Starting phenix.real_space_refine on Sat Aug 23 01:54:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v7z_43011/08_2025/8v7z_43011.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v7z_43011/08_2025/8v7z_43011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v7z_43011/08_2025/8v7z_43011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v7z_43011/08_2025/8v7z_43011.map" model { file = "/net/cci-nas-00/data/ceres_data/8v7z_43011/08_2025/8v7z_43011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v7z_43011/08_2025/8v7z_43011.cif" } resolution = 3.4 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 5880 2.51 5 N 1472 2.21 5 O 1571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 8977 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1104, 8846 Classifications: {'peptide': 1104} Link IDs: {'PTRANS': 30, 'TRANS': 1073} Chain breaks: 6 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 131 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'POV': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 5, 'POV:plan-2': 5, 'POV:plan-3': 5} Unresolved non-hydrogen planarities: 59 Time building chain proxies: 2.21, per 1000 atoms: 0.25 Number of scatterers: 8977 At special positions: 0 Unit cell: (86.756, 82.524, 136.482, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 6 15.00 Mg 2 11.99 O 1571 8.00 N 1472 7.00 C 5880 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 341.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 68.9% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 20 through 30 removed outlier: 3.976A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 64 Processing helix chain 'A' and resid 68 through 106 removed outlier: 3.613A pdb=" N ALA A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Proline residue: A 99 - end of helix Processing helix chain 'A' and resid 120 through 166 removed outlier: 4.336A pdb=" N ILE A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY A 126 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.601A pdb=" N LEU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 removed outlier: 3.725A pdb=" N LEU A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 removed outlier: 3.801A pdb=" N PHE A 200 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 201 " --> pdb=" O ALA A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 197 through 201' Processing helix chain 'A' and resid 202 through 219 removed outlier: 3.702A pdb=" N LEU A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 268 removed outlier: 3.588A pdb=" N PHE A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.356A 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: 3.651A pdb=" N MET A 281 " --> pdb=" O TRP A 277 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 313 through 330 Proline residue: A 324 - end of helix removed outlier: 4.881A pdb=" N ILE A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.838A pdb=" N THR A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 376 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 531 Processing helix chain 'A' and resid 549 through 564 removed outlier: 3.551A pdb=" N LYS A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 591 Processing helix chain 'A' and resid 606 through 613 Processing helix chain 'A' and resid 629 through 634 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 858 through 885 Processing helix chain 'A' and resid 910 through 927 removed outlier: 3.528A pdb=" N TYR A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL A 915 " --> pdb=" O SER A 911 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE A 916 " --> pdb=" O SER A 912 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ASP A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR A 925 " --> pdb=" O GLY A 921 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 926 " --> pdb=" O VAL A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 959 removed outlier: 3.622A pdb=" N SER A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'A' and resid 980 through 985 Processing helix chain 'A' and resid 985 through 1012 removed outlier: 4.092A pdb=" N LEU A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1061 removed outlier: 4.234A pdb=" N PHE A1016 " --> pdb=" O GLN A1012 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) Proline residue: A1021 - end of helix removed outlier: 3.908A pdb=" N ALA A1025 " --> pdb=" O PRO A1021 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) Proline