Starting phenix.real_space_refine on Thu Mar 5 10:18:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s61_24846/03_2026/7s61_24846.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s61_24846/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7s61_24846/03_2026/7s61_24846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s61_24846/03_2026/7s61_24846.map" model { file = "/net/cci-nas-00/data/ceres_data/7s61_24846/03_2026/7s61_24846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s61_24846/03_2026/7s61_24846.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.47, per 1000 atoms: 0.21 Number of scatterers: 20985 At special positions: 0 Unit cell: (133.9, 149.5, 136.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 P 5 15.00 Mg 2 11.99 O 3725 8.00 N 3569 7.00 C 13564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.01 Simple disulfide: pdb=" N VAL C 291 " - pdb=" CG2 VAL C 291 " distance=2.75 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.01 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.01 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 985.9 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: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 67 through 97 Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.619A pdb=" N ALA A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.647A pdb=" N ILE A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 67 through 97 Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.619A pdb=" N ALA B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 129 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 172 removed outlier: 3.647A pdb=" N ILE B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 67 through 97 Processing helix chain 'C' and resid 116 through 129 removed outlier: 3.619A pdb=" N ALA C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 172 removed outlier: 3.648A pdb=" N ILE C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 67 through 97 Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.619A pdb=" N ALA D 120 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 129 " --> pdb=" O ILE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 172 removed outlier: 3.647A pdb=" N ILE D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'D' and resid 305 through 307 No H-bonds generated for 'chain 'D' and resid 305 through 307' Processing helix chain 'E' and resid 21 through 24 Processing helix chain 'E' and resid 25 through 34 Processing helix chain 'E' and resid 34 through 52 removed outlier: 3.959A pdb=" N PHE E 45 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 71 through 98 removed outlier: 3.866A pdb=" N TRP E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 129 Processing helix chain 'E' and resid 137 through 161 removed outlier: 3.594A pdb=" N VAL E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS E 161 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 193 removed outlier: 3.516A pdb=" N GLY E 181 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'E' and resid 234 through 242 removed outlier: 3.921A pdb=" N HIS E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 313 removed outlier: 6.258A pdb=" N ARG E 298 " --> pdb=" O HIS E 294 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU E 300 " --> pdb=" O PHE E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 328 Processing helix chain 'E' and resid 348 through 353 Processing helix chain 'E' and resid 355 through 401 Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 414 through 457 removed outlier: 3.591A pdb=" N VAL E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR E 426 " --> pdb=" O VAL E 422 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASN E 427 " --> pdb=" O ALA E 423 " (cutoff:3.500A) Proline residue: E 437 - end of helix Proline residue: E 443 - end of helix Processing helix chain 'E' and resid 459 through 465 removed outlier: 4.095A pdb=" N ILE E 463 " --> pdb=" O VAL E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 506 removed outlier: 4.410A pdb=" N ALA E 472 " --> pdb=" O ILE E 468 " (cutoff:3.500A) Proline residue: E 473 - end of helix removed outlier: 3.740A pdb=" N GLY E 506 " --> pdb=" O GLU E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 513 removed outlier: 3.729A pdb=" N LEU E 512 " --> pdb=" O LYS E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 565 Proline residue: E 552 - end of helix removed outlier: 4.069A pdb=" N VAL E 564 " --> pdb=" O PHE E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 589 removed outlier: 4.021A pdb=" N ALA E 577 " --> pdb=" O SER E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 593 through 615 Processing helix chain 'E' and resid 721 through 728 Processing helix chain 'E' and resid 783 through 790 Processing helix chain 'E' and resid 795 through 806 Processing helix chain 'E' and resid 832 through 844 removed outlier: 3.911A pdb=" N GLN E 836 " --> pdb=" O GLY E 832 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 871 Processing helix chain 'E' and resid 875 through 880 removed outlier: 3.779A pdb=" N ASP E 879 " --> pdb=" O GLU E 875 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP E 880 " --> pdb=" O LEU E 876 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 875 through 880' Processing helix chain 'E' and resid 913 through 920 Processing helix chain 'E' and resid 921 through 932 removed outlier: 3.545A pdb=" N LEU E 931 " --> pdb=" O HIS E 927 " (cutoff:3.500A) Processing helix chain 'E' and resid 998 through 1009 removed outlier: 3.646A pdb=" N ALA E1002 " --> pdb=" O TRP E 998 " (cutoff:3.500A) Processing helix chain 'E' and resid 1009 through 1039 Processing helix chain 'E' and resid 1062 through 1097 removed outlier: 5.197A pdb=" N PHE E1068 " --> pdb=" O TYR E1064 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E1074 " --> pdb=" O VAL E1070 " (cutoff:3.500A) Processing helix chain 'E' and resid 1100 through 1106 Processing helix chain 'E' and resid 1109 through 1116 removed outlier: 3.657A pdb=" N PHE E1113 " --> pdb=" O PRO E1109 " (cutoff:3.500A) Processing helix chain 'E' and resid 1117 through 1135 removed outlier: 3.762A pdb=" N ILE E1121 " --> pdb=" O PRO E1117 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1135 through 1161 removed outlier: 3.759A pdb=" N THR E1161 " --> pdb=" O ILE E1157 " (cutoff:3.500A) Processing helix chain 'E' and resid 1162 through 1210 removed outlier: 4.377A pdb=" N VAL E1166 " --> pdb=" O PRO E1162 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 4.573A pdb=" N VAL E1184 " --> pdb=" O LYS E1180 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA E1185 " --> pdb=" O TYR E1181 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP E1188 " --> pdb=" O VAL E1184 " (cutoff:3.500A) Proline residue: E1199 - end of helix removed outlier: 3.715A pdb=" N GLU E1209 " --> pdb=" O ALA E1205 " (cutoff:3.500A) Processing helix chain 'E' and resid 1210 through 1218 removed outlier: 3.545A pdb=" N ARG E1218 " --> pdb=" O ILE E1214 " (cutoff:3.500A) Processing helix chain 'E' and resid 1219 through 1274 removed outlier: 3.695A pdb=" N VAL E1259 " --> pdb=" O ILE E1255 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL E1260 " --> pdb=" O GLY E1256 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS E1273 " --> pdb=" O SER E1269 " (cutoff:3.500A) Processing helix chain 'E' and resid 1280 through 1320 removed outlier: 5.627A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP E1297 " --> pdb=" O ASN E1293 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA E1311 " --> pdb=" O LEU E1307 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1384 through 1391 removed outlier: 3.713A pdb=" N SER E1389 " --> pdb=" O LYS E1385 " (cutoff:3.500A) Processing helix chain 'E' and resid 1414 through 1422 removed outlier: 3.791A pdb=" N ARG E1421 " --> pdb=" O THR E1417 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E1422 " --> pdb=" O LEU E1418 " (cutoff:3.500A) Processing helix chain 'E' and resid 1436 through 1441 Processing helix chain 'E' and resid 1447 through 1457 Processing helix chain 'E' and resid 1460 through 1466 Processing helix chain 'E' and resid 1483 through 1498 removed outlier: 4.075A pdb=" N ARG E1498 " --> pdb=" O ARG E1494 " (cutoff:3.500A) Processing helix chain 'E' and resid 1513 through 1528 removed outlier: 3.514A pdb=" N ALA E1527 " --> pdb=" O VAL E1523 " (cutoff:3.500A) Processing helix chain 'E' and resid 1562 through 1570 removed outlier: 4.367A pdb=" N LYS E1570 " --> pdb=" O LEU E1566 " (cutoff:3.500A) Processing helix chain 'E' and resid 1572 through 1582 removed outlier: 3.899A pdb=" N LYS E1582 " --> pdb=" O VAL E1578 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.615A pdb=" N VAL A 202 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 255 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.995A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 230 through 238 removed outlier: 5.273A pdb=" N THR A 223 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 221 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER A 212 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL A 290 " --> pdb=" O SER A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 322 Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.614A pdb=" N VAL B 202 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 255 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.996A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 230 through 238 removed outlier: 5.273A pdb=" N THR B 223 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 221 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER B 212 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL B 290 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AB1, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AB2, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.615A pdb=" N VAL C 202 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 255 " --> pdb=" O VAL C 202 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.996A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 230 through 238 removed outlier: 5.274A pdb=" N THR C 223 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 221 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER C 212 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL C 290 " --> pdb=" O SER C 212 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AB6, first strand: chain 'C' and resid 319 through 322 Processing sheet with id=AB7, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.614A pdb=" N VAL D 202 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 255 " --> pdb=" O VAL D 202 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.996A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 230 through 238 removed outlier: 5.274A pdb=" N THR D 223 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG D 221 " --> pdb=" O HIS D 234 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER D 212 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL D 290 " --> pdb=" O SER D 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 313 through 315 Processing sheet with id=AC2, first strand: chain 'D' and resid 319 through 322 Processing sheet with id=AC3, first strand: chain 'E' and resid 678 through 680 removed outlier: 4.129A pdb=" N VAL E 680 " --> pdb=" O ILE E 704 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 697 through 701 removed outlier: 4.498A pdb=" N ASN E 699 " --> pdb=" O GLY E 685 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLY E 685 " --> pdb=" O ASN E 699 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR E 701 " --> pdb=" O MET E 683 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N MET E 683 " --> pdb=" O THR E 701 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN E 732 " --> pdb=" O THR E 688 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 771 through 773 removed outlier: 6.108A pdb=" N ALA E 771 " --> pdb=" O PHE E 852 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL E 851 " --> pdb=" O VAL E 885 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL E 887 " --> pdb=" O VAL E 851 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU E 853 " --> pdb=" O VAL E 887 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU E 709 " --> pdb=" O TRP E 899 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE E 901 " --> pdb=" O LEU E 709 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N MET E 711 " --> pdb=" O ILE E 901 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N MET E 903 " --> pdb=" O MET E 711 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL E 713 " --> pdb=" O MET E 903 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE E 900 " --> pdb=" O GLU E 911 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU E 911 " --> pdb=" O ILE E 900 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA E 902 " --> pdb=" O GLN E 909 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 1365 through 1369 removed outlier: 5.392A pdb=" N VAL E1365 " --> pdb=" O ASN E1349 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU E1350 " --> pdb=" O GLU E1400 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLU E1400 " --> pdb=" O LEU E1350 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL E1352 " --> pdb=" O THR E1398 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR E1398 " --> pdb=" O VAL E1352 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 1423 through 1425 removed outlier: 6.170A pdb=" N SER E1423 " --> pdb=" O ILE E1504 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS E1374 " --> pdb=" O LEU E1548 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ILE E1550 " --> pdb=" O LYS E1374 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY E1376 " --> pdb=" O ILE E1550 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU E1552 " --> pdb=" O GLY E1376 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYS E1378 " --> pdb=" O LEU E1552 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU E1559 " --> pdb=" O VAL E1551 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS E1553 " --> pdb=" O ILE E1557 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE E1557 " --> pdb=" O LYS E1553 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 1434 through 1435 removed outlier: 3.617A pdb=" N GLY E1434 " --> pdb=" O ILE E1475 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 3246 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.29 Time building geometry restraints manager: 1.92 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: 12287 35.49 - 70.98: 436 70.98 - 106.47: 24 106.47 - 141.96: 0 141.96 - 177.45: 1 Dihedral angle restraints: 12748 sinusoidal: 4980 harmonic: 7768 Sorted by residual: dihedral pdb=" CA VAL E 193 " pdb=" C VAL E 193 " pdb=" N ARG E 194 " pdb=" CA ARG E 194 " ideal model delta harmonic sigma weight residual -180.00 -106.53 -73.47 0 5.00e+00 4.00e-02 2.16e+02 dihedral pdb=" CA GLY E 21 " pdb=" C GLY E 21 " pdb=" N VAL E 22 " pdb=" CA VAL E 22 " ideal model delta harmonic sigma weight residual 180.00 -132.58 -47.42 0 5.00e+00 4.00e-02 9.00e+01 dihedral pdb=" CB VAL C 291 " pdb=" N VAL C 291 " pdb=" CG2 VAL C 291 " pdb=" CB VAL C 291 " ideal model delta sinusoidal sigma weight residual -86.00 -0.00 -86.00 1 1.00e+01 1.00e-02 8.93e+01 ... (remaining 12745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 3282 0.169 - 0.338: 156 0.338 - 0.508: 13 0.508 - 0.677: 2 0.677 - 0.846: 1 Chirality restraints: 3454 Sorted by residual: chirality pdb=" CG LEU E1227 " pdb=" CB LEU E1227 " pdb=" CD1 LEU E1227 " pdb=" CD2 LEU E1227 " both_signs ideal model delta sigma weight residual False -2.59 -1.74 -0.85 2.00e-01 2.50e+01 1.79e+01 chirality pdb=" CG LEU E 183 " pdb=" CB LEU E 183 " pdb=" CD1 LEU E 183 " pdb=" CD2 LEU E 183 " both_signs ideal model delta sigma weight residual False -2.59 -1.96 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CB VAL E 556 " pdb=" CA VAL E 556 " pdb=" CG1 VAL E 556 " pdb=" CG2 VAL E 556 " both_signs ideal model delta sigma weight residual False -2.63 -2.09 -0.54 2.00e-01 2.50e+01 7.25e+00 ... (remaining 3451 not shown) Planarity restraints: 3624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 267 " 0.024 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C LEU E 267 " -0.081 2.00e-02 2.50e+03 pdb=" O LEU E 267 " 0.031 2.00e-02 2.50e+03 pdb=" N CYS E 268 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 589 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO E 590 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E1017 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C VAL E1017 " -0.067 2.00e-02 2.50e+03 pdb=" O VAL E1017 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE E1018 " 0.022 2.00e-02 2.50e+03 ... (remaining 3621 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 269 2.60 - 3.18: 15762 3.18 - 3.75: 35089 3.75 - 4.33: 46327 4.33 - 4.90: 74583 Nonbonded interactions: 172030 Sorted by model distance: nonbonded pdb=" SG CYS E 7 " pdb=" SG CYS E 27 " model vdw 2.028 3.760 nonbonded pdb=" O1B ADP E1601 " pdb="MG MG E1603 " model vdw 2.160 2.170 nonbonded pdb="MG MG E1602 " pdb=" O3B ATP E1604 " model vdw 2.162 2.170 nonbonded pdb="MG MG E1602 " pdb=" O2B ATP E1604 " model vdw 2.170 2.170 nonbonded pdb=" NE2 GLN E 775 " pdb="MG MG E1602 " model vdw 2.246 2.250 ... (remaining 172025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 18.940 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.717 21446 Z= 0.527 Angle : 1.654 70.859 29149 Z= 0.901 Chirality : 0.083 0.846 3454 Planarity : 0.013 0.104 3624 Dihedral : 17.700 177.446 7685 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.57 % Favored : 95.32 % Rotamer: Outliers : 8.22 % Allowed : 10.60 % Favored : 81.18 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.86 (0.12), residues: 2650 helix: -4.05 (0.07), residues: 1289 sheet: -1.03 (0.30), residues: 275 loop : -2.51 (0.15), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 314 TYR 0.051 0.004 TYR E1287 PHE 0.047 0.004 PHE E1164 TRP 0.034 0.004 TRP E1247 HIS 0.014 0.003 HIS E1098 Details of bonding type rmsd covalent geometry : bond 0.00968 (21440) covalent geometry : angle 1.58125 (29139) SS BOND : bond 0.32123 ( 5) SS BOND : angle 26.25139 ( 10) hydrogen bonds : bond 0.15559 ( 1092) hydrogen bonds : angle 8.17319 ( 3246) Misc. bond : bond 0.00039 ( 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 : 0.767 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: 0.1463 time to fit residues: 169.7679 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 : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 359 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN B 57 GLN B 128 GLN B 277 HIS ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS C 277 HIS ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN D 277 HIS ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN E 265 GLN E 407 ASN E 438 ASN E 548 ASN E 563 HIS E 795 ASN E 820 GLN E 836 GLN E 935 GLN E1197 GLN ** E1373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.060245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.050390 restraints weight = 107232.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.051989 restraints weight = 54800.