037 0.001 PHE E 42 TRP 0.038 0.001 TRP E 52 HIS 0.007 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (21440) covalent geometry : angle 0.75348 / 0.36 (29139) SS BOND : bond 0.00138 / 0.07 ( 5) SS BOND : angle 1.07004 / 0.56 ( 10) hydrogen bonds : bond 0.04262 / 2.86 ( 1092) hydrogen bonds : angle 4.37057 / 3.06 ( 3246) Misc. bond : bond 0.00062 / 0.03 ( 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 429 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 355 time to evaluate : 0.622 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: 0.9468 (mmmt) cc_final: 0.9124 (mmmt) REVERT: A 77 MET cc_start: 0.8518 (tpp) cc_final: 0.7783 (tmm) REVERT: A 170 LYS cc_start: 0.8776 (tptp) cc_final: 0.8412 (tppt) REVERT: A 209 MET cc_start: 0.8298 (mmp) cc_final: 0.7718 (mmp) REVERT: A 279 GLN cc_start: 0.8742 (tp40) cc_final: 0.8389 (tm-30) REVERT: A 288 GLU cc_start: 0.8017 (tt0) cc_final: 0.7781 (mm-30) REVERT: A 332 LYS cc_start: 0.9438 (mttt) cc_final: 0.9197 (mttp) REVERT: B 63 LEU cc_start: 0.9645 (tt) cc_final: 0.9411 (pp) REVERT: B 77 MET cc_start: 0.8813 (tpt) cc_final: 0.8262 (tmm) REVERT: B 169 MET cc_start: 0.8949 (mmm) cc_final: 0.8563 (ttm) REVERT: B 170 LYS cc_start: 0.9067 (tptp) cc_final: 0.8504 (tptm) REVERT: B 185 LYS cc_start: 0.9198 (ttpp) cc_final: 0.8945 (pptt) REVERT: B 288 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7968 (mt-10) REVERT: B 305 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8697 (mt) REVERT: B 330 TYR cc_start: 0.8668 (m-80) cc_final: 0.8402 (m-80) REVERT: B 332 LYS cc_start: 0.9547 (mttt) cc_final: 0.9196 (mmtt) REVERT: C 39 LYS cc_start: 0.9407 (mmtt) cc_final: 0.9069 (mmmt) REVERT: C 47 LYS cc_start: 0.8855 (tppt) cc_final: 0.8413 (tppt) REVERT: C 163 MET cc_start: 0.9007 (mmm) cc_final: 0.8649 (mmm) REVERT: C 185 LYS cc_start: 0.9437 (tppp) cc_final: 0.9035 (tppp) REVERT: C 235 GLN cc_start: 0.8891 (mt0) cc_final: 0.8273 (mt0) REVERT: C 268 TYR cc_start: 0.9117 (t80) cc_final: 0.8648 (t80) REVERT: C 296 ILE cc_start: 0.9341 (mt) cc_final: 0.8939 (tt) REVERT: C 332 LYS cc_start: 0.9366 (ttpp) cc_final: 0.8966 (ttpp) REVERT: D 77 MET cc_start: 0.8904 (tpp) cc_final: 0.8440 (tpp) REVERT: D 185 LYS cc_start: 0.9110 (ttpp) cc_final: 0.8862 (tptt) REVERT: D 240 MET cc_start: 0.8223 (tmm) cc_final: 0.7706 (tmm) REVERT: D 247 ASN cc_start: 0.8017 (p0) cc_final: 0.7689 (p0) REVERT: D 250 PHE cc_start: 0.9205 (t80) cc_final: 0.8164 (t80) REVERT: D 257 ILE cc_start: 0.9408 (mt) cc_final: 0.9164 (mp) REVERT: D 268 TYR cc_start: 0.8644 (t80) cc_final: 0.8232 (t80) REVERT: D 332 LYS cc_start: 0.9501 (mttt) cc_final: 0.9194 (mmmt) REVERT: E 42 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8710 (t80) REVERT: E 109 MET cc_start: 0.8495 (tpp) cc_final: 0.7871 (tpp) REVERT: E 113 MET cc_start: 0.9193 (mmt) cc_final: 0.8782 (mmp) REVERT: E 144 TRP cc_start: 0.8986 (m100) cc_final: 0.8424 (m100) REVERT: E 182 MET cc_start: 0.9295 (mmm) cc_final: 0.8803 (mmm) REVERT: E 183 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.7964 (mm) REVERT: E 430 MET cc_start: 0.9127 (ttp) cc_final: 0.8913 (ttm) REVERT: E 584 PHE cc_start: 0.8572 (m-10) cc_final: 0.8195 (m-80) REVERT: E 586 ILE cc_start: 0.9594 (pt) cc_final: 0.9358 (pt) REVERT: E 711 MET cc_start: 0.8895 (mmm) cc_final: 0.8620 (mpp) REVERT: E 798 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7896 (ttt180) REVERT: E 801 MET cc_start: 0.8663 (ptt) cc_final: 0.8336 (ptp) REVERT: E 1066 MET cc_start: 0.8471 (mmm) cc_final: 0.8251 (mmp) REVERT: E 