residue: A1050 - end of helix removed outlier: 3.718A pdb=" N THR A1057 " --> pdb=" O THR A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1069 Processing helix chain 'A' and resid 1070 through 1103 removed outlier: 3.853A pdb=" N ASN A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1116 Processing helix chain 'A' and resid 1134 through 1168 removed outlier: 3.952A pdb=" N ASN A1138 " --> pdb=" O THR A1134 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TRP A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1258 removed outlier: 3.679A 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 1299 through 1305 Processing helix chain 'A' and resid 1311 through 1320 removed outlier: 3.864A pdb=" N LYS A1317 " --> pdb=" O GLN A1313 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL A1318 " --> pdb=" O GLU A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1329 removed outlier: 3.687A pdb=" N GLU A1329 " --> pdb=" O ARG A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 3.845A pdb=" N GLY A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1362 Processing helix chain 'A' and resid 1377 through 1391 removed outlier: 3.554A pdb=" N GLN A1382 " --> pdb=" O PRO A1378 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1409 removed outlier: 4.196A pdb=" N GLU A1409 " --> pdb=" O GLU A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1431 Processing sheet with id=AA1, first strand: chain 'A' and resid 444 through 448 removed outlier: 5.921A pdb=" N ILE A 444 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A 396 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N MET A 394 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LYS A 483 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASN A 396 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LYS A 481 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 479 " --> pdb=" O THR A 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 488 through 491 removed outlier: 6.659A pdb=" N SER A 489 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR A 569 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL A 603 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU A 571 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA A 455 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU A 619 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA A 457 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 626 " --> pdb=" O ILE A 618 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS A 620 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N SER A 624 " --> pdb=" O HIS A 620 " (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 1210 through 1215 removed outlier: 3.860A pdb=" N ASP A1214 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE A1230 " --> pdb=" O ASP A1214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1240 through 1243 Processing sheet with id=AA6, first strand: chain 'A' and resid 1287 through 1289 removed outlier: 6.473A pdb=" N GLY A1287 " --> pdb=" O LEU A1368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 509 hydrogen bonds defined for protein. 1515 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: 1.50 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2749 1.34 - 1.46: 1740 1.46 - 1.58: 4586 1.58 - 1.69: 10 1.69 - 1.81: 77 Bond restraints: 9162 Sorted by residual: bond pdb=" CB ASP A 373 " pdb=" CG ASP A 373 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.20e-01 bond pdb=" CA ASN A1138 " pdb=" CB ASN A1138 " ideal model delta sigma weight residual 1.528 1.542 -0.014 1.59e-02 3.96e+03 7.45e-01 bond pdb=" CB MET A 469 " pdb=" CG MET A 469 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 7.01e-01 bond pdb=" CA ASP A 373 " pdb=" CB ASP A 373 " ideal model delta sigma weight residual 1.528 1.541 -0.012 1.56e-02 4.11e+03 6.38e-01 bond pdb=" CB MET A 244 " pdb=" CG MET A 244 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.21e-01 ... (remaining 9157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 12214 2.04 - 4.08: 146 4.08 - 6.12: 19 6.12 - 8.16: 6 8.16 - 10.19: 4 Bond angle restraints: 12389 Sorted by residual: angle pdb=" N ILE A1117 " pdb=" CA ILE A1117 " pdb=" C ILE A1117 " ideal model delta sigma weight residual 113.53 108.71 4.82 9.80e-01 1.04e+00 2.42e+01 angle pdb=" N VAL A1108 " pdb=" CA VAL A1108 " pdb=" C VAL A1108 " ideal model delta sigma weight residual 111.56 108.02 3.54 8.60e-01 1.35e+00 1.70e+01 angle pdb=" CA LEU