Starting phenix.real_space_refine on Sat Aug 23 03:43:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubr_42101/08_2025/8ubr_42101.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubr_42101/08_2025/8ubr_42101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ubr_42101/08_2025/8ubr_42101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubr_42101/08_2025/8ubr_42101.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubr_42101/08_2025/8ubr_42101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubr_42101/08_2025/8ubr_42101.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 49 5.16 5 C 6180 2.51 5 N 1547 2.21 5 O 1653 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9440 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1156, 9265 Classifications: {'peptide': 1156} Link IDs: {'PTRANS': 30, 'TRANS': 1125} Chain breaks: 6 Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 175 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 2, 'LBN': 2, 'WG5': 1} Classifications: {'undetermined': 9, 'water': 4} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'LBN:plan-1': 2, 'LBN:plan-2': 2, 'LBN:plan-3': 2} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 2.80, per 1000 atoms: 0.30 Number of scatterers: 9440 At special positions: 0 Unit cell: (75.712, 87.204, 142.636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 49 16.00 P 6 15.00 Mg 2 11.99 F 3 9.00 O 1653 8.00 N 1547 7.00 C 6180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 328.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 71.5% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.611A pdb=" N ALA A 9 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 16 Processing helix chain 'A' and resid 17 through 19 No H-bonds generated for 'chain 'A' and resid 17 through 19' Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 45 through 64 Processing helix chain 'A' and resid 68 through 109 removed outlier: 3.931A pdb=" N ALA A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Proline residue: A 99 - end of helix Processing helix chain 'A' and resid 119 through 165 removed outlier: 3.737A pdb=" N PHE A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 132 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.539A pdb=" N LEU A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.718A pdb=" N ASP A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.602A pdb=" N LEU A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.871A pdb=" N GLU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 199 through 220 Proline residue: A 205 - end of helix removed outlier: 4.032A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 268 removed outlier: 4.453A pdb=" N GLY A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 277 through 308 removed outlier: 3.736A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.532A pdb=" N PHE A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 329 removed outlier: 3.612A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.515A pdb=" N ILE A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 376 removed outlier: 3.575A pdb=" N TRP A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 473 Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 526 through 533 removed outlier: 3.950A pdb=" N LYS A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 538 Processing helix chain 'A' and resid 549 through 564 Processing helix chain 'A' and resid 579 through 591 Processing helix chain 'A' and resid 606 through 612 removed outlier: 3.907A pdb=" N LYS A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 846 through 854 Processing helix chain 'A' and resid 856 through 886 removed outlier: 3.778A pdb=" N ILE A 860 " --> pdb=" O HIS A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 922 removed outlier: 4.038A pdb=" N TYR A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 927 Processing helix chain 'A' and resid 934 through 959 Processing helix chain 'A' and resid 960 through 965 Processing helix chain 'A' and resid 968 through 985 removed outlier: 3.723A pdb=" N ASP A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1012 removed outlier: 4.447A pdb=" N LEU A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A1010 " --> pdb=" O ALA A1006 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1047 removed outlier: 4.048A pdb=" N PHE A1016 " --> pdb=" O GLN A1012 " (cutoff:3.500A) Proline residue: A1021 - end of helix removed outlier: 3.877A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 Processing helix chain 'A' and resid 1061 through 1069 Processing helix chain 'A' and resid 1070 through 1121 removed outlier: 4.018A pdb=" N ASN A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1168 removed outlier: 3.962A pdb=" N ARG A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1259 