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.053087 restraints weight = 34372.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.053851 restraints weight = 24558.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.054340 restraints weight = 19177.178| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.195 21446 Z= 0.147 Angle : 0.844 58.518 29149 Z= 0.428 Chirality : 0.047 0.314 3454 Planarity : 0.006 0.080 3624 Dihedral : 8.659 172.164 2975 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 3.78 % Allowed : 19.17 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.14), residues: 2650 helix: -1.08 (0.13), residues: 1283 sheet: -0.67 (0.30), residues: 283 loop : -1.89 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E1300 TYR 0.022 0.002 TYR D 268 PHE 0.028 0.002 PHE D 86 TRP 0.023 0.002 TRP D 90 HIS 0.005 0.001 HIS E1098 Details of bonding type rmsd covalent geometry : bond 0.00323 (21440) covalent geometry : angle 0.75394 (29139) SS BOND : bond 0.00583 ( 5) SS BOND : angle 20.47214 ( 10) hydrogen bonds : bond 0.04924 ( 1092) hydrogen bonds : angle 4.96928 ( 3246) Misc. bond : bond 0.00042 ( 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 545 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 459 time to evaluate : 0.818 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: 0.8697 (m-40) cc_final: 0.8339 (t0) REVERT: A 47 LYS cc_start: 0.9198 (mmmt) cc_final: 0.8923 (mmmt) REVERT: A 66 LEU cc_start: 0.9323 (mt) cc_final: 0.9011 (mt) REVERT: A 77 MET cc_start: 0.8706 (tpp) cc_final: 0.7612 (tmm) REVERT: A 137 MET cc_start: 0.8286 (ptt) cc_final: 0.7969 (ptp) REVERT: A 170 LYS cc_start: 0.8832 (tptp) cc_final: 0.8495 (tppt) REVERT: A 173 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8603 (pt0) REVERT: A 199 MET cc_start: 0.8814 (mtm) cc_final: 0.8579 (mtt) REVERT: A 209 MET cc_start: 0.8458 (mmp) cc_final: 0.6990 (mmp) REVERT: A 279 GLN cc_start: 0.9180 (tp40) cc_final: 0.8101 (tm-30) REVERT: A 292 GLU cc_start: 0.8123 (pt0) cc_final: 0.7286 (pt0) REVERT: A 330 TYR cc_start: 0.8879 (m-80) cc_final: 0.8541 (m-80) REVERT: A 332 LYS cc_start: 0.9368 (mttt) cc_final: 0.9077 (mttm) REVERT: B 38 LYS cc_start: 0.9496 (mmmm) cc_final: 0.9237 (mmmm) REVERT: B 43 ASN cc_start: 0.8817 (m110) cc_final: 0.8502 (m-40) REVERT: B 52 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7369 (mm110) REVERT: B 63 LEU cc_start: 0.9642 (tt) cc_final: 0.9234 (pp) REVERT: B 77 MET cc_start: 0.8612 (tpp) cc_final: 0.8261 (tmm) REVERT: B 81 CYS cc_start: 0.8186 (t) cc_final: 0.7919 (t) REVERT: B 169 MET cc_start: 0.9307 (mmm) cc_final: 0.8785 (ttm) REVERT: B 170 LYS cc_start: 0.9045 (tptp) cc_final: 0.8631 (tptm) REVERT: B 237 ASP cc_start: 0.7608 (p0) cc_final: 0.6426 (p0) REVERT: B 240 MET cc_start: 0.8210 (tmm) cc_final: 0.7727 (tmm) REVERT: B 288 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8239 (mt-10) REVERT: B 305 LEU cc_start: 0.8862 (mt) cc_final: 0.8473 (mt) REVERT: B 330 TYR cc_start: 0.8704 (m-80) cc_final: 0.8446 (m-80) REVERT: C 39 LYS cc_start: 0.9406 (mmtt) cc_final: 0.9038 (tptt) REVERT: C 86 PHE cc_start: 0.9477 (m-80) cc_final: 0.9219 (m-10) REVERT: C 88 MET cc_start: 0.8879 (ttt) cc_final: 0.7963 (tmm) REVERT: C 152 GLN cc_start: 0.9076 (tt0) cc_final: 0.8400 (tt0) REVERT: C 170 LYS cc_start: 0.9220 (tptp) cc_final: 0.8923 (tptm) REVERT: C 207 LYS cc_start: 0.9244 (mmmm) cc_final: 0.8994 (mmmm) REVERT: C 288 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8247 (mt-10) REVERT: C 293 THR cc_start: 0.9572 (p) cc_final: 0.9249 (t) REVERT: C 296 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8871 (tt) REVERT: C 313 GLN cc_start: 0.8778 (mt0) cc_final: 0.8524 (mt0) REVERT: C 335 ASN cc_start: 0.9332 (m-40) cc_final: 0.9080 (m110) REVERT: D 44 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8872 (t) REVERT: D 47 LYS cc_start: 0.8830 (mmmt) cc_final: 0.7832 (mptt) REVERT: D 77 MET cc_start: 0.8772 (tpp) cc_final: 0.8506 (tmm) REVERT: D 86 PHE cc_start: 0.8937 (m-80) cc_final: 0.8286 (m-10) REVERT: D 128 GLN cc_start: 0.8961 (tt0) cc_final: 0.8665 (tm-30) REVERT: D 137 MET cc_start: 0.8168 (ptm) cc_final: 0.7862 (ttm) REVERT: D 183 PHE cc_start: 0.9048 (m-80) cc_final: 0.8561 (m-10) REVERT: D 185 LYS cc_start: 0.8945 (ttpp) cc_final: 0.8466 (tptt) REVERT: D 202 VAL cc_start: 0.9274 (OUTLIER) cc_final: 0.9004 (p) REVERT: D 211 ILE cc_start: 0.9377 (mp) cc_final: 0.8245 (mp) REVERT: D 212 SER cc_start: 0.9133 (p) cc_final: 0.8928 (p) REVERT: D 217 MET cc_start: 0.8640 (mtm) cc_final: 0.7926 (mtm) REVERT: D 218 GLN cc_start: 0.9292 (mm-40) cc_final: 0.8982 (mm-40) REVERT: D 235 GLN cc_start: 0.8938 (mt0) cc_final: 0.8550 (pm20) REVERT: D 240 MET cc_start: 0.8227 (tmm) cc_final: 0.7829 (tmm) REVERT: D 247 ASN cc_start: 0.7982 (p0) cc_final: 0.7377 (p0) REVERT: D 299 GLN cc_start: 0.9553 (tt0) cc_final: 0.8646 (tm-30) REVERT: E 39 PHE cc_start: 0.9161 (t80) cc_final: 0.8737 (t80) REVERT: E 45 PHE cc_start: 0.8808 (t80) cc_final: 0.8132 (t80) REVERT: E 89 GLU cc_start: 0.9111 (tp30) cc_final: 0.8845 (tm-30) REVERT: E 109 MET cc_start: 0.8191 (tpp) cc_final: 0.7475 (tpp) REVERT: E 113 MET cc_start: 0.9178 (mmt) cc_final: 0.8680 (mmp) REVERT: E 128 ILE cc_start: 0.9647 (tp) cc_final: 0.9361 (tp) REVERT: E 182 MET cc_start: 0.9283 (mmm) cc_final: 0.8725 (mmm) REVERT: E 369 LEU cc_start: 0.9404 (tp) cc_final: 0.9172 (tp) REVERT: E 430 MET cc_start: 0.9081 (ttp) cc_final: 0.8866 (ttp) REVERT: E 584 PHE cc_start: 0.8686 (m-10) cc_final: 0.8329 (m-80) REVERT: E 711 MET cc_start: 0.9024 (mmm) cc_final: 0.8528 (mpp) REVERT: E 1021 LEU cc_start: 0.9646 (mm) cc_final: 0.9360 (pp) REVERT: E 1261 LEU cc_start: 0.9650 (tp) cc_final: 0.9448 (tp) REVERT: E 1276 LEU cc_start: 0.8056 (mp) cc_final: 0.7379 (tt) REVERT: E 1298 MET cc_start: 0.8956 (ttt) cc_final: 0.8436 (tmm) outliers start: 86 outliers final: 37 residues processed: 516 average time/residue: 0.1424 time to fit residues: 116.9799 Evaluate side-chains 415 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 374 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 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 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: chunk 98 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 161 optimal weight: 0.7980 chunk 195 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS B 175 HIS B 186 HIS B 335 ASN C 48 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN D 97 HIS D 160 ASN D 175 HIS ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 224 ASN ** 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 = 0.3173 r_free = 0.3173 target = 0.058513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.048859 restraints weight = 108248.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.050420 restraints weight = 56429.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.051472 restraints weight = 35860.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.052222 restraints weight = 25864.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.052700 restraints weight = 20308.684| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.191 21446 Z= 0.160 Angle : 0.806 58.542 29149 Z= 0.404 Chirality : 0.046 0.342 3454 Planarity : 0.004 0.065 3624 Dihedral : 7.021 162.726 2911 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 3.69 % Allowed : 21.28 % Favored : 75.02 % 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: -0.95 (0.15), residues: 2650 helix: 0.12 (0.14), residues: 1325 sheet: -0.54 (0.30), residues: 303 loop : -1.58 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 835 TYR 0.025 0.002 TYR D 268 PHE 0.026 0.001 PHE C 86 TRP 0.018 0.001 TRP E1247 HIS 0.029 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00353 (21440) covalent geometry : angle 0.71116 (29139) SS BOND : bond 0.00458 ( 5) SS BOND : angle 20.47955 ( 10) hydrogen bonds : bond 0.04487 ( 1092) hydrogen bonds : angle 4.54460 ( 3246) Misc. bond : bond 0.00042 ( 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 462 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 378 time to evaluate : 0.814 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: 0.8815 (m-40) cc_final: 0.8258 (t0) REVERT: A 66 LEU cc_start: 0.9368 (mt) cc_final: 0.9140 (mt) REVERT: A 77 MET cc_start: 0.8774 (tpp) cc_final: 0.7920 (tmm) REVERT: A 84 LEU cc_start: 0.9326 (tp) cc_final: 0.9101 (mp) REVERT: A 137 MET cc_start: 0.8527 (ptt) cc_final: 0.8160 (ptp) REVERT: A 170 LYS cc_start: 0.8837 (tptp) cc_final: 0.8478 (tppt) REVERT: A 173 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8653 (pt0) REVERT: A 208 SER cc_start: 0.9093 (p) cc_final: 0.8798 (p) REVERT: A 209 MET cc_start: 0.8368 (mmp) cc_final: 0.7118 (mmp) REVERT: A 211 ILE cc_start: 0.9476 (OUTLIER) cc_final: 0.9133 (mp) REVERT: A 234 HIS cc_start: 0.8056 (t-170) cc_final: 0.7713 (t-90) REVERT: A 279 GLN cc_start: 0.8944 (tp40) cc_final: 0.8349 (tm-30) REVERT: A 292 GLU cc_start: 0.8237 (pt0) cc_final: 0.7453 (pt0) REVERT: A 332 LYS cc_start: 0.9453 (mttt) cc_final: 0.9130 (mttp) REVERT: B 38 LYS cc_start: 0.9554 (mmmm) cc_final: 0.9338 (mmmm) REVERT: B 43 ASN cc_start: 0.8819 (m110) cc_final: 0.7681 (p0) REVERT: B 63 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9292 (pp) REVERT: B 169 MET cc_start: 0.9227 (mmm) cc_final: 0.8736 (ttm) REVERT: B 170 LYS cc_start: 0.9052 (tptp) cc_final: 0.8566 (tptm) REVERT: B 288 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8219 (mt-10) REVERT: B 305 LEU cc_start: 0.8996 (mt) cc_final: 0.8570 (mt) REVERT: B 330 TYR cc_start: 0.8780 (m-80) cc_final: 0.8480 (m-80) REVERT: C 39 LYS cc_start: 0.9370 (mmtt) cc_final: 0.9000 (tptt) REVERT: C 207 LYS cc_start: 0.9285 (mmmm) cc_final: 0.9064 (mmmm) REVERT: C 209 MET cc_start: 0.8453 (tpp) cc_final: 0.8087 (tpt) REVERT: C 288 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8152 (mt-10) REVERT: C 296 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8955 (tt) REVERT: C 332 LYS cc_start: 0.9551 (mtpp) cc_final: 0.9225 (ttpp) REVERT: C 335 ASN cc_start: 0.9349 (m-40) cc_final: 0.9038 (m110) REVERT: D 77 MET cc_start: 0.8747 (tpp) cc_final: 0.8523 (tmm) REVERT: D 128 GLN cc_start: 0.9115 (tt0) cc_final: 0.8793 (tm-30) REVERT: D 163 MET cc_start: 0.9103 (mmm) cc_final: 0.8792 (mmm) REVERT: D 183 PHE cc_start: 0.9125 (m-80) cc_final: 0.8505 (m-10) REVERT: D 185 LYS cc_start: 0.8943 (ttpp) cc_final: 0.8535 (tptt) REVERT: D 202 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.8868 (p) REVERT: D 207 LYS cc_start: 0.8848 (mmtt) cc_final: 0.7997 (tmtt) REVERT: D 211 ILE cc_start: 0.9317 (mp) cc_final: 0.8319 (mp) REVERT: D 212 SER cc_start: 0.9125 (p) cc_final: 0.8913 (p) REVERT: D 217 MET cc_start: 0.8536 (mtm) cc_final: 0.7968 (mtm) REVERT: D 218 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8876 (mm-40) REVERT: D 240 MET cc_start: 0.8061 (tmm) cc_final: 0.7218 (tmm) REVERT: D 247 ASN cc_start: 0.8127 (p0) cc_final: 0.7821 (p0) REVERT: D 262 ASP cc_start: 0.8992 (t70) cc_final: 0.8249 (t70) REVERT: D 299 GLN cc_start: 0.9641 (tt0) cc_final: 0.8857 (tm-30) REVERT: E 39 PHE cc_start: 0.9151 (t80) cc_final: 0.8783 (t80) REVERT: E 45 PHE cc_start: 0.8829 (t80) cc_final: 0.8603 (t80) REVERT: E 109 MET cc_start: 0.8366 (tpp) cc_final: 0.7765 (tpp) REVERT: E 113 MET cc_start: 0.9212 (mmt) cc_final: 0.8708 (mmp) REVERT: E 182 MET cc_start: 0.9289 (mmm) cc_final: 0.8778 (mmm) REVERT: E 234 MET cc_start: 0.9141 (mmm) cc_final: 0.8777 (mmm) REVERT: E 369 LEU cc_start: 0.9460 (tp) cc_final: 0.9215 (tp) REVERT: E 584 PHE cc_start: 0.8695 (m-10) cc_final: 0.8344 (m-80) REVERT: E 711 MET cc_start: 0.8894 (mmm) cc_final: 0.8559 (mpp) REVERT: E 1021 LEU cc_start: 0.9648 (mm) cc_final: 0.9392 (pp) REVERT: E 1252 MET cc_start: 0.9195 (mmm) cc_final: 0.8937 (mmm) REVERT: E 1298 MET cc_start: 0.9060 (ttt) cc_final: 0.8508 (tmm) REVERT: E 1301 ASN cc_start: 0.9260 (m-40) cc_final: 0.8809 (m-40) REVERT: E 1514 MET cc_start: 0.9041 (mtm) cc_final: 0.8805 (mtm) outliers start: 84 outliers final: 49 residues processed: 443 average time/residue: 0.1380 time to fit residues: 98.1788 Evaluate side-chains 399 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 345 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain 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 175 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 1078 LEU Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1130 ASN Chi-restraints excluded: chain E residue 1161 THR 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: chunk 236 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 251 optimal weight: 8.9990 chunk 245 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 97 HIS A 128 GLN ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 160 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS ** E 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1346 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 = 0.3091 r_free = 0.3091 target = 0.055152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.045592 restraints weight = 111064.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.047077 restraints weight = 58260.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.048094 restraints weight = 37377.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.048815 restraints weight = 27266.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.049321 restraints weight = 21551.461| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.189 21446 Z= 0.257 Angle : 0.850 58.578 29149 Z= 0.432 Chirality : 0.047 0.335 3454 Planarity : 0.004 0.055 3624 Dihedral : 6.620 129.271 2905 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Rotamer: Outliers : 5.36 % Allowed : 22.03 % Favored : 72.60 % 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: -0.30 (0.16), residues: 2650 helix: 0.64 (0.14), residues: 1340 sheet: -0.48 (0.30), residues: 299 loop : -1.17 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 192 TYR 0.022 0.002 TYR E1004 PHE 0.027 0.002 PHE C 86 TRP 0.017 0.002 TRP E1247 HIS 0.010 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00550 (21440) covalent geometry : angle 0.75997 (29139) SS BOND : bond 0.00558 ( 5) SS BOND : angle 20.51537 ( 10) hydrogen bonds : bond 0.04579 ( 1092) hydrogen bonds : angle 4.61608 ( 3246) Misc. bond : bond 0.00111 ( 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 456 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 334 time to evaluate : 0.756 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 43 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8089 (t0) REVERT: A 66 LEU cc_start: 0.9407 (mt) cc_final: 0.9174 (mt) REVERT: A 77 MET cc_start: 0.8717 (tpp) cc_final: 0.7994 (tmm) REVERT: A 137 MET cc_start: 0.8667 (ptt) cc_final: 0.8324 (ptp) REVERT: A 170 LYS cc_start: 0.8818 (tptp) cc_final: 0.8505 (tppt) REVERT: A 208 SER cc_start: 0.8943 (p) cc_final: 0.8628 (p) REVERT: A 209 MET cc_start: 0.8280 (mmp) cc_final: 0.7389 (mmp) REVERT: A 211 ILE cc_start: 0.9519 (OUTLIER) cc_final: 0.9261 (mp) REVERT: A 234 HIS cc_start: 0.8270 (t-170) cc_final: 0.7912 (t-90) REVERT: A 279 GLN cc_start: 0.8920 (tp40) cc_final: 0.8278 (tm-30) REVERT: A 288 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7882 (tt0) REVERT: A 292 GLU cc_start: 0.8389 (pt0) cc_final: 0.7454 (pt0) REVERT: A 313 GLN cc_start: 0.8235 (mt0) cc_final: 0.7584 (mp10) REVERT: A 332 LYS cc_start: 0.9429 (mttt) cc_final: 0.9173 (mttp) REVERT: B 43 ASN cc_start: 0.8741 (m110) cc_final: 0.5932 (p0) REVERT: B 88 MET cc_start: 0.9023 (ttm) cc_final: 0.8752 (ttm) REVERT: B 129 VAL cc_start: 0.9353 (OUTLIER) cc_final: 0.9130 (p) REVERT: B 169 MET cc_start: 0.9067 (mmm) cc_final: 0.8615 (ttm) REVERT: B 170 LYS cc_start: 0.9160 (tptp) cc_final: 0.8848 (tptm) REVERT: B 211 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8618 (mp) REVERT: B 288 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8342 (mt-10) REVERT: B 296 ILE cc_start: 0.8825 (mp) cc_final: 0.8512 (pt) REVERT: B 305 LEU cc_start: 0.9091 (mt) cc_final: 0.8588 (mt) REVERT: B 330 TYR cc_start: 0.8786 (m-80) cc_final: 0.8445 (m-80) REVERT: B 332 LYS cc_start: 0.9288 (mppt) cc_final: 0.8876 (mptt) REVERT: C 39 LYS cc_start: 0.9388 (mmtt) cc_final: 0.9018 (mmmt) REVERT: C 296 ILE cc_start: 0.9441 (mt) cc_final: 0.9122 (tt) REVERT: C 326 TYR cc_start: 0.8673 (m-80) cc_final: 0.7447 (m-80) REVERT: C 332 LYS cc_start: 0.9673 (mtpp) cc_final: 0.9338 (ttpp) REVERT: D 77 MET cc_start: 0.8874 (tpp) cc_final: 0.8527 (tmm) REVERT: D 86 PHE cc_start: 0.9074 (m-80) cc_final: 0.8667 (m-10) REVERT: D 183 PHE cc_start: 0.9104 (m-80) cc_final: 0.8490 (m-10) REVERT: D 185 LYS cc_start: 0.9125 (ttpp) cc_final: 0.8779 (tptt) REVERT: D 202 VAL cc_start: 0.9304 (OUTLIER) cc_final: 0.8932 (p) REVERT: D 207 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8761 (mmtt) REVERT: D 240 MET cc_start: 0.8097 (tmm) cc_final: 0.7249 (tmm) REVERT: D 247 ASN cc_start: 0.8298 (p0) cc_final: 0.7923 (p0) REVERT: E 39 PHE cc_start: 0.9263 (t80) cc_final: 0.8875 (t80) REVERT: E 109 MET cc_start: 0.8552 (tpp) cc_final: 0.8177 (tpp) REVERT: E 113 MET cc_start: 0.9201 (mmt) cc_final: 0.8829 (mmp) REVERT: E 182 MET cc_start: 0.9324 (mmm) cc_final: 0.8925 (mmm) REVERT: E 234 MET cc_start: 0.9255 (mmm) cc_final: 0.9003 (mmm) REVERT: E 364 PHE cc_start: 0.9051 (t80) cc_final: 0.8837 (t80) REVERT: E 369 LEU cc_start: 0.9498 (tp) cc_final: 0.9266 (tp) REVERT: E 584 PHE cc_start: 0.8613 (m-10) cc_final: 0.8203 (m-80) REVERT: E 711 MET cc_start: 0.8837 (mmm) cc_final: 0.8586 (mpp) REVERT: E 801 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8711 (ptp) REVERT: E 1016 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9146 (tt) REVERT: E 1021 LEU cc_start: 0.9654 (mm) cc_final: 0.9378 (pp) REVERT: E 1252 MET cc_start: 0.9174 (mmm) cc_final: 0.8865 (mmm) REVERT: E 1289 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9116 (tt) REVERT: E 1295 LEU cc_start: 0.9685 (tp) cc_final: 0.9473 (tt) REVERT: E 1298 MET cc_start: 0.9076 (ttt) cc_final: 0.8600 (tmm) REVERT: E 1301 ASN cc_start: 0.9251 (m-40) cc_final: 0.8832 (m-40) REVERT: E 1525 MET cc_start: 0.9220 (mmm) cc_final: 0.8835 (mmm) outliers start: 122 outliers final: 70 residues processed: 423 average time/residue: 0.1367 time to fit residues: 92.9575 Evaluate side-chains 387 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 309 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 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 291 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 801 MET Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 907 THR Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1039 ASP Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1130 ASN Chi-restraints excluded: chain E residue 1161 THR Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1289 LEU Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 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: chunk 90 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 201 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 123 optimal weight: 0.4980 chunk 179 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 186 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.058022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.048230 restraints weight = 108224.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.049772 restraints weight = 56893.