A 184 " pdb=" CB LEU A 184 " pdb=" CG LEU A 184 " ideal model delta sigma weight residual 116.30 126.49 -10.19 3.50e+00 8.16e-02 8.48e+00 angle pdb=" CG1 ILE A1267 " pdb=" CB ILE A1267 " pdb=" CG2 ILE A1267 " ideal model delta sigma weight residual 110.70 102.21 8.49 3.00e+00 1.11e-01 8.00e+00 angle pdb=" CA LEU A 61 " pdb=" CB LEU A 61 " pdb=" CG LEU A 61 " ideal model delta sigma weight residual 116.30 126.02 -9.72 3.50e+00 8.16e-02 7.71e+00 ... (remaining 12384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4529 17.84 - 35.67: 707 35.67 - 53.51: 234 53.51 - 71.34: 57 71.34 - 89.18: 7 Dihedral angle restraints: 5534 sinusoidal: 2323 harmonic: 3211 Sorted by residual: dihedral pdb=" CA ASP A 614 " pdb=" CB ASP A 614 " pdb=" CG ASP A 614 " pdb=" OD1 ASP A 614 " ideal model delta sinusoidal sigma weight residual -30.00 -88.43 58.43 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CG ARG A 560 " pdb=" CD ARG A 560 " pdb=" NE ARG A 560 " pdb=" CZ ARG A 560 " ideal model delta sinusoidal sigma weight residual -90.00 -133.42 43.42 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CB GLU A 527 " pdb=" CG GLU A 527 " pdb=" CD GLU A 527 " pdb=" OE1 GLU A 527 " ideal model delta sinusoidal sigma weight residual 0.00 -84.22 84.22 1 3.00e+01 1.11e-03 9.59e+00 ... (remaining 5531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1137 0.049 - 0.098: 253 0.098 - 0.147: 46 0.147 - 0.196: 1 0.196 - 0.245: 2 Chirality restraints: 1439 Sorted by residual: chirality pdb=" CB ILE A1267 " pdb=" CA ILE A1267 " pdb=" CG1 ILE A1267 " pdb=" CG2 ILE A1267 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB ILE A1366 " pdb=" CA ILE A1366 " pdb=" CG1 ILE A1366 " pdb=" CG2 ILE A1366 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE A 601 " pdb=" CA ILE A 601 " pdb=" CG1 ILE A 601 " pdb=" CG2 ILE A 601 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1436 not shown) Planarity restraints: 1497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A1103 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.04e+00 pdb=" C ILE A1103 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE A1103 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU A1104 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1063 " -0.017 2.00e-02 2.50e+03 1.47e-02 5.41e+00 pdb=" CG TRP A1063 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A1063 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A1063 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A1063 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1063 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1063 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1063 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1063 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A1063 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 98 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO A 99 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.026 5.00e-02 4.00e+02 ... (remaining 1494 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 64 2.58 - 3.16: 7296 3.16 - 3.74: 14530 3.74 - 4.32: 19133 4.32 - 4.90: 32771 Nonbonded interactions: 73794 Sorted by model distance: nonbonded pdb=" OE1 GLN A 493 " pdb="MG MG A1501 " model vdw 2.004 2.170 nonbonded pdb=" OE1 GLN A1291 " pdb="MG MG A1502 " model vdw 2.026 2.170 nonbonded pdb=" OG SER A1251 " pdb="MG MG A1502 " model vdw 2.030 2.170 nonbonded pdb=" OG1 THR A 465 " pdb="MG MG A1501 " model vdw 2.168 2.170 nonbonded pdb=" NE2 GLN A 493 " pdb="MG MG A1501 " model vdw 2.207 2.250 ... (remaining 73789 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.700 Find NCS groups from input model: 0.050 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:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 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 : 0.002 0.029 9164 Z= 0.117 Angle : 0.585 10.194 12389 Z= 0.300 Chirality : 0.041 0.245 1439 Planarity : 0.004 0.046 1497 Dihedral : 19.314 89.179 3456 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.41 % Allowed : 35.12 % Favored : 64.47 % 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: -0.10 (0.26), residues: 1090 helix: 0.82 (0.20), residues: 731 sheet: -1.19 (0.63), residues: 68 loop : -2.00 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1386 TYR 0.011 0.001 TYR A 919 PHE 0.026 0.001 PHE A1033 TRP 0.040 0.002 TRP A1063 HIS 0.003 0.001 HIS A1085 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9162) covalent