removed outlier: 3.608A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1284 Processing helix chain 'A' and resid 1300 through 1305 Processing helix chain 'A' and resid 1311 through 1322 Processing helix chain 'A' and resid 1324 through 1329 Processing helix chain 'A' and resid 1347 through 1362 Processing helix chain 'A' and resid 1377 through 1391 removed outlier: 4.535A pdb=" N ILE A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1410 removed outlier: 3.848A pdb=" N CYS A1410 " --> pdb=" O MET A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.633A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1441 removed outlier: 3.722A pdb=" N ARG A1438 " --> pdb=" O ARG A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1450 Processing sheet with id=AA1, first strand: chain 'A' and resid 441 through 448 removed outlier: 6.585A pdb=" N LYS A 442 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR A 398 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE A 444 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN A 396 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 446 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N MET A 394 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LYS A 483 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASN A 396 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LYS A 481 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 488 through 491 removed outlier: 6.224A pdb=" N SER A 489 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ASP A 572 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N CYS A 491 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR A 569 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL A 603 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU A 571 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU A 454 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 500 through 501 Processing sheet with id=AA4, first strand: chain 'A' and resid 1227 through 1234 removed outlier: 5.694A pdb=" N GLU A1228 " --> pdb=" O ALA A1217 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA A1217 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE A1232 " --> pdb=" O LYS A1213 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LYS A1213 " --> pdb=" O PHE A1232 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE A1234 " --> pdb=" O THR A1211 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR A1211 " --> pdb=" O ILE A1234 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A1215 " --> pdb=" O GLU A1264 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLU A1264 " --> pdb=" O LEU A1215 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA A1217 " --> pdb=" O ASN A1262 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN A1262 " --> pdb=" O ALA A1217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1286 through 1289 removed outlier: 6.569A pdb=" N LEU A1367 " --> pdb=" O ILE A1398 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N CYS A1400 " --> pdb=" O LEU A1367 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A1369 " --> pdb=" O CYS A1400 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A1240 " --> pdb=" O LEU A1399 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1298 through 1299 585 hydrogen bonds defined for protein. 1707 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: 1.51 Time building geometry restraints manager: 1.62 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: 1592 1.32 - 1.45: 2466 1.45 - 1.57: 5490 1.57 - 1.69: 11 1.69 - 1.81: 81 Bond restraints: 9640 Sorted by residual: bond pdb=" N ILE A 488 " pdb=" CA ILE A 488 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.14e-02 7.69e+03 1.16e+01 bond pdb=" N PHE A 77 " pdb=" CA PHE A 77 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.19e-02 7.06e+03 1.12e+01 bond pdb=" N LEU A 987 " pdb=" CA LEU A 987 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.04e-02 9.25e+03 1.12e+01 bond pdb=" N VAL A1017 " pdb=" CA VAL A1017 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.09e+01 bond pdb=" N ILE A 106 " pdb=" CA ILE A 106 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.17e-02 7.31e+03 9.39e+00 ... (remaining 9635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 11799 1.31 - 2.62: 980 2.62 - 3.93: 234 3.93 - 5.24: 31 5.24 - 6.55: 8 Bond angle restraints: 13052 Sorted by residual: angle pdb=" PB ATP A1503 " pdb=" O3B ATP A1503 " pdb=" PG ATP A1503 " ideal model delta sigma weight residual 139.87 133.72 6.15 1.00e+00 1.00e+00 3.79e+01 angle pdb=" PB ATP A1502 " pdb=" O3B ATP A1502 " pdb=" PG ATP A1502 " ideal model delta sigma weight residual 139.87 135.09 4.78 1.00e+00 1.00e+00 2.29e+01 angle pdb=" N VAL A 922 " pdb=" CA VAL A 922 " pdb=" C VAL A 922 " ideal model