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.050821 restraints weight = 36475.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.051547 restraints weight = 26563.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.052056 restraints weight = 21084.516| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.194 21446 Z= 0.144 Angle : 0.814 58.423 29149 Z= 0.398 Chirality : 0.047 0.354 3454 Planarity : 0.004 0.054 3624 Dihedral : 6.402 133.060 2901 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 4.57 % Allowed : 23.18 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.16), residues: 2650 helix: 0.88 (0.14), residues: 1339 sheet: -0.40 (0.30), residues: 295 loop : -1.02 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1251 TYR 0.017 0.001 TYR E1004 PHE 0.026 0.001 PHE E1164 TRP 0.029 0.001 TRP E 52 HIS 0.008 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00329 (21440) covalent geometry : angle 0.72007 (29139) SS BOND : bond 0.00510 ( 5) SS BOND : angle 20.45333 ( 10) hydrogen bonds : bond 0.04340 ( 1092) hydrogen bonds : angle 4.35325 ( 3246) Misc. bond : bond 0.00069 ( 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 458 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 354 time to evaluate : 0.900 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 47 LYS cc_start: 0.9410 (mmmt) cc_final: 0.9141 (mmmt) REVERT: A 66 LEU cc_start: 0.9366 (mt) cc_final: 0.9165 (mp) REVERT: A 77 MET cc_start: 0.8739 (tpp) cc_final: 0.7861 (tmm) REVERT: A 137 MET cc_start: 0.8438 (ptt) cc_final: 0.8200 (ptp) REVERT: A 170 LYS cc_start: 0.8769 (tptp) cc_final: 0.8453 (tppt) REVERT: A 175 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.8220 (p-80) REVERT: A 209 MET cc_start: 0.8295 (mmp) cc_final: 0.7660 (mmp) REVERT: A 234 HIS cc_start: 0.8271 (t-170) cc_final: 0.7905 (t-90) REVERT: A 279 GLN cc_start: 0.8828 (tp40) cc_final: 0.8380 (tm-30) REVERT: A 332 LYS cc_start: 0.9416 (mttt) cc_final: 0.9159 (mttm) REVERT: B 63 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9432 (pp) REVERT: B 88 MET cc_start: 0.9035 (ttm) cc_final: 0.8766 (ttm) REVERT: B 129 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.9001 (p) REVERT: B 169 MET cc_start: 0.9066 (mmm) cc_final: 0.8604 (ttm) REVERT: B 170 LYS cc_start: 0.9129 (tptp) cc_final: 0.8828 (tptm) REVERT: B 305 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8620 (mt) REVERT: B 330 TYR cc_start: 0.8700 (m-80) cc_final: 0.8369 (m-80) REVERT: C 39 LYS cc_start: 0.9394 (mmtt) cc_final: 0.9063 (mppt) REVERT: C 147 LEU cc_start: 0.9585 (tt) cc_final: 0.9299 (mm) REVERT: C 209 MET cc_start: 0.8464 (tpp) cc_final: 0.8024 (tpt) REVERT: C 296 ILE cc_start: 0.9335 (mt) cc_final: 0.8948 (tt) REVERT: C 332 LYS cc_start: 0.9603 (mtpp) cc_final: 0.9119 (ttpp) REVERT: C 335 ASN cc_start: 0.9369 (m-40) cc_final: 0.9123 (m110) REVERT: D 77 MET cc_start: 0.8916 (tpp) cc_final: 0.8432 (tpp) REVERT: D 86 PHE cc_start: 0.9053 (m-80) cc_final: 0.8627 (m-10) REVERT: D 183 PHE cc_start: 0.9103 (m-80) cc_final: 0.8450 (m-10) REVERT: D 185 LYS cc_start: 0.9113 (ttpp) cc_final: 0.8786 (tptt) REVERT: D 202 VAL cc_start: 0.9255 (p) cc_final: 0.8851 (p) REVERT: D 209 MET cc_start: 0.6876 (mmp) cc_final: 0.6443 (mmp) REVERT: D 240 MET cc_start: 0.7985 (tmm) cc_final: 0.7004 (tmm) REVERT: D 247 ASN cc_start: 0.8311 (p0) cc_final: 0.7916 (p0) REVERT: D 250 PHE cc_start: 0.9090 (t80) cc_final: 0.8283 (t80) REVERT: D 262 ASP cc_start: 0.8985 (t70) cc_final: 0.8503 (t0) REVERT: E 39 PHE cc_start: 0.9262 (t80) cc_final: 0.8938 (t80) REVERT: E 109 MET cc_start: 0.8528 (tpp) cc_final: 0.7934 (tpp) REVERT: E 113 MET cc_start: 0.9146 (mmt) cc_final: 0.8665 (mmp) REVERT: E 128 ILE cc_start: 0.9658 (tp) cc_final: 0.9423 (tp) REVERT: E 144 TRP cc_start: 0.9042 (m100) cc_final: 0.8352 (m100) REVERT: E 182 MET cc_start: 0.9408 (mmm) cc_final: 0.8887 (mmm) REVERT: E 369 LEU cc_start: 0.9410 (tp) cc_final: 0.9111 (tp) REVERT: E 430 MET cc_start: 0.9122 (ttp) cc_final: 0.8781 (ptm) REVERT: E 584 PHE cc_start: 0.8714 (m-10) cc_final: 0.8333 (m-80) REVERT: E 586 ILE cc_start: 0.9521 (pt) cc_final: 0.9321 (pt) REVERT: E 711 MET cc_start: 0.8871 (mmm) cc_final: 0.8618 (mpp) REVERT: E 1021 LEU cc_start: 0.9653 (mm) cc_final: 0.9371 (pp) REVERT: E 1022 LEU cc_start: 0.9407 (mt) cc_final: 0.9187 (mt) REVERT: E 1164 PHE cc_start: 0.8487 (t80) cc_final: 0.8269 (t80) REVERT: E 1252 MET cc_start: 0.9200 (mmm) cc_final: 0.8884 (mmm) REVERT: E 1289 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9134 (tt) REVERT: E 1295 LEU cc_start: 0.9673 (tp) cc_final: 0.9461 (tt) REVERT: E 1298 MET cc_start: 0.9101 (ttt) cc_final: 0.8586 (tmm) REVERT: E 1301 ASN cc_start: 0.9144 (m-40) cc_final: 0.8737 (m-40) outliers start: 104 outliers final: 58 residues processed: 430 average time/residue: 0.1354 time to fit residues: 94.0426 Evaluate side-chains 386 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 323 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain 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 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 182 ILE 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 290 VAL 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 142 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 907 THR Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1039 ASP Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1289 LEU Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 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: chunk 9 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 249 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS C 46 HIS ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS C 277 HIS ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN D 216 HIS ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN ** E 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1427 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.053126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.043923 restraints weight = 112535.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.045346 restraints weight = 59118.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.046324 restraints weight = 37922.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.046989 restraints weight = 27583.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.047465 restraints weight = 21865.205| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.188 21446 Z= 0.345 Angle : 0.935 58.582 29149 Z= 0.476 Chirality : 0.050 0.328 3454 Planarity : 0.005 0.050 3624 Dihedral : 6.651 121.918 2899 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.50 % Allowed : 23.22 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.09 (0.16), residues: 2650 helix: 0.76 (0.14), residues: 1345 sheet: -0.52 (0.30), residues: 291 loop : -0.94 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E1251 TYR 0.021 0.002 TYR E1064 PHE 0.028 0.002 PHE C 86 TRP 0.044 0.003 TRP E 52 HIS 0.007 0.002 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00728 (21440) covalent geometry : angle 0.85372 (29139) SS BOND : bond 0.00681 ( 5) SS BOND : angle 20.55269 ( 10) hydrogen bonds : bond 0.04783 ( 1092) hydrogen bonds : angle 4.88850 ( 3246) Misc. bond : bond 0.00121 ( 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 427 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 302 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8786 (tpp) cc_final: 0.7793 (tmm) REVERT: A 81 CYS cc_start: 0.8974 (p) cc_final: 0.8655 (p) REVERT: A 137 MET cc_start: 0.8736 (ptt) cc_final: 0.8382 (ptp) REVERT: A 155 VAL cc_start: 0.9753 (OUTLIER) cc_final: 0.9508 (p) REVERT: A 160 ASN cc_start: 0.9336 (m-40) cc_final: 0.9122 (m-40) REVERT: A 170 LYS cc_start: 0.8883 (tptp) cc_final: 0.8529 (tppt) REVERT: A 209 MET cc_start: 0.8326 (mmp) cc_final: 0.7775 (mmp) REVERT: A 262 ASP cc_start: 0.9304 (OUTLIER) cc_final: 0.8944 (t70) REVERT: A 279 GLN cc_start: 0.8840 (tp40) cc_final: 0.8334 (tm-30) REVERT: A 288 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7840 (tt0) REVERT: A 332 LYS cc_start: 0.9458 (mttt) cc_final: 0.9157 (mttm) REVERT: B 129 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.9116 (p) REVERT: B 169 MET cc_start: 0.8976 (mmm) cc_final: 0.8649 (ttm) REVERT: B 170 LYS cc_start: 0.9216 (tptp) cc_final: 0.8997 (tptp) REVERT: B 211 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8904 (mp) REVERT: B 305 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8652 (mt) REVERT: B 330 TYR cc_start: 0.8854 (m-80) cc_final: 0.8461 (m-80) REVERT: C 38 LYS cc_start: 0.9462 (mmmm) cc_final: 0.9235 (mmmm) REVERT: C 39 LYS cc_start: 0.9410 (mmtt) cc_final: 0.9198 (mppt) REVERT: C 47 LYS cc_start: 0.8881 (tppt) cc_final: 0.8571 (tppt) REVERT: C 185 LYS cc_start: 0.9474 (tppp) cc_final: 0.9133 (tppp) REVERT: C 296 ILE cc_start: 0.9503 (mt) cc_final: 0.9254 (tt) REVERT: C 332 LYS cc_start: 0.9650 (mtpp) cc_final: 0.9269 (mtmm) REVERT: D 77 MET cc_start: 0.8912 (tpp) cc_final: 0.8377 (tpp) REVERT: D 88 MET cc_start: 0.9080 (tpp) cc_final: 0.8855 (mmm) REVERT: D 137 MET cc_start: 0.8390 (ttp) cc_final: 0.8077 (ttp) REVERT: D 185 LYS cc_start: 0.9165 (ttpp) cc_final: 0.8853 (tptt) REVERT: D 202 VAL cc_start: 0.9329 (OUTLIER) cc_final: 0.9076 (p) REVERT: D 240 MET cc_start: 0.8309 (tmm) cc_final: 0.7585 (tmm) REVERT: D 247 ASN cc_start: 0.8597 (p0) cc_final: 0.8346 (p0) REVERT: D 262 ASP cc_start: 0.8754 (t70) cc_final: 0.8538 (t70) REVERT: E 39 PHE cc_start: 0.9296 (t80) cc_final: 0.8803 (t80) REVERT: E 43 ILE cc_start: 0.9654 (tp) cc_final: 0.9397 (pt) REVERT: E 109 MET cc_start: 0.8666 (tpp) cc_final: 