geometry : angle 0.58491 (12389) hydrogen bonds : bond 0.09973 ( 509) hydrogen bonds : angle 4.87131 ( 1515) Misc. bond : bond 0.00042 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 152 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.6815 (mttt) cc_final: 0.6566 (mmmt) REVERT: A 243 MET cc_start: 0.7876 (tmm) cc_final: 0.7545 (ttt) REVERT: A 286 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: A 469 MET cc_start: 0.8246 (mmm) cc_final: 0.7873 (mmt) REVERT: A 933 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7424 (mtp-110) REVERT: A 961 MET cc_start: 0.7121 (mmm) cc_final: 0.6790 (tpt) REVERT: A 1341 ASP cc_start: 0.6434 (t0) cc_final: 0.5874 (t0) outliers start: 4 outliers final: 1 residues processed: 156 average time/residue: 0.1174 time to fit residues: 24.6968 Evaluate side-chains 142 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 323 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.0770 chunk 106 optimal weight: 3.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 ASN A1412 GLN A1423 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.179745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.160880 restraints weight = 10093.879| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.45 r_work: 0.3654 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9164 Z= 0.127 Angle : 0.531 8.147 12389 Z= 0.267 Chirality : 0.040 0.190 1439 Planarity : 0.004 0.041 1497 Dihedral : 8.181 59.891 1348 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.53 % Allowed : 30.69 % Favored : 64.78 % 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: -0.02 (0.26), residues: 1090 helix: 0.93 (0.20), residues: 726 sheet: -1.07 (0.69), residues: 58 loop : -2.04 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 251 TYR 0.011 0.001 TYR A 919 PHE 0.011 0.001 PHE A 236 TRP 0.023 0.001 TRP A1063 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9162) covalent geometry : angle 0.53103 (12389) hydrogen bonds : bond 0.03682 ( 509) hydrogen bonds : angle 4.32976 ( 1515) Misc. bond : bond 0.00047 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 0.353 Fit side-chains REVERT: A 64 LYS cc_start: 0.7145 (mttt) cc_final: 0.6907 (mmmt) REVERT: A 199 HIS cc_start: 0.8049 (OUTLIER) cc_final: 0.7572 (t70) REVERT: A 243 MET cc_start: 0.7947 (tmm) cc_final: 0.7744 (ttp) REVERT: A 286 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: A 319 PHE cc_start: 0.6258 (OUTLIER) cc_final: 0.5994 (t80) REVERT: A 881 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.6093 (mp) REVERT: A 933 ARG cc_start: 0.8181 (ptm160) cc_final: 0.7569 (mtp-110) outliers start: 44 outliers final: 23 residues processed: 188 average time/residue: 0.1133 time to fit residues: 28.8601 Evaluate side-chains 177 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 47 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 84 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.153308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.136269 restraints weight = 10024.309| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.14 r_work: 0.3637 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9164 Z= 0.143 Angle : 0.543 8.416 12389 Z= 0.272 Chirality : 0.041 0.187 1439 Planarity : 0.004 0.039 1497 Dihedral : 7.641 56.932 1346 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 5.15 % Allowed : 32.34 % Favored : 62.51 % 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: -0.06 (0.26), residues: 1090 helix: 0.92 (0.20), residues: 720 sheet: -1.19 (0.68), residues: 58 loop : -2.06 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1386 TYR 0.011 0.001 TYR A 919 PHE 0.016 0.001 PHE A 236 TRP 0.028 0.001 TRP A1063 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9162) covalent geometry : angle 0.54346 (12389) hydrogen bonds : bond 0.03753 ( 509) hydrogen bonds : angle 4.28419 ( 1515) Misc. bond : bond 0.00059 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 0.387 Fit side-chains REVERT: A 60 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: A 64 LYS cc_start: 0.7090 (mttt) cc_final: 0.6772 (mmmt) REVERT: A 199 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.7579 (t70) REVERT: A 243 MET cc_start: 0.8045 (tmm) cc_final: 0.7758 (ttp) REVERT: A 286 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: A 881 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.5931 (mp) REVERT: A 933 ARG cc_start: 0.8143 (ptm160) cc_final: 0.7532 (mtp-110) outliers start: 50 outliers final: 32 residues processed: 188 average time/residue: 0.1094 time to fit residues: 28.1761 Evaluate side-chains 176 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 16 optimal weight: 0.0030 chunk 18 optimal weight: 3.