delta sigma weight residual 112.29 108.59 3.70 9.40e-01 1.13e+00 1.55e+01 angle pdb=" O VAL A1007 " pdb=" C VAL A1007 " pdb=" N VAL A1008 " ideal model delta sigma weight residual 121.83 117.96 3.87 1.03e+00 9.43e-01 1.41e+01 angle pdb=" CA VAL A1010 " pdb=" C VAL A1010 " pdb=" O VAL A1010 " ideal model delta sigma weight residual 120.85 116.93 3.92 1.06e+00 8.90e-01 1.37e+01 ... (remaining 13047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.47: 5116 19.47 - 38.93: 558 38.93 - 58.40: 152 58.40 - 77.86: 28 77.86 - 97.33: 11 Dihedral angle restraints: 5865 sinusoidal: 2506 harmonic: 3359 Sorted by residual: dihedral pdb=" C32 LBN A1505 " pdb=" C33 LBN A1505 " pdb=" C4 LBN A1505 " pdb=" C7 LBN A1505 " ideal model delta sinusoidal sigma weight residual 179.89 -82.78 -97.33 1 3.00e+01 1.11e-03 1.20e+01 dihedral pdb=" CB GLU A1228 " pdb=" CG GLU A1228 " pdb=" CD GLU A1228 " pdb=" OE1 GLU A1228 " ideal model delta sinusoidal sigma weight residual 0.00 89.01 -89.01 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA ASP A 579 " pdb=" CB ASP A 579 " pdb=" CG ASP A 579 " pdb=" OD1 ASP A 579 " ideal model delta sinusoidal sigma weight residual -30.00 -85.48 55.48 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 5862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1206 0.062 - 0.123: 227 0.123 - 0.185: 59 0.185 - 0.246: 14 0.246 - 0.308: 1 Chirality restraints: 1507 Sorted by residual: chirality pdb=" CA ILE A 906 " pdb=" N ILE A 906 " pdb=" C ILE A 906 " pdb=" CB ILE A 906 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA LYS A 329 " pdb=" N LYS A 329 " pdb=" C LYS A 329 " pdb=" CB LYS A 329 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA CYS A1344 " pdb=" N CYS A1344 " pdb=" C CYS A1344 " pdb=" CB CYS A1344 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1504 not shown) Planarity restraints: 1574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A1009 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.52e+00 pdb=" C ALA A1009 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA A1009 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL A1010 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 WG5 A1508 " -0.029 2.00e-02 2.50e+03 1.47e-02 4.33e+00 pdb=" C12 WG5 A1508 " 0.014 2.00e-02 2.50e+03 pdb=" C13 WG5 A1508 " 0.012 2.00e-02 2.50e+03 pdb=" C14 WG5 A1508 " 0.005 2.00e-02 2.50e+03 pdb=" C15 WG5 A1508 " 0.001 2.00e-02 2.50e+03 pdb=" C16 WG5 A1508 " 0.005 2.00e-02 2.50e+03 pdb=" C17 WG5 A1508 " 0.011 2.00e-02 2.50e+03 pdb=" C18 WG5 A1508 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1007 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.15e+00 pdb=" C VAL A1007 " 0.031 2.00e-02 2.50e+03 pdb=" O VAL A1007 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A1008 " -0.010 2.00e-02 2.50e+03 ... (remaining 1571 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 13 2.49 - 3.09: 6324 3.09 - 3.69: 13741 3.69 - 4.30: 20712 4.30 - 4.90: 34105 Nonbonded interactions: 74895 Sorted by model distance: nonbonded pdb=" O3G ATP A1503 " pdb="MG MG A1509 " model vdw 1.887 2.170 nonbonded pdb="MG MG A1509 " pdb=" O HOH A1602 " model vdw 1.904 2.170 nonbonded pdb="MG MG A1509 " pdb=" O HOH A1601 " model vdw 1.926 2.170 nonbonded pdb=" OG SER A1251 " pdb="MG MG A1509 " model vdw 2.009 2.170 nonbonded pdb=" OG1 THR A 465 " pdb="MG MG A1501 " model vdw 2.045 2.170 ... (remaining 74890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 : 0.006 0.043 9640 Z= 0.418 Angle : 0.831 6.554 13052 Z= 0.566 Chirality : 0.056 0.308 1507 Planarity : 0.004 0.031 1574 Dihedral : 17.606 97.329 3693 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.10 % Allowed : 19.82 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.24), residues: 1142 helix: 1.32 (0.19), residues: 757 sheet: -1.22 (0.44), residues: 88 loop : -0.95 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 3 TYR 0.024 0.002 TYR A 38 PHE 0.019 0.002 PHE A 446 TRP 0.028 0.002 TRP A1063 HIS 0.005 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00608 ( 9640) covalent geometry : angle 0.83111 (13052) hydrogen bonds : bond 0.15416 ( 585) hydrogen bonds : angle 5.33676 ( 1707) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.225 Fit side-chains REVERT: A 536 LYS cc_start: 0.7542 (mmtt) cc_final: 0.7329 (mppt) REVERT: A 1010 VAL cc_start: 0.6843 (t) cc_final: 0.6636 (t) REVERT: A 1109 ILE cc_start: 0.7663 (mt) cc_final: 0.7325 (tt) REVERT: A 1341 ASP cc_start: 0.7051 (t0) cc_final: 0.6699 (t70) outliers start: 1 outliers final: 1 residues processed: 138 average time/residue: 0.4776 time to fit residues: 70.0966 Evaluate side-chains 108 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1166 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 HIS A1038 GLN A1224 ASN A1375 HIS A1402 HIS A1423 