0.8279 (tpp) REVERT: E 113 MET cc_start: 0.9220 (mmt) cc_final: 0.8821 (mmp) REVERT: E 128 ILE cc_start: 0.9690 (tp) cc_final: 0.9429 (tp) REVERT: E 144 TRP cc_start: 0.9178 (m100) cc_final: 0.8418 (m100) REVERT: E 182 MET cc_start: 0.9404 (mmm) cc_final: 0.8935 (mmm) REVERT: E 234 MET cc_start: 0.9470 (mmm) cc_final: 0.9162 (mmm) REVERT: E 369 LEU cc_start: 0.9436 (tp) cc_final: 0.9144 (tp) REVERT: E 401 MET cc_start: 0.8908 (tpp) cc_final: 0.8685 (mmm) REVERT: E 584 PHE cc_start: 0.8548 (m-10) cc_final: 0.8147 (m-80) REVERT: E 586 ILE cc_start: 0.9543 (pt) cc_final: 0.9338 (pt) REVERT: E 720 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.9035 (mtpp) REVERT: E 1136 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.9306 (mm) REVERT: E 1164 PHE cc_start: 0.8613 (t80) cc_final: 0.8365 (t80) REVERT: E 1252 MET cc_start: 0.9269 (mmm) cc_final: 0.9005 (mmm) REVERT: E 1295 LEU cc_start: 0.9689 (tp) cc_final: 0.9482 (tt) REVERT: E 1298 MET cc_start: 0.9091 (ttt) cc_final: 0.8621 (tmm) REVERT: E 1313 LYS cc_start: 0.9174 (tppt) cc_final: 0.8874 (tppt) outliers start: 125 outliers final: 87 residues processed: 397 average time/residue: 0.1366 time to fit residues: 86.2244 Evaluate side-chains 386 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 291 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 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 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 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 217 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ILE 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 184 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 400 ILE Chi-restraints excluded: chain E residue 408 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 907 THR Chi-restraints excluded: chain E residue 910 ARG 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 1168 LEU Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 1368 LEU Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1435 THR Chi-restraints excluded: chain E residue 1474 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 233 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 157 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 253 optimal weight: 0.0670 chunk 248 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS C 235 GLN D 160 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 933 ASN E1459 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.057886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.048506 restraints weight = 109863.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.049999 restraints weight = 57567.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.051071 restraints weight = 37259.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.051783 restraints weight = 26905.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.052222 restraints weight = 21215.731| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.196 21446 Z= 0.136 Angle : 0.836 58.374 29149 Z= 0.404 Chirality : 0.047 0.359 3454 Planarity : 0.004 0.053 3624 Dihedral : 6.259 132.536 2899 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 3.96 % Allowed : 25.24 % Favored : 70.80 % 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: 0.27 (0.16), residues: 2650 helix: 1.11 (0.14), residues: 1334 sheet: -0.45 (0.30), residues: 291 loop : -0.80 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 17 TYR 0.012 0.001 TYR E 379 PHE 0.022 0.001 PHE E 364 TRP 0.041 0.001 TRP E 52 HIS 0.007 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00309 (21440) covalent geometry : angle 0.74568 (29139) SS BOND : bond 0.00516 ( 5) SS BOND : angle 20.43986 ( 10) hydrogen bonds : bond 0.04359 ( 1092) hydrogen bonds : angle 4.35534 ( 3246) Misc. bond : bond 0.00065 ( 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 431 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 341 time to evaluate : 0.845 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 77 MET cc_start: 0.8718 (tpp) cc_final: 0.7876 (tmm) REVERT: A 160 ASN cc_start: 0.9262 (m-40) cc_final: 0.9012 (m-40) REVERT: A 170 LYS cc_start: 0.8921 (tptp) cc_final: 0.8446 (tppt) REVERT: A 209 MET cc_start: 0.8204 (mmp) cc_final: 0.7665 (mmp) REVERT: A 262 ASP cc_start: 0.9117 (OUTLIER) cc_final: 0.8420 (m-30) REVERT: A 279 GLN cc_start: 0.8675 (tp40) cc_final: 0.8282 (tm-30) REVERT: A 288 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7635 (tt0) REVERT: A 332 LYS cc_start: 0.9418 (mttt) cc_final: 0.9171 (mttp) REVERT: B 63 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9429 (pp) REVERT: B 169 MET cc_start: 0.8964 (mmm) cc_final: 0.8617 (ttm) REVERT: B 170 LYS cc_start: 0.9179 (tptp) cc_final: 0.8643 (tptm) REVERT: B 181 LEU cc_start: 0.9597 (mm) cc_final: 0.9244 (mm) REVERT: B 211 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8874 (mp) REVERT: B 305 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8669 (mt) REVERT: B 330 TYR cc_start: 0.8729 (m-80) cc_final: 0.8409 (m-80) REVERT: C 39 LYS cc_start: 0.9399 (mmtt) cc_final: 0.9148 (mppt) REVERT: C 47 LYS cc_start: 0.8911 (tppt) cc_final: 0.8470 (tppt) REVERT: C 147 LEU cc_start: 0.9555 (tt) cc_final: 0.9287 (mm) REVERT: C 163 MET cc_start: 0.9181 (mmm) cc_final: 0.8546 (mmm) REVERT: C 268 TYR cc_start: 0.9115 (t80) cc_final: 0.8618 (t80) REVERT: C 296 ILE cc_start: 0.9392 (mt) cc_final: 0.9134 (tt) REVERT: C 332 LYS cc_start: 0.9583 (mtpp) cc_final: 0.9181 (ttpp) REVERT: D 77 MET cc_start: 0.8824 (tpp) cc_final: 0.8360 (tpp) REVERT: D 217 MET cc_start: 0.8522 (mtm) cc_final: 0.8100 (mtm) REVERT: D 240 MET cc_start: 0.8126 (tmm) cc_final: 0.7612 (tmm) REVERT: D 250 PHE cc_start: 0.9075 (t80) cc_final: 0.8239 (t80) REVERT: E 43 ILE cc_start: 0.9605 (tp) cc_final: 0.9336 (pt) REVERT: E 109 MET cc_start: 0.8494 (tpp) cc_final: 0.7895 (tpp) REVERT: E 113 MET cc_start: 0.9137 (mmt) cc_final: 0.8627 (mmp) REVERT: E 144 TRP cc_start: 0.8976 (m100) cc_final: 0.8449 (m100) REVERT: E 182 MET cc_start: 0.9304 (mmm) cc_final: 0.8780 (mmm) REVERT: E 183 LEU cc_start: 0.9573 (mm) cc_final: 0.7893 (mm) REVERT: E 369 LEU cc_start: 0.9397 (tp) cc_final: 0.9063 (tp) REVERT: E 430 MET cc_start: 0.9057 (ttp) cc_final: 0.8657 (ptm) REVERT: E 584 PHE cc_start: 0.8622 (m-10) cc_final: 0.8256 (m-80) REVERT: E 1021 LEU cc_start: 0.9546 (mm) cc_final: 0.9313 (pp) REVERT: E 1066 MET cc_start: 0.8495 (mmm) cc_final: 0.8270 (mmp) REVERT: E 1088 TRP cc_start: 0.7920 (OUTLIER) cc_final: 0.7609 (t-100) REVERT: E 1110 MET cc_start: 0.8596 (mmm) cc_final: 0.8287 (mmt) REVERT: E 1246 ARG cc_start: 0.8770 (mmp80) cc_final: 0.8312 (mmp80) REVERT: E 1252 MET cc_start: 0.9117 (mmm) cc_final: 0.8820 (mmm) REVERT: E 1298 MET cc_start: 0.9069 (ttt) cc_final: 0.8550 (tmm) REVERT: E 1301 ASN cc_start: 0.9085 (m-40) cc_final: 0.8691 (m-40) REVERT: E 1444 ARG cc_start: 0.7374 (mmp80) cc_final: 0.6942 (mmp80) REVERT: E 1514 MET cc_start: 0.8711 (mtm) cc_final: 0.8490 (mpp) outliers start: 90 outliers final: 63 residues processed: 413 average time/residue: 0.1404 time to fit residues: 93.3423 Evaluate side-chains 387 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 319 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 SER 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 63 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 77 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 291 VAL Chi-restraints excluded: chain C residue 337 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 220 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL 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 184 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 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 884 VAL Chi-restraints excluded: chain E residue 907 THR Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1039 ASP Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1088 TRP Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 1368 LEU Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1435 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 34 optimal weight: 0.3980 chunk 192 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 53 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.057834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.048508 restraints weight = 109706.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.050036 restraints weight = 58077.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.051055 restraints weight = 37243.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.051783 restraints weight = 27106.