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1148 ASN A1375 HIS ** A1412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.158042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136383 restraints weight = 9915.404| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.64 r_work: 0.3398 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9164 Z= 0.125 Angle : 0.525 8.655 12389 Z= 0.262 Chirality : 0.040 0.159 1439 Planarity : 0.003 0.039 1497 Dihedral : 7.426 57.608 1346 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 6.08 % Allowed : 32.54 % Favored : 61.38 % 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: 0.02 (0.26), residues: 1090 helix: 0.95 (0.20), residues: 725 sheet: -1.19 (0.68), residues: 58 loop : -1.96 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1386 TYR 0.010 0.001 TYR A 919 PHE 0.013 0.001 PHE A 236 TRP 0.027 0.001 TRP A1063 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9162) covalent geometry : angle 0.52518 (12389) hydrogen bonds : bond 0.03577 ( 509) hydrogen bonds : angle 4.24920 ( 1515) Misc. bond : bond 0.00044 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 149 time to evaluate : 0.349 Fit side-chains REVERT: A 60 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: A 64 LYS cc_start: 0.6731 (mttt) cc_final: 0.6419 (mmmt) REVERT: A 199 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7527 (t70) REVERT: A 286 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: A 851 ARG cc_start: 0.5891 (ttp80) cc_final: 0.5630 (ttp-170) REVERT: A 881 LEU cc_start: 0.5850 (OUTLIER) cc_final: 0.5529 (mp) REVERT: A 933 ARG cc_start: 0.7968 (ptm160) cc_final: 0.7307 (mtp-110) outliers start: 59 outliers final: 37 residues processed: 196 average time/residue: 0.1083 time to fit residues: 29.0807 Evaluate side-chains 186 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 87 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS A 974 ASN ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 ASN A1348 HIS A1375 HIS ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.177532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.158565 restraints weight = 10126.478| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.44 r_work: 0.3468 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9164 Z= 0.149 Angle : 0.551 8.308 12389 Z= 0.275 Chirality : 0.041 0.192 1439 Planarity : 0.004 0.039 1497 Dihedral : 7.371 54.128 1346 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.50 % Favored : 94.40 % Rotamer: Outliers : 6.59 % Allowed : 32.23 % Favored : 61.17 % 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: -0.06 (0.26), residues: 1090 helix: 0.91 (0.20), residues: 721 sheet: -1.00 (0.69), residues: 56 loop : -2.06 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 334 TYR 0.011 0.001 TYR A 512 PHE 0.016 0.001 PHE A 236 TRP 0.035 0.001 TRP A1063 HIS 0.003 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9162) covalent geometry : angle 0.55090 (12389) hydrogen bonds : bond 0.03740 ( 509) hydrogen bonds : angle 4.27326 ( 1515) Misc. bond : bond 0.00052 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 151 time to evaluate : 0.361 Fit side-chains REVERT: A 60 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7247 (tm-30) REVERT: A 64 LYS cc_start: 0.7023 (mttt) cc_final: 0.6698 (mmmt) REVERT: A 199 HIS cc_start: 0.8097 (OUTLIER) cc_final: 0.7671 (t70) REVERT: A 286 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: A 552 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8135 (mt0) REVERT: A 881 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5927 (mp) REVERT: A 933 ARG cc_start: 0.8141 (ptm160) cc_final: 0.7535 (mtp-110) REVERT: A 958 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7594 (mp10) REVERT: A 1165 LYS cc_start: 0.5787 (pttm) cc_final: 0.4919 (ttmm) REVERT: A 1417 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.6754 (pp20) outliers start: 64 outliers final: 43 residues processed: 204 average time/residue: 0.0855 time to fit residues: 24.2602 Evaluate side-chains 195 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 145 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 958 GLN Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1348 HIS