1088 TRP cc_start: 0.7854 (OUTLIER) cc_final: 0.7630 (t-100) REVERT: E 1110 MET cc_start: 0.8529 (mmm) cc_final: 0.8244 (mmt) REVERT: E 1228 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9072 (mp) REVERT: E 1261 LEU cc_start: 0.9593 (tp) cc_final: 0.9148 (mt) REVERT: E 1298 MET cc_start: 0.9140 (ttt) cc_final: 0.8341 (tmm) REVERT: E 1301 ASN cc_start: 0.9152 (m-40) cc_final: 0.8733 (m110) outliers start: 74 outliers final: 65 residues processed: 407 average time/residue: 0.1292 time to fit residues: 84.3016 Evaluate side-chains 407 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 336 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 115 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 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 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 144 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 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 220 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 49 ILE 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 202 VAL Chi-restraints excluded: chain D residue 212 SER 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 343 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 PHE 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 219 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 224 ASN 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 798 ARG 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 1140 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 1190 GLN Chi-restraints excluded: chain E residue 1227 LEU 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 Chi-restraints excluded: chain E residue 1368 LEU Chi-restraints excluded: chain E residue 1435 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: [64, 102, 207, 104, 215, 231, 82, 218, 221, 156, 121] chunk 64 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 231 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** D 160 ASN D 175 HIS E 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.056870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.047318 restraints weight = 110036.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.048846 restraints weight = 58025.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.049865 restraints weight = 37186.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.050596 restraints weight = 27117.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.051111 restraints weight = 21410.933| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21446 Z= 0.155 Angle : 0.763 13.439 29149 Z= 0.370 Chirality : 0.047 0.300 3454 Planarity : 0.004 0.054 3624 Dihedral : 5.630 126.068 2868 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 3.43 % Allowed : 27.97 % Favored : 68.60 % 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: 0.44 (0.16), residues: 2650 helix: 1.25 (0.14), residues: 1331 sheet: -0.53 (0.31), residues: 283 loop : -0.64 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1251 TYR 0.025 0.001 TYR E1004 PHE 0.033 0.001 PHE E 42 TRP 0.019 0.001 TRP D 83 HIS 0.007 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (21440) covalent geometry : angle 0.76255 / 0.37 (29139) SS BOND : bond 0.00175 / 0.09 ( 5) SS BOND : angle 1.19087 / 0.62 ( 10) hydrogen bonds : bond 0.04261 / 2.85 ( 1092) hydrogen bonds : angle 4.41888 / 3.09 ( 3246) Misc. bond : bond 0.00067 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3244.36 seconds wall clock time: 57 minutes 9.72 seconds (3429.72 seconds total)