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.052311 restraints weight = 21292.847| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.196 21446 Z= 0.143 Angle : 0.829 58.358 29149 Z= 0.400 Chirality : 0.047 0.352 3454 Planarity : 0.004 0.052 3624 Dihedral : 6.039 127.273 2899 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 3.65 % Allowed : 26.03 % Favored : 70.32 % 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: 0.41 (0.16), residues: 2650 helix: 1.19 (0.14), residues: 1335 sheet: -0.43 (0.31), residues: 283 loop : -0.65 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 17 TYR 0.012 0.001 TYR E 379 PHE 0.022 0.001 PHE C 86 TRP 0.035 0.001 TRP E 52 HIS 0.006 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00328 (21440) covalent geometry : angle 0.73740 (29139) SS BOND : bond 0.00554 ( 5) SS BOND : angle 20.43933 ( 10) hydrogen bonds : bond 0.04251 ( 1092) hydrogen bonds : angle 4.33302 ( 3246) Misc. bond : bond 0.00069 ( 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 414 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 331 time to evaluate : 0.794 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 77 MET cc_start: 0.8574 (tpp) cc_final: 0.7868 (tmm) REVERT: A 160 ASN cc_start: 0.9212 (m-40) cc_final: 0.8990 (m-40) REVERT: A 170 LYS cc_start: 0.8908 (tptp) cc_final: 0.8437 (tppt) REVERT: A 209 MET cc_start: 0.8249 (mmp) cc_final: 0.7704 (mmp) REVERT: A 262 ASP cc_start: 0.9066 (OUTLIER) cc_final: 0.8358 (m-30) REVERT: A 279 GLN cc_start: 0.8698 (tp40) cc_final: 0.8307 (tm-30) REVERT: A 288 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7725 (tt0) REVERT: A 332 LYS cc_start: 0.9426 (mttt) cc_final: 0.9179 (mttp) REVERT: B 63 LEU cc_start: 0.9665 (OUTLIER) cc_final: 0.9430 (pp) REVERT: B 169 MET cc_start: 0.8957 (mmm) cc_final: 0.8601 (ttm) REVERT: B 170 LYS cc_start: 0.9177 (tptp) cc_final: 0.8634 (tptm) REVERT: B 181 LEU cc_start: 0.9594 (mm) cc_final: 0.9256 (mm) REVERT: B 288 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7969 (mt-10) REVERT: B 305 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8780 (mt) REVERT: B 330 TYR cc_start: 0.8688 (m-80) cc_final: 0.8455 (m-80) REVERT: B 332 LYS cc_start: 0.9296 (mppt) cc_final: 0.8860 (mptt) REVERT: C 38 LYS cc_start: 0.9442 (mmmm) cc_final: 0.9193 (mmmm) REVERT: C 39 LYS cc_start: 0.9434 (mmtt) cc_final: 0.9121 (mppt) REVERT: C 47 LYS cc_start: 0.8891 (tppt) cc_final: 0.8485 (tppt) REVERT: C 147 LEU cc_start: 0.9572 (tt) cc_final: 0.9268 (mm) REVERT: C 163 MET cc_start: 0.9203 (mmm) cc_final: 0.8510 (mmm) REVERT: C 268 TYR cc_start: 0.9129 (t80) cc_final: 0.8666 (t80) REVERT: C 296 ILE cc_start: 0.9380 (mt) cc_final: 0.9019 (tt) REVERT: C 332 LYS cc_start: 0.9564 (mtpp) cc_final: 0.9147 (mtmm) REVERT: D 77 MET cc_start: 0.8853 (tpp) cc_final: 0.8372 (tpp) REVERT: D 185 LYS cc_start: 0.9097 (ttpp) cc_final: 0.8842 (tptt) REVERT: D 240 MET cc_start: 0.8002 (tmm) cc_final: 0.7212 (tmm) REVERT: D 247 ASN cc_start: 0.8251 (p0) cc_final: 0.7638 (p0) REVERT: D 250 PHE cc_start: 0.9173 (t80) cc_final: 0.8224 (t80) REVERT: E 42 PHE cc_start: 0.8702 (m-80) cc_final: 0.8479 (t80) REVERT: E 43 ILE cc_start: 0.9577 (tp) cc_final: 0.9279 (pt) REVERT: E 89 GLU cc_start: 0.9134 (tp30) cc_final: 0.8607 (tm-30) REVERT: E 109 MET cc_start: 0.8499 (tpp) cc_final: 0.7958 (tpp) REVERT: E 113 MET cc_start: 0.9147 (mmt) cc_final: 0.8676 (mmm) REVERT: E 144 TRP cc_start: 0.8989 (m100) cc_final: 0.8375 (m100) REVERT: E 182 MET cc_start: 0.9248 (mmm) cc_final: 0.8726 (mmm) REVERT: E 183 LEU cc_start: 0.9590 (mm) cc_final: 0.7988 (mm) REVERT: E 369 LEU cc_start: 0.9391 (tp) cc_final: 0.9060 (tp) REVERT: E 430 MET cc_start: 0.9041 (ttp) cc_final: 0.8662 (ptm) REVERT: E 584 PHE cc_start: 0.8556 (m-10) cc_final: 0.8175 (m-80) REVERT: E 1066 MET cc_start: 0.8392 (mmm) cc_final: 0.8165 (mmp) REVERT: E 1088 TRP cc_start: 0.7951 (OUTLIER) cc_final: 0.7688 (t-100) REVERT: E 1110 MET cc_start: 0.8556 (mmm) cc_final: 0.8275 (mmt) REVERT: E 1228 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9101 (mp) REVERT: E 1246 ARG cc_start: 0.8815 (mmp80) cc_final: 0.8368 (mmp80) REVERT: E 1252 MET cc_start: 0.9085 (mmm) cc_final: 0.8859 (mmm) REVERT: E 1261 LEU cc_start: 0.9567 (tp) cc_final: 0.9113 (mt) REVERT: E 1298 MET cc_start: 0.9086 (ttt) cc_final: 0.8270 (tmm) REVERT: E 1301 ASN cc_start: 0.9118 (m-40) cc_final: 0.8722 (m-40) REVERT: E 1313 LYS cc_start: 0.9046 (tppt) cc_final: 0.8759 (tppt) REVERT: E 1444 ARG cc_start: 0.7396 (mmp80) cc_final: 0.7024 (mmp80) REVERT: E 1514 MET cc_start: 0.8707 (mtm) cc_final: 0.8500 (mpp) outliers start: 83 outliers final: 65 residues processed: 394 average time/residue: 0.1460 time to fit residues: 91.6885 Evaluate side-chains 389 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 319 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 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 208 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain 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 220 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 556 VAL Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1039 ASP Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1088 TRP Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1171 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1228 LEU 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 1425 ILE Chi-restraints excluded: chain E residue 1435 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 106 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 264 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 143 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1427 GLN E1488 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.057840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.048794 restraints weight = 109881.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.050250 restraints weight = 57558.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.051335 restraints weight = 37094.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.052044 restraints weight = 26459.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.052535 restraints weight = 20671.071| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.196 21446 Z= 0.143 Angle : 0.835 58.388 29149 Z= 0.401 Chirality : 0.047 0.360 3454 Planarity : 0.003 0.052 3624 Dihedral : 5.962 127.700 2899 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 3.47 % Allowed : 26.52 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.16), residues: 2650 helix: 1.24 (0.14), residues: 1328 sheet: -0.35 (0.31), residues: 283 loop : -0.56 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 50 TYR 0.012 0.001 TYR E 379 PHE 0.020 0.001 PHE C 86 TRP 0.032 0.001 TRP E 52 HIS 0.007 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00330 (21440) covalent geometry : angle 0.74482 (29139) SS BOND : bond 0.00535 ( 5) SS BOND : angle 20.44212 ( 10) hydrogen bonds : bond 0.04184 ( 1092) hydrogen bonds : angle 4.32685 ( 3246) Misc. bond : bond 0.00061 ( 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 419 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 340 time to evaluate : 0.852 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 47 LYS cc_start: 0.9477 (mmmt) cc_final: 0.9244 (mmmt) REVERT: A 77 MET cc_start: 0.8576 (tpp) cc_final: 0.7852 (tmm) REVERT: A 160 ASN cc_start: 0.9231 (m-40) cc_final: 0.8979 (m-40) REVERT: A 170 LYS cc_start: 0.8855 (tptp) cc_final: 0.8450 (tppt) REVERT: A 209 MET cc_start: 0.8234 (mmp) cc_final: 0.7686 (mmp) REVERT: A 262 ASP cc_start: 0.9076 (OUTLIER) cc_final: 0.8438 (m-30) REVERT: A 279 GLN cc_start: 0.8678 (tp40) cc_final: 0.8326 (tm-30) REVERT: A 288 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7662 (tt0) REVERT: A 332 LYS cc_start: 0.9435 (mttt) cc_final: 0.9192 (mttp) REVERT: B 63 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9423 (pp) REVERT: B 169 MET cc_start: 0.8852 (mmm) cc_final: 0.8534 (ttm) REVERT: B 170 LYS cc_start: 0.9180 (tptp) cc_final: 0.8622 (tptm) REVERT: B 181 LEU cc_start: 0.9576 (mm) cc_final: 0.9223 (mm) REVERT: B 288 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7906 (mt-10) REVERT: B 305 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8729 (mt) REVERT: B 332 LYS cc_start: 0.9258 (mppt) cc_final: 0.8832 (mptt) REVERT: C 39 LYS cc_start: 0.9424 (mmtt) cc_final: 0.9136 (mppt) REVERT: C 47 LYS cc_start: 0.8796 (tppt) cc_final: 0.8371 (tppt) REVERT: C 147 LEU cc_start: 0.9574 (tt) cc_final: 0.9269 (mm) REVERT: C 163 MET cc_start: 0.9195 (mmm) cc_final: 0.8580 (mmm) REVERT: C 185 LYS cc_start: 0.9415 (tppp) cc_final: 0.8993 (tppp) REVERT: C 235 GLN cc_start: 0.8812 (mt0) cc_final: 0.8054 (mt0) REVERT: C 268 TYR cc_start: 0.9111 (t80) cc_final: 0.8658 (t80) REVERT: C 296 ILE cc_start: 0.9393 (mt) cc_final: 0.8994 (tt) REVERT: C 332 LYS cc_start: 0.9482 (mtpp) cc_final: 0.9112 (mtmm) REVERT: D 77 MET cc_start: 0.8870 (tpp) cc_final: 0.8369 (tpp) REVERT: D 126 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8304 (mm-30) REVERT: D 185 LYS cc_start: 0.9063 (ttpp) cc_final: 0.8840 (tptt) REVERT: D 240 MET cc_start: 0.7962 (tmm) cc_final: 0.7189 (tmm) REVERT: D 247 ASN cc_start: 0.8102 (p0) cc_final: 0.7480 (p0) REVERT: D 250 PHE cc_start: 0.9093 (t80) cc_final: 0.7813 (t80) REVERT: E 39 PHE cc_start: 0.9208 (t80) cc_final: 0.8730 (t80) REVERT: E 42 PHE cc_start: 0.8659 (m-80) cc_final: 0.8366 (t80) REVERT: E 43 ILE cc_start: 0.9591 (tp) cc_final: 0.9231 (pt) REVERT: E 109 MET cc_start: 0.8584 (tpp) cc_final: 0.7983 (tpp) REVERT: E 113 MET cc_start: 0.9140 (mmt) cc_final: 0.8682 (mmm) REVERT: E 144 TRP cc_start: 0.9019 (m100) cc_final: 0.8416 (m100) REVERT: E 182 MET cc_start: 0.9021 (mmm) cc_final: 0.8630 (mmm) REVERT: E 183 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.7721 (mm) REVERT: E 369 LEU cc_start: 0.9390 (tp) cc_final: 0.9061 (tp) REVERT: E 430 MET cc_start: 0.9012 (ttp) cc_final: 0.8631 (ptm) REVERT: E 453 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9393 (mm) REVERT: E 584 PHE cc_start: 0.8501 (m-10) cc_final: 0.8223 (m-80) REVERT: E 586 ILE cc_start: 0.9499 (pt) cc_final: 0.9252 (pt) REVERT: E 711 MET cc_start: 0.8899 (mmm) cc_final: 0.8693 (mpp) REVERT: E 1066 MET cc_start: 0.8352 (mmm) cc_final: 0.8125 (mmp) REVERT: E 1088 TRP cc_start: 0.7922 (OUTLIER) cc_final: 0.7681 (t-100) REVERT: E 1110 MET cc_start: 0.8534 (mmm) cc_final: 0.8265 (mmt) REVERT: E 1228 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9096 (mp) REVERT: E 1246 ARG cc_start: 0.8839 (mmp80) cc_final: 0.8411 (mmp80) REVERT: E 1252 MET cc_start: 0.9061 (mmm) cc_final: 0.8836 (mmm) REVERT: E 1261 LEU cc_start: 0.9566 (tp) cc_final: 0.9149 (mt) REVERT: E 1298 MET cc_start: 0.9071 (ttt) cc_final: 0.8265 (tmm) REVERT: E 1301 ASN cc_start: 0.9128 (m-40) cc_final: 0.8733 (m-40) REVERT: E 1313 LYS cc_start: 0.8993 (tppt) cc_final: 0.8714 (tppt) REVERT: E 1444 ARG cc_start: 0.7410 (mmp80) cc_final: 0.7094 (mmp80) outliers start: 79 outliers final: 65 residues processed: 404 average time/residue: 0.1470 time to fit residues: 94.4373 Evaluate side-chains 395 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 323 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 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 208 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 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 138 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 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 884 VAL Chi-restraints excluded: chain E residue 907 THR Chi-restraints excluded: chain E residue 1039 ASP Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1088 TRP Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 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 1283 LEU Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 1368 LEU Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1435 THR Chi-restraints excluded: chain E residue 1474 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 2 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 240 optimal weight: 3.9990 chunk 88 optimal weight: 0.0670 chunk 155 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 130 optimal weight: 0.5980 chunk 134 optimal weight: 0.3980 chunk 257 optimal weight: 0.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN D 160 ASN D 242 ASN E 127 ASN E 846 GLN E 867 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.059516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.050296 restraints weight = 109810.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.051814 restraints weight = 57258.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.052881 restraints weight = 36527.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.053608 restraints weight = 26252.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.054094 restraints weight = 20542.727| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.196 21446 Z= 0.134 Angle : 0.847 58.367 29149 Z= 0.404 Chirality : 0.048 0.358 3454 Planarity : 0.003 0.053 3624 Dihedral : 5.905 128.639 2899 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 3.12 % Allowed : 27.18 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.16), residues: 2650 helix: 1.24 (0.14), residues: 1341 sheet: -0.24 (0.30), residues: 291 loop : -0.59 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 17 TYR 0.021 0.001 TYR E 397 PHE 0.019 0.001 PHE C 86 TRP 0.033 0.001 TRP E 52 HIS 0.007 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00307 (21440) covalent geometry : angle 0.75761 (29139) SS BOND : bond 0.00513 ( 5) SS BOND : angle 20.43514 ( 10) hydrogen bonds : bond 0.04154 ( 1092) hydrogen bonds : angle 4.29131 ( 3246) Misc. bond : bond 0.00055 ( 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 422 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 351 time to evaluate : 0.796 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: 0.9396 (mmmt) cc_final: 0.9005 (mmmt) REVERT: A 77 MET cc_start: 0.8499 (tpp) cc_final: 0.7714 (tmm) REVERT: A 88 MET cc_start: 0.8558 (mtt) cc_final: 0.8299 (mtt) REVERT: A 170 LYS cc_start: 0.8917 (tptp) cc_final: 0.8435 (tppt) REVERT: A 262 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8460 (m-30) REVERT: A 279 GLN cc_start: 0.8694 (tp40) cc_final: 0.8364 (tm-30) REVERT: A 288 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7647 (tt0) REVERT: A 332 LYS cc_start: 0.9449 (mttt) cc_final: 0.9193 (mttp) REVERT: B 43 ASN cc_start: 0.8349 (m110) cc_final: 0.8083 (m-40) REVERT: B 169 MET cc_start: 0.8833 (mmm) cc_final: 0.8528 (ttm) REVERT: B 170 LYS cc_start: 0.9155 (tptp) cc_final: 0.8589 (tptm) REVERT: B 181 LEU cc_start: 0.9584 (mm) cc_final: 0.9244 (mm) REVERT: B 288 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7839 (mt-10) REVERT: B 305 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8767 (mt) REVERT: C 39 LYS cc_start: 0.9347 (mmtt) cc_final: 0.9021 (mppt) REVERT: C 47 LYS cc_start: 0.8795 (tppt) cc_final: 0.8331 (tppt) REVERT: C 147 LEU cc_start: 0.9563 (tt) cc_final: 0.9320 (mm) REVERT: C 163 MET cc_start: 0.9192 (mmm) cc_final: 0.8592 (mmm) REVERT: C 185 LYS cc_start: 0.9427 (tppp) cc_final: 0.9005 (tppp) REVERT: C 211 ILE cc_start: 0.9437 (mp) cc_final: 0.9038 (mp) REVERT: C 235 GLN cc_start: 0.8817 (mt0) cc_final: 0.7992 (mt0) REVERT: C 268 TYR cc_start: 0.9085 (t80) cc_final: 0.7361 (t80) REVERT: C 296 ILE cc_start: 0.9351 (mt) cc_final: 0.8954 (tt) REVERT: C 332 LYS cc_start: 0.9494 (mtpp) cc_final: 0.9156 (mtmm) REVERT: D 77 MET cc_start: 0.8857 (tpp) cc_final: 0.8395 (tpp) REVERT: D 126 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8204 (mm-30) REVERT: D 185 LYS cc_start: 0.9040 (ttpp) cc_final: 0.8799 (tptt) REVERT: D 240 MET cc_start: 0.7882 (tmm) cc_final: 0.7079 (tmm) REVERT: D 247 ASN cc_start: 0.8173 (p0) cc_final: 0.7546 (p0) REVERT: D 250 PHE cc_start: 0.9039 (t80) cc_final: 0.7851 (t80) REVERT: E 39 PHE cc_start: 0.9261 (t80) cc_final: 0.8898 (t80) REVERT: E 42 PHE cc_start: 0.8532 (m-80) cc_final: 0.8276 (t80) REVERT: E 109 MET cc_start: 0.8554 (tpp) cc_final: 0.8072 (tpp) REVERT: E 113 MET cc_start: 0.9132 (mmt) cc_final: 0.8734 (mmp) REVERT: E 144 TRP cc_start: 0.8979 (m100) cc_final: 0.8458 (m100) REVERT: E 182 MET cc_start: 0.8995 (mmm) cc_final: 0.8602 (mmm) REVERT: E 183 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.7662 (mm) REVERT: E 190 VAL cc_start: 0.8810 (p) cc_final: 0.8595 (p) REVERT: E 369 LEU cc_start: 0.9380 (tp) cc_final: 0.8966 (tp) REVERT: E 430 MET cc_start: 0.9004 (ttp) cc_final: 0.8589 (ptm) REVERT: E 453 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9371 (mm) REVERT: E 584 PHE cc_start: 0.8510 (m-10) cc_final: 0.8188 (m-80) REVERT: E 711 MET cc_start: 0.8890 (mmm) cc_final: 0.8654 (mpp) REVERT: E 801 MET cc_start: 0.8650 (ptp) cc_final: 0.8328 (ptp) REVERT: E 1066 MET cc_start: 0.8347 (mmm) cc_final: 0.8126 (mmp) REVERT: E 1088 TRP cc_start: 0.7849 (OUTLIER) cc_final: 0.7644 (t-100) REVERT: E 1110 MET cc_start: 0.8490 (mmm) cc_final: 0.8232 (mmt) REVERT: E 1228 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9073 (mp) REVERT: E 1246 ARG cc_start: 0.8833 (mmp80) cc_final: 0.8382 (mmp80) REVERT: E 1252 MET cc_start: 0.9026 (mmm) cc_final: 0.8796 (mmm) REVERT: E 1261 LEU cc_start: 0.9572 (tp) cc_final: 0.9144 (mt) REVERT: E 1298 MET cc_start: 0.9039 (ttt) cc_final: 0.8220 (tmm) REVERT: E 1301 ASN cc_start: 0.9142 (m-40) cc_final: 0.8699 (m-40) REVERT: E 1313 LYS cc_start: 0.8927 (tppt) cc_final: 0.8694 (tppt) REVERT: E 1444 ARG cc_start: 0.7295 (mmp80) cc_final: 0.7085 (mmp80) REVERT: E 1514 MET cc_start: 0.8564 (mpp) cc_final: 0.8198 (mmp) outliers start: 71 outliers final: 56 residues processed: 405 average time/residue: 0.1417 time to fit residues: 91.7589 Evaluate side-chains 393 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 331 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 319 VAL 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 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 138 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 534 LEU Chi-restraints excluded: chain E residue 770 VAL Chi-restraints excluded: chain E residue 884 VAL Chi-restraints excluded: chain E residue 1039 ASP Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1088 TRP Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1171 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1253 GLU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1307 LEU Chi-restraints excluded: chain E residue 1368 LEU Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1474 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 64 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 207 optimal weight: 0.0670 chunk 104 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 231 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 218 optimal weight: 0.7980 chunk 221 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.059645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.050433 restraints weight = 109814.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.051964 restraints weight = 57865.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.052996 restraints weight = 36866.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.053752 restraints weight = 26580.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.054284 restraints weight = 20747.937| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.196 21446 Z= 0.136 Angle : 0.865 58.380 29149 Z= 0.411 Chirality : 0.048 0.357 3454 Planarity : 0.004 0.053 3624 Dihedral : 5.853 127.121 2899 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 3.25 % Allowed : 27.62 % Favored : 69.13 % 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: 0.55 (0.17), residues: 2650 helix: 1.25 (0.14), residues: 1341 sheet: -0.21 (0.32), residues: 283 loop : -0.58 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 17 TYR 0.017 0.001 TYR E1004 PHE 0.036 0.001 PHE D 183 TRP 0.030 0.001 TRP E 52 HIS 0.007 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00314 (21440) covalent geometry : angle 0.77798 (29139) SS BOND : bond 0.00514 ( 5) SS BOND : angle 20.43718 ( 10) hydrogen bonds : bond 0.04107 ( 1092) hydrogen bonds : angle 4.33344 ( 3246) Misc. bond : bond 0.00054 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3402.00 seconds wall clock time: 59 minutes 58.26 seconds (3598.26 seconds total)