Chi-restraints excluded: chain A residue 1371 GLN Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 3.9990 chunk 72 optimal weight: 0.0980 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1375 HIS ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.176422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.157386 restraints weight = 10193.838| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.44 r_work: 0.3596 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9164 Z= 0.170 Angle : 0.581 9.327 12389 Z= 0.288 Chirality : 0.042 0.196 1439 Planarity : 0.004 0.039 1497 Dihedral : 7.386 52.677 1346 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.50 % Favored : 94.40 % Rotamer: Outliers : 6.90 % Allowed : 31.82 % Favored : 61.28 % 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: -0.19 (0.25), residues: 1090 helix: 0.82 (0.20), residues: 720 sheet: -1.04 (0.69), residues: 56 loop : -2.12 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1102 TYR 0.013 0.001 TYR A 512 PHE 0.016 0.001 PHE A 236 TRP 0.038 0.002 TRP A1063 HIS 0.008 0.001 HIS A1348 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 9162) covalent geometry : angle 0.58080 (12389) hydrogen bonds : bond 0.03893 ( 509) hydrogen bonds : angle 4.32215 ( 1515) Misc. bond : bond 0.00063 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 150 time to evaluate : 0.248 Fit side-chains REVERT: A 32 LEU cc_start: 0.4777 (OUTLIER) cc_final: 0.4173 (mt) REVERT: A 60 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: A 199 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7656 (t70) REVERT: A 265 MET cc_start: 0.8076 (tmm) cc_final: 0.7594 (ttp) REVERT: A 286 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: A 482 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7562 (mt) REVERT: A 552 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8023 (mt0) REVERT: A 881 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.5937 (mp) REVERT: A 933 ARG cc_start: 0.8137 (ptm160) cc_final: 0.7449 (mtp-110) REVERT: A 958 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7384 (mp10) REVERT: A 1417 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.6783 (pp20) outliers start: 67 outliers final: 43 residues processed: 205 average time/residue: 0.0934 time to fit residues: 26.3067 Evaluate side-chains 198 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 958 GLN Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 93 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 ASN ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.164316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.143636 restraints weight = 10259.084| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.53 r_work: 0.3612 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9164 Z= 0.156 Angle : 0.569 9.626 12389 Z= 0.283 Chirality : 0.041 0.202 1439 Planarity : 0.004 0.039 1497 Dihedral : 7.321 53.756 1346 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 6.49 % Allowed : 32.03 % Favored : 61.48 % 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: -0.18 (0.25), residues: 1090 helix: 0.82 (0.20), residues: 724 sheet: -1.07 (0.69), residues: 56 loop : -2.14 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 334 TYR 0.011 0.001 TYR A 512 PHE 0.015 0.001 PHE A 236 TRP 0.048 0.002 TRP A1063 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9162) covalent geometry : angle 0.56904 (12389) hydrogen bonds : bond 0.03813 ( 509) hydrogen bonds : angle 4.32534 ( 1515) Misc. bond : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 146 time to evaluate : 0.364 Fit side-chains REVERT: A 32 LEU cc_start: 0.5105 (OUTLIER) cc_final: 0.4476 (mt) REVERT: A 33 GLU cc_start: 0.4249 (OUTLIER) cc_final: 0.3991 (pm20) REVERT: A 60 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: A 199 HIS cc_start: 0.8110 (OUTLIER) cc_final: 0.7685 (t70) REVERT: A 286 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: A 482 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7717 (mt) REVERT: A 552 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: A 588 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7533 (mt-10) REVERT: A 881 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.5992 (mp) REVERT: A 933 ARG cc_start: 0.8183 (ptm160) cc_final: 0.7528 (mtp-110) REVERT: A 958 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7545 (mp10) REVERT: A 1242 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7986 (tt) REVERT: A 1417 