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.123612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.104163 restraints weight = 11808.127| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.50 r_work: 0.3057 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9640 Z= 0.220 Angle : 0.669 9.253 13052 Z= 0.357 Chirality : 0.045 0.145 1507 Planarity : 0.005 0.047 1574 Dihedral : 9.015 76.103 1491 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.93 % Allowed : 17.26 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.24), residues: 1142 helix: 1.65 (0.18), residues: 758 sheet: -0.23 (0.49), residues: 92 loop : -0.99 (0.30), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 248 TYR 0.016 0.002 TYR A 304 PHE 0.019 0.002 PHE A 446 TRP 0.011 0.002 TRP A1063 HIS 0.007 0.002 HIS A 856 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 9640) covalent geometry : angle 0.66924 (13052) hydrogen bonds : bond 0.09376 ( 585) hydrogen bonds : angle 4.56274 ( 1707) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 109 time to evaluate : 0.215 Fit side-chains REVERT: A 36 ASP cc_start: 0.7996 (m-30) cc_final: 0.7790 (m-30) REVERT: A 47 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6747 (p0) REVERT: A 279 GLU cc_start: 0.7006 (mp0) cc_final: 0.6699 (mp0) REVERT: A 442 LYS cc_start: 0.8200 (tttp) cc_final: 0.7974 (ttmt) REVERT: A 476 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: A 536 LYS cc_start: 0.7541 (mmtt) cc_final: 0.7246 (mmmm) REVERT: A 920 VAL cc_start: 0.7255 (t) cc_final: 0.6863 (p) REVERT: A 1010 VAL cc_start: 0.6710 (t) cc_final: 0.6474 (t) REVERT: A 1091 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8321 (tt) REVERT: A 1109 ILE cc_start: 0.7732 (mt) cc_final: 0.7299 (tp) REVERT: A 1137 MET cc_start: 0.7297 (tpp) cc_final: 0.7078 (mmm) REVERT: A 1165 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7985 (mmtm) REVERT: A 1309 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7957 (pt0) REVERT: A 1341 ASP cc_start: 0.7576 (t0) cc_final: 0.7102 (t70) outliers start: 50 outliers final: 15 residues processed: 149 average time/residue: 0.4329 time to fit residues: 69.0634 Evaluate side-chains 126 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1317 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 114 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 98 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A1224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109299 restraints weight = 11980.432| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.33 r_work: 0.3109 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9640 Z= 0.152 Angle : 0.518 6.316 13052 Z= 0.280 Chirality : 0.040 0.126 1507 Planarity : 0.004 0.031 1574 Dihedral : 8.469 74.332 1491 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.04 % Allowed : 18.93 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.24), residues: 1142 helix: 2.12 (0.19), residues: 758 sheet: 0.03 (0.51), residues: 92 loop : -0.93 (0.31), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 3 TYR 0.013 0.002 TYR A1073 PHE 0.013 0.002 PHE A 446 TRP 0.017 0.001 TRP A 865 HIS 0.004 0.001 HIS A 856 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9640) covalent geometry : angle 0.51756 (13052) hydrogen bonds : bond 0.07650 ( 585) hydrogen bonds : angle 4.26664 ( 1707) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 0.276 Fit side-chains REVERT: A 36 ASP cc_start: 0.7930 (m-30) cc_final: 0.7702 (m-30) REVERT: A 118 SER cc_start: 0.3365 (OUTLIER) cc_final: 0.3124 (t) REVERT: A 384 GLU cc_start: 0.3635 (OUTLIER) cc_final: 0.2890 (pm20) REVERT: A 442 LYS cc_start: 0.8216 (tttp) cc_final: 0.7651 (mmpt) REVERT: A 536 LYS cc_start: 0.7685 (mmtt) cc_final: 0.7445 (mmmm) REVERT: A 610 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8122 (mp) REVERT: A 920 VAL cc_start: 0.7326 (t) cc_final: 0.6946 (p) REVERT: A 1091 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8304 (tt) REVERT: A 1109 ILE cc_start: 0.7787 (mt) cc_final: 0.7374 (tp) REVERT: A 1137 MET cc_start: 0.7306 (tpp) cc_final: 0.7083 (tpp) REVERT: A 1165 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7830 (mmtm) REVERT: A 1309 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8019 (pt0) REVERT: A 1317 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7327 (tttp) REVERT: A 1341 ASP cc_start: 0.7614 (t0) cc_final: 0.7171 (t70) outliers start: 41 outliers final: 13 residues processed: 144 average time/residue: 0.4252 time to fit residues: 65.5848 Evaluate side-chains 121 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1317 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 5 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1224 ASN A1428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.125151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.107167 restraints weight = 12055.944| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.33 r_work: 0.3059 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9640 Z= 0.170 Angle : 0.556 6.566 13052 Z= 0.298 Chirality : 0.041 0.131 1507 Planarity : 0.004 0.033 1574 Dihedral : 8.371 74.140 1491 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.24 % Allowed : 20.12 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.24), residues: 1142 helix: 2.06 (0.19), residues: 759 sheet: 0.14 (0.51), residues: 92 loop : -0.95 (0.31), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 975 TYR 0.014 0.002 TYR A1073 PHE 0.013 0.002 PHE A 446 TRP 0.018 0.001 TRP A1063 HIS 0.005 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9640) covalent geometry : angle 0.55557 (13052) hydrogen bonds : bond 0.08155 ( 585) hydrogen bonds : angle 4.30433 ( 1707) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 101 time to evaluate : 0.226 Fit side-chains REVERT: A 36 ASP cc_start: 0.7989 (m-30) cc_final: 0.7777 (m-30) REVERT: A 47 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.6778 (p0) REVERT: A 279 GLU cc_start: 0.6979 (mp0) cc_final: 0.6666 (mp0) REVERT: A 373 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7088 (t0) REVERT: A 384 GLU cc_start: 0.3588 (OUTLIER) cc_final: 0.2841 (pm20) REVERT: A 543 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6418 (tt0) REVERT: A 610 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8142 (mp) REVERT: A 1091 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8313 (tt) REVERT: A 1109 ILE cc_start: 0.7811 (mt) cc_final: 0.7404 (tp) REVERT: A 1137 MET cc_start: 0.7354 (tpp) cc_final: 0.7105 (tpp) REVERT: A 1165 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7903 (mmtm) REVERT: A 1309 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: A 1341 ASP cc_start: 0.7628 (t0) cc_final: 0.7188 (t70) outliers start: 43 outliers final: 18 residues processed: 137 average time/residue: 0.4441 time to fit residues: 65.2460 Evaluate side-chains 126 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1317 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 113 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 90 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1224 ASN A1428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.125417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.107536 restraints weight = 12149.269| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.34 r_work: 0.3087 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9640 Z= 0.159 Angle : 0.532 6.435 13052 Z= 0.286 Chirality : 0.040 0.129 1507 Planarity : 0.004 0.031 1574 Dihedral : 8.208 72.975 1491 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.75 % Allowed : 21.70 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.24), residues: 1142 helix: 2.10 (0.19), residues: 759 sheet: 0.40 (0.54), residues: 85 loop : -1.02 (0.30), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 975 TYR 0.014 0.002 TYR A1073 PHE 0.013 0.002 PHE A 446 TRP 0.018 0.001 TRP A1063 HIS 0.005 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9640) covalent geometry : angle 0.53249 (13052) hydrogen bonds : bond 0.07804 ( 585) hydrogen bonds : angle 4.25643 ( 1707) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.274 Fit side-chains REVERT: A 36 ASP cc_start: 0.7992 (m-30) cc_final: 0.7765 (m-30) REVERT: A 47 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6776 (p0) REVERT: A 373 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7050 (t0) REVERT: A 384 GLU cc_start: 0.3580 (OUTLIER) cc_final: 0.2838 (pm20) REVERT: A 443 ASP cc_start: 0.7662 (t70) cc_final: 0.7377 (t0) REVERT: A 450 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.7094 (ttp-110) REVERT: A 514 GLU cc_start: 0.7504 (tp30) cc_final: 0.7299 (tp30) REVERT: A 536 LYS cc_start: 0.7609 (mmmm) cc_final: 0.7332 (mmtp) REVERT: A 543 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6416 (tt0) REVERT: A 610 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8144 (mp) REVERT: A 1091 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8301 (tt) REVERT: A 1109 ILE cc_start: 0.7758 (mt) cc_final: 0.7353 (tp) REVERT: A 1137 MET cc_start: 0.7354 (tpp) cc_final: 0.7142 (mmm) REVERT: A 1165 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7912 (mmtm) REVERT: A 1309 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8010 (pt0) REVERT: A 1341 ASP cc_start: 0.7648 (t0) cc_final: 0.7217 (t70) REVERT: A 1405 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6851 (mp0) outliers start: 38 outliers final: 16 residues processed: 134 average time/residue: 0.5113 time to fit residues: 72.8539 Evaluate side-chains 125 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 450 