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.6822 (pp20) outliers start: 63 outliers final: 42 residues processed: 197 average time/residue: 0.1054 time to fit residues: 28.6670 Evaluate side-chains 197 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 958 GLN Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1348 HIS Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.157286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.135061 restraints weight = 9709.317| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.68 r_work: 0.3380 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9164 Z= 0.132 Angle : 0.552 9.969 12389 Z= 0.275 Chirality : 0.040 0.206 1439 Planarity : 0.004 0.038 1497 Dihedral : 7.162 55.465 1346 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.14 % Favored : 94.77 % Rotamer: Outliers : 5.87 % Allowed : 32.54 % Favored : 61.59 % 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: -0.04 (0.26), residues: 1090 helix: 0.92 (0.20), residues: 724 sheet: -1.08 (0.69), residues: 56 loop : -2.07 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1386 TYR 0.013 0.001 TYR A 304 PHE 0.014 0.001 PHE A 236 TRP 0.052 0.001 TRP A1063 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9162) covalent geometry : angle 0.55178 (12389) hydrogen bonds : bond 0.03640 ( 509) hydrogen bonds : angle 4.28874 ( 1515) Misc. bond : bond 0.00037 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 152 time to evaluate : 0.243 Fit side-chains REVERT: A 32 LEU cc_start: 0.4392 (OUTLIER) cc_final: 0.3767 (mt) REVERT: A 33 GLU cc_start: 0.4008 (OUTLIER) cc_final: 0.3739 (pm20) REVERT: A 60 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7165 (tm-30) REVERT: A 199 HIS cc_start: 0.8098 (OUTLIER) cc_final: 0.7607 (t70) REVERT: A 249 ASP cc_start: 0.7845 (m-30) cc_final: 0.7631 (m-30) REVERT: A 286 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: A 482 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7588 (mt) REVERT: A 552 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8031 (mt0) REVERT: A 588 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7356 (mt-10) REVERT: A 881 LEU cc_start: 0.5851 (OUTLIER) cc_final: 0.5525 (mp) REVERT: A 933 ARG cc_start: 0.8015 (ptm160) cc_final: 0.7237 (mtp-110) REVERT: A 958 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: A 1242 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7819 (tt) REVERT: A 1394 ASP cc_start: 0.6297 (OUTLIER) cc_final: 0.5332 (t0) outliers start: 57 outliers final: 40 residues processed: 200 average time/residue: 0.0936 time to fit residues: 25.7851 Evaluate side-chains 195 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 958 GLN Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1348 HIS Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.163473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142957 restraints weight = 10193.764| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.50 r_work: 0.3522 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9164 Z= 0.175 Angle : 0.603 11.081 12389 Z= 0.299 Chirality : 0.042 0.220 1439 Planarity : 0.004 0.039 1497 Dihedral : 7.266 55.566 1346 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.69 % Favored : 94.22 % Rotamer: Outliers : 6.59 % Allowed : 31.10 % Favored : 62.31 % 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: -0.25 (0.26), residues: 1090 helix: 0.76 (0.20), residues: 724 sheet: -1.14 (0.68), residues: 56 loop : -2.13 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1386 TYR 0.013 0.001 TYR A 512 PHE 0.020 0.002 PHE A1331 TRP 0.060 0.002 TRP A1063 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 9162) covalent geometry : angle 0.60335 (12389) hydrogen bonds : bond 0.03959 ( 509) hydrogen bonds : angle 4.37450 ( 1515) Misc. bond : bond 0.00057 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 145 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.4897 (OUTLIER) cc_final: 0.4320 (mt) REVERT: A 33 GLU cc_start: 0.4236 (OUTLIER) cc_final: 0.4004 (pm20) REVERT: A 60 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: A 199 HIS cc_start: 0.8113 (OUTLIER) cc_final: 0.7676 (t70) REVERT: A 243 MET cc_start: 0.8126 (tmm) cc_final: 0.7628 (ttp) REVERT: A 286 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: A 552 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8152 (mt0) REVERT: A 588 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7510 (mt-10) REVERT: A 881 LEU cc_start: 0.6302 (OUTLIER) cc_final: 0.5950 (mp) REVERT: A 933 ARG cc_start: 0.8160 (ptm160) cc_final: 0.7425 (mtp-110) REVERT: A 958 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7479 (mp10) REVERT: A 1242 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8020 (tt) REVERT: A 1394 ASP cc_start: 0.6577 (OUTLIER) cc_final: 0.5607 (t0) REVERT: A 1417 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.6869 (pp20) outliers start: 64 outliers final: 47 residues processed: 200 average time/residue: 0.0860 time to fit residues: 23.8777 Evaluate side-chains 203 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 145 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 958 GLN Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1218 LYS Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1348 HIS Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.154964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135727 restraints weight = 9956.935| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.35 r_work: 0.3622 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9164 Z= 0.126 Angle : 0.559 11.834 12389 Z= 0.276 Chirality : 0.040 0.215 1439 Planarity : 0.003 0.038 1497 Dihedral : 7.010 57.620 1346 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 5.66 % Allowed : 32.13 % Favored : 62.20 % 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: -0.03 (0.26), residues: 1090 helix: 0.94 (0.20), residues: 723 sheet: -1.13 (0.69), residues: 56 loop : -2.05 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1386 TYR 0.011 0.001 TYR A 304 PHE 0.018 0.001 PHE A1331 TRP 0.055 0.002 TRP A1063 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9162) covalent geometry : angle 0.55904 (12389) hydrogen bonds : bond 0.03571 ( 509) hydrogen bonds : angle 4.29212 ( 1515) Misc. bond : bond 0.00031 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.4659 (OUTLIER) cc_final: 0.4089 (mt) REVERT: A 33 GLU cc_start: 0.4174 (OUTLIER) cc_final: 0.3944 (pm20) REVERT: A 60 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: A 199 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7630 (t70) REVERT: A 249 ASP cc_start: 0.7997 (m-30) cc_final: 0.7723 (m-30) REVERT: A 286 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: A 469 MET cc_start: 0.8246 (mmm) cc_final: 0.7923 (mmt) REVERT: A 552 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: A 588 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7515 (mt-10) REVERT: A 881 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6122 (mp) REVERT: A 933 ARG cc_start: 0.8038 (ptm160) cc_final: 0.7378 (mtp-110) REVERT: A 1218 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8214 (mttp) REVERT: A 1242 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7909 (tt) REVERT: A 1354 MET cc_start: 0.7807 (ttm) cc_final: 0.7419 (ttt) REVERT: A 1390 GLN cc_start: 0.8012 (tt0) cc_final: 0.7427 (tt0) REVERT: A 1394 ASP cc_start: 0.6386 (OUTLIER) cc_final: 0.5402 (t0) outliers start: 55 outliers final: 42 residues processed: 192 average time/residue: 0.0835 time to fit residues: 22.3661 Evaluate side-chains 193 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 141 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1218 LYS Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1348 HIS Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.153464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.136813 restraints weight = 9904.114| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.12 r_work: 0.3686 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9164 Z= 0.149 Angle : 0.586 12.945 12389 Z= 0.288 Chirality : 0.041 0.221 1439 Planarity : 0.004 0.039 1497 Dihedral : 7.020 57.137 1346 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.32 % Favored : 94.59 % Rotamer: Outliers : 5.66 % Allowed : 31.82 % Favored : 62.51 % 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: -0.11 (0.26), residues: 1090 helix: 0.87 (0.20), residues: 723 sheet: -1.11 (0.68), residues: 56 loop : -2.06 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1386 TYR 0.011 0.001 TYR A 304 PHE 0.016 0.001 PHE A1033 TRP 0.061 0.002 TRP A1063 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9162) covalent geometry : angle 0.58648 (12389) hydrogen bonds : bond 0.03734 ( 509) hydrogen bonds : angle 4.32122 ( 1515) Misc. bond : bond 0.00047 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1942.70 seconds wall clock time: 34 minutes 9.83 seconds (2049.83 seconds total)