ARG Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1405 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 74 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1224 ASN A1428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.123791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.104587 restraints weight = 11849.862| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.50 r_work: 0.3054 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9640 Z= 0.178 Angle : 0.571 6.563 13052 Z= 0.305 Chirality : 0.041 0.130 1507 Planarity : 0.004 0.033 1574 Dihedral : 8.242 73.690 1491 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.04 % Allowed : 21.89 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.24), residues: 1142 helix: 1.97 (0.18), residues: 759 sheet: 0.40 (0.54), residues: 85 loop : -1.06 (0.30), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 975 TYR 0.014 0.002 TYR A 917 PHE 0.014 0.002 PHE A1296 TRP 0.023 0.002 TRP A1063 HIS 0.005 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9640) covalent geometry : angle 0.57144 (13052) hydrogen bonds : bond 0.08366 ( 585) hydrogen bonds : angle 4.33339 ( 1707) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 0.230 Fit side-chains REVERT: A 36 ASP cc_start: 0.8003 (m-30) cc_final: 0.7763 (m-30) REVERT: A 47 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6763 (p0) REVERT: A 279 GLU cc_start: 0.7017 (mp0) cc_final: 0.6692 (mp0) REVERT: A 373 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7152 (t0) REVERT: A 384 GLU cc_start: 0.3588 (OUTLIER) cc_final: 0.2832 (pm20) REVERT: A 443 ASP cc_start: 0.7711 (t70) cc_final: 0.7332 (t0) REVERT: A 450 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.7086 (ttp-110) REVERT: A 483 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7826 (mtmm) REVERT: A 536 LYS cc_start: 0.7556 (mmmm) cc_final: 0.7335 (mmtp) REVERT: A 543 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6413 (tt0) REVERT: A 610 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8096 (mp) REVERT: A 1091 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8291 (tt) REVERT: A 1109 ILE cc_start: 0.7762 (mt) cc_final: 0.7335 (tp) REVERT: A 1137 MET cc_start: 0.7289 (tpp) cc_final: 0.7050 (mmm) REVERT: A 1165 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8033 (mmtm) REVERT: A 1309 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8013 (pt0) REVERT: A 1341 ASP cc_start: 0.7635 (t0) cc_final: 0.7178 (t70) REVERT: A 1405 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6809 (mp0) outliers start: 41 outliers final: 21 residues processed: 138 average time/residue: 0.4528 time to fit residues: 66.8844 Evaluate side-chains 129 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 450 ARG Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1405 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A1224 ASN A1428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.102745 restraints weight = 11833.536| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.50 r_work: 0.3025 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9640 Z= 0.223 Angle : 0.649 8.013 13052 Z= 0.344 Chirality : 0.044 0.137 1507 Planarity : 0.005 0.042 1574 Dihedral : 8.544 75.509 1491 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.44 % Allowed : 21.50 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.24), residues: 1142 helix: 1.65 (0.18), residues: 759 sheet: 0.26 (0.53), residues: 85 loop : -1.22 (0.30), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 975 TYR 0.016 0.002 TYR A 304 PHE 0.017 0.002 PHE A1296 TRP 0.027 0.002 TRP A1063 HIS 0.005 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 9640) covalent geometry : angle 0.64936 (13052) hydrogen bonds : bond 0.09463 ( 585) hydrogen bonds : angle 4.50145 ( 1707) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 98 time to evaluate : 0.411 Fit side-chains REVERT: A 36 ASP cc_start: 0.7987 (m-30) cc_final: 0.7768 (m-30) REVERT: A 47 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6764 (p0) REVERT: A 279 GLU cc_start: 0.7077 (mp0) cc_final: 0.6749 (mp0) REVERT: A 384 GLU cc_start: 0.3619 (OUTLIER) cc_final: 0.2825 (pm20) REVERT: A 390 THR cc_start: 0.5278 (OUTLIER) cc_final: 0.4961 (p) REVERT: A 443 ASP cc_start: 0.7694 (t70) cc_final: 0.7217 (OUTLIER) REVERT: A 450 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.7131 (ttp-110) REVERT: A 483 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7832 (mtmm) REVERT: A 536 LYS cc_start: 0.7517 (mmmm) cc_final: 0.7253 (mmtp) REVERT: A 610 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8141 (mp) REVERT: A 1091 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8296 (tt) REVERT: A 1109 ILE cc_start: 0.7825 (mt) cc_final: 0.7387 (tp) REVERT: A 1137 MET cc_start: 0.7296 (tpp) cc_final: 0.7075 (mmm) REVERT: A 1165 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8118 (mmtm) REVERT: A 1309 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8015 (pt0) REVERT: A 1341 ASP cc_start: 0.7605 (t0) cc_final: 0.7129 (t70) REVERT: A 1405 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6924 (mp0) outliers start: 45 outliers final: 23 residues processed: 140 average time/residue: 0.4820 time to fit residues: 72.2230 Evaluate side-chains 128 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 450 ARG Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1405 GLU Chi-restraints excluded: chain A residue 1415 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A1224 ASN A1428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.103828 restraints weight = 11869.610| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.50 r_work: 0.3044 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9640 Z= 0.186 Angle : 0.590 6.554 13052 Z= 0.314 Chirality : 0.042 0.131 1507 Planarity : 0.004 0.035 1574 Dihedral : 8.453 73.925 1491 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.73 % Allowed : 21.20 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.24), residues: 1142 helix: 1.77 (0.18), residues: 759 sheet: 0.30 (0.54), residues: 85 loop : -1.21 (0.30), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 975 TYR 0.015 0.002 TYR A 917 PHE 0.014 0.002 PHE A1296 TRP 0.032 0.002 TRP A1063 HIS 0.005 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9640) covalent geometry : angle 0.58953 (13052) hydrogen bonds : bond 0.08653 ( 585) hydrogen bonds : angle 4.38658 ( 1707) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 95 time to evaluate : 0.366 Fit side-chains REVERT: A 36 ASP cc_start: 0.7985 (m-30) cc_final: 0.7748 (m-30) REVERT: A 47 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.6767 (p0) REVERT: A 279 GLU cc_start: 0.7043 (mp0) cc_final: 0.6711 (mp0) REVERT: A 384 GLU cc_start: 0.3574 (OUTLIER) cc_final: 0.2800 (pm20) REVERT: A 443 ASP cc_start: 0.7646 (t70) cc_final: 0.7140 (OUTLIER) REVERT: A 450 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.7084 (ttp-110) REVERT: A 483 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7830 (mtmm) REVERT: A 543 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6418 (tt0) REVERT: A 598 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.7909 (mmtt) REVERT: A 610 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8103 (mp) REVERT: A 1091 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8294 (tt) REVERT: A 1109 ILE cc_start: 0.7763 (mt) cc_final: 0.7336 (tp) REVERT: A 1137 MET cc_start: 0.7284 (tpp) cc_final: 0.7057 (mmm) REVERT: A 1165 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8039 (mmtm) REVERT: A 1309 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8000 (pt0) REVERT: A 1341 ASP cc_start: 0.7608 (t0) cc_final: 0.7137 (t70) REVERT: A 1405 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6882 (mp0) outliers start: 48 outliers final: 26 residues processed: 137 average time/residue: 0.4761 time to fit residues: 69.7010 Evaluate side-chains 129 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 450 ARG Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1405 GLU Chi-restraints excluded: chain A residue 1415 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 55 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1224 ASN A1428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.107182 restraints weight = 11926.831| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.33 r_work: 0.3075 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9640 Z= 0.160 Angle : 0.543 6.660 13052 Z= 0.290 Chirality : 0.040 0.129 1507 Planarity : 0.004 0.033 1574 Dihedral : 8.278 72.168 1491 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.85 % Allowed : 21.99 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.24), residues: 1142 helix: 1.99 (0.19), residues: 759 sheet: 0.35 (0.54), residues: 85 loop : -1.17 (0.31), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 975 TYR 0.014 0.002 TYR A 917 PHE 0.012 0.002 PHE A1296 TRP 0.039 0.002 TRP A1063 HIS 0.004 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9640) covalent geometry : angle 0.54292 (13052) hydrogen bonds : bond 0.07853 ( 585) hydrogen bonds : angle 4.24832 ( 1707) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 0.218 Fit side-chains REVERT: A 36 ASP cc_start: 0.7993 (m-30) cc_final: 0.7771 (m-30) REVERT: A 47 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6743 (p0) REVERT: A 279 GLU cc_start: 0.6953 (mp0) cc_final: 0.6653 (mp0) REVERT: A 384 GLU cc_start: 0.3648 (OUTLIER) cc_final: 0.2850 (pm20) REVERT: A 443 ASP cc_start: 0.7586 (t70) cc_final: 0.7110 (OUTLIER) REVERT: A 479 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7270 (tp30) REVERT: A 543 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6435 (tt0) REVERT: A 598 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.7926 (mmtt) REVERT: A 610 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8159 (mp) REVERT: A 1091 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8294 (tt) REVERT: A 1109 ILE cc_start: 0.7800 (mt) cc_final: 0.7391 (tp) REVERT: A 1137 MET cc_start: 0.7221 (tpp) cc_final: 0.7010 (mmm) REVERT: A 1165 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7932 (mmtm) REVERT: A 1309 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.8043 (pt0) REVERT: A 1341 ASP cc_start: 0.7637 (t0) cc_final: 0.7224 (t70) REVERT: A 1405 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6852 (mp0) outliers start: 39 outliers final: 22 residues processed: 136 average time/residue: 0.4889 time to fit residues: 70.8890 Evaluate side-chains 129 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1405 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1224 ASN A1428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.104536 restraints weight = 11764.895| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.43 r_work: 0.3057 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9640 Z= 0.183 Angle : 0.588 6.524 13052 Z= 0.312 Chirality : 0.042 0.131 1507 Planarity : 0.004 0.035 1574 Dihedral : 8.364 73.105 1491 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.55 % Allowed : 22.19 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.24), residues: 1142 helix: 1.87 (0.18), residues: 759 sheet: 0.32 (0.54), residues: 85 loop : -1.22 (0.31), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 975 TYR 0.015 0.002 TYR A 917 PHE 0.014 0.002 PHE A1296 TRP 0.049 0.002 TRP A1063 HIS 0.005 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9640) covalent geometry : angle 0.58761 (13052) hydrogen bonds : bond 0.08475 ( 585) hydrogen bonds : angle 4.32424 ( 1707) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.353 Fit side-chains REVERT: A 36 ASP cc_start: 0.7987 (m-30) cc_final: 0.7750 (m-30) REVERT: A 47 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.6750 (p0) REVERT: A 279 GLU cc_start: 0.7016 (mp0) cc_final: 0.6701 (mp0) REVERT: A 373 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7188 (t0) REVERT: A 384 GLU cc_start: 0.3591 (OUTLIER) cc_final: 0.2805 (pm20) REVERT: A 443 ASP cc_start: 0.7608 (t70) cc_final: 0.7082 (OUTLIER) REVERT: A 479 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7271 (tp30) REVERT: A 483 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7818 (mtmm) REVERT: A 543 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6401 (tt0) REVERT: A 598 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7899 (mmtt) REVERT: A 610 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8089 (mp) REVERT: A 1091 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8288 (tt) REVERT: A 1109 ILE cc_start: 0.7749 (mt) cc_final: 0.7334 (tp) REVERT: A 1137 MET cc_start: 0.7191 (tpp) cc_final: 0.6966 (mmm) REVERT: A 1165 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8024 (mmtm) REVERT: A 1309 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8045 (pt0) REVERT: A 1341 ASP cc_start: 0.7609 (t0) cc_final: 0.7143 (t70) REVERT: A 1405 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6871 (mp0) outliers start: 36 outliers final: 20 residues processed: 130 average time/residue: 0.4982 time to fit residues: 69.0299 Evaluate side-chains 126 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1405 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 111 optimal weight: 0.0870 chunk 28 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1224 ASN A1428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.125829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107907 restraints weight = 11812.252| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.31 r_work: 0.3086 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9640 Z= 0.147 Angle : 0.515 6.525 13052 Z= 0.277 Chirality : 0.039 0.129 1507 Planarity : 0.004 0.032 1574 Dihedral : 8.137 71.072 1491 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.06 % Allowed : 22.68 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.25), residues: 1142 helix: 2.14 (0.19), residues: 759 sheet: 0.37 (0.55), residues: 85 loop : -1.10 (0.31), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 3 TYR 0.014 0.001 TYR A 917 PHE 0.011 0.001 PHE A1296 TRP 0.052 0.002 TRP A1063 HIS 0.004 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9640) covalent geometry : angle 0.51540 (13052) hydrogen bonds : bond 0.07420 ( 585) hydrogen bonds : angle 4.16956 ( 1707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2590.31 seconds wall clock time: 44 minutes 50.55 seconds (2690.55 seconds total)