Starting phenix.real_space_refine on Tue Nov 14 04:59:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d3r_7793/11_2023/6d3r_7793_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d3r_7793/11_2023/6d3r_7793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d3r_7793/11_2023/6d3r_7793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d3r_7793/11_2023/6d3r_7793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d3r_7793/11_2023/6d3r_7793_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d3r_7793/11_2023/6d3r_7793_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 sd= 0.035 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 27 5.16 5 C 4854 2.51 5 N 1348 2.21 5 O 1375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1056": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1309": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 7610 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 7610 Unusual residues: {'ATP': 2} Classifications: {'peptide': 1127, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 423} Link IDs: {'PTRANS': 27, 'TRANS': 1099, None: 2} Not linked: pdbres="GLN A1441 " pdbres="ATP A1501 " Not linked: pdbres="ATP A1501 " pdbres="ATP A1502 " Chain breaks: 3 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1524 Unresolved non-hydrogen angles: 1957 Unresolved non-hydrogen dihedrals: 1274 Unresolved non-hydrogen chiralities: 149 Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 8, 'TYR:plan': 19, 'ASN:plan1': 10, 'TRP:plan': 6, 'ASP:plan': 27, 'PHE:plan': 29, 'GLU:plan': 36, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 834 Time building chain proxies: 4.75, per 1000 atoms: 0.62 Number of scatterers: 7610 At special positions: 0 Unit cell: (74.3748, 97.7891, 136.354, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 6 15.00 O 1375 8.00 N 1348 7.00 C 4854 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.6 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2116 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 5 sheets defined 65.8% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 46 through 62 Processing helix chain 'A' and resid 70 through 110 removed outlier: 3.842A pdb=" N CYS A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N TRP A 80 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS A 81 " --> pdb=" O CYS A 77 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N PHE A 84 " --> pdb=" O TRP A 80 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Proline residue: A 100 - end of helix removed outlier: 3.954A pdb=" N TYR A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 167 Proline residue: A 141 - end of helix removed outlier: 3.699A pdb=" N LYS A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 178 through 186 Processing helix chain 'A' and resid 192 through 214 removed outlier: 4.035A pdb=" N LEU A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ALA A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 199 " --> pdb=" O GLY A 195 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N HIS A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N PHE A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TRP A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 223 through 276 removed outlier: 3.716A pdb=" N ASN A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLN A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N SER A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 327 removed outlier: 3.504A pdb=" N GLU A 291 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 298 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 306 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.927A pdb=" N THR A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 376 removed outlier: 3.588A pdb=" N SER A 358 " --> pdb=" O GLN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 515 through 524 Processing helix chain 'A' and resid 528 through 533 removed outlier: 5.103A pdb=" N LYS A 533 " --> pdb=" O GLU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 551 through 564 Processing helix chain 'A' and resid 581 through 591 Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 639 through 647 Processing helix chain 'A' and resid 651 through 653 No H-bonds generated for 'chain 'A' and resid 651 through 653' Processing helix chain 'A' and resid 656 through 669 Processing helix chain 'A' and resid 851 through 859 Processing helix chain 'A' and resid 861 through 887 removed outlier: 3.950A pdb=" N LEU A 885 " --> pdb=" O SER A 881 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N PHE A 887 " --> pdb=" O VAL A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 961 removed outlier: 3.889A pdb=" N GLY A 938 " --> pdb=" O GLY A 934 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 939 " --> pdb=" O ILE A 935 " (cutoff:3.500A) Proline residue: A 940 - end of helix removed outlier: 3.564A pdb=" N HIS A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 970 Processing helix chain 'A' and resid 974 through 1015 Proline residue: A 992 - end of helix removed outlier: 4.970A pdb=" N PHE A 996 " --> pdb=" O PRO A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1064 Proline residue: A1025 - end of helix removed outlier: 4.062A pdb=" N GLN A1046 " --> pdb=" O GLN A1042 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A1047 " --> pdb=" O GLN A1043 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU A1048 " --> pdb=" O LEU A1044 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A1049 " --> pdb=" O LYS A1045 " (cutoff:3.500A) Proline residue: A1054 - end of helix Processing helix chain 'A' and resid 1066 through 1071 Processing helix chain 'A' and resid 1075 through 1124 Processing helix chain 'A' and resid 1130 through 1170 removed outlier: 3.976A pdb=" N ILE A1135 " --> pdb=" O ARG A1132 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A1142 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET A1144 " --> pdb=" O MET A1141 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY A1145 " --> pdb=" O ASN A1142 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A1146 " --> pdb=" O ILE A1143 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A1169 " --> pdb=" O ARG A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1259 removed outlier: 3.625A pdb=" N LEU A1256 " --> pdb=" O LYS A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1278 No H-bonds generated for 'chain 'A' and resid 1276 through 1278' Processing helix chain 'A' and resid 1281 through 1287 Processing helix chain 'A' and resid 1302 through 1306 Processing helix chain 'A' and resid 1314 through 1323 Processing helix chain 'A' and resid 1327 through 1332 Processing helix chain 'A' and resid 1336 through 1338 No H-bonds generated for 'chain 'A' and resid 1336 through 1338' Processing helix chain 'A' and resid 1350 through 1363 Processing helix chain 'A' and resid 1374 through 1376 No H-bonds generated for 'chain 'A' and resid 1374 through 1376' Processing helix chain 'A' and resid 1380 through 1393 removed outlier: 4.847A pdb=" N VAL A1385 " --> pdb=" O ILE A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1411 removed outlier: 4.870A pdb=" N GLU A1411 " --> pdb=" O GLU A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1438 Processing sheet with id= A, first strand: chain 'A' and resid 447 through 449 Processing sheet with id= B, first strand: chain 'A' and resid 624 through 629 removed outlier: 6.688A pdb=" N ILE A 619 " --> pdb=" O TYR A 626 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR A 628 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 617 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG A 601 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL A 457 " --> pdb=" O ARG A 601 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 603 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N GLY A 459 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1234 through 1236 Processing sheet with id= D, first strand: chain 'A' and resid 1218 through 1220 Processing sheet with id= E, first strand: chain 'A' and resid 1422 through 1426 562 hydrogen bonds defined for protein. 1434 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: 2.87 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1652 1.32 - 1.45: 2199 1.45 - 1.57: 3802 1.57 - 1.70: 22 1.70 - 1.83: 51 Bond restraints: 7726 Sorted by residual: bond pdb=" O5' ATP A1502 " pdb=" PA ATP A1502 " ideal model delta sigma weight residual 1.579 1.725 -0.146 1.10e-02 8.26e+03 1.77e+02 bond pdb=" O5' ATP A1501 " pdb=" PA ATP A1501 " ideal model delta sigma weight residual 1.579 1.700 -0.121 1.10e-02 8.26e+03 1.22e+02 bond pdb=" C1' ATP A1502 " pdb=" N9 ATP A1502 " ideal model delta sigma weight residual 1.459 1.592 -0.133 1.40e-02 5.10e+03 8.97e+01 bond pdb=" C1' ATP A1501 " pdb=" N9 ATP A1501 " ideal model delta sigma weight residual 1.459 1.558 -0.099 1.40e-02 5.10e+03 5.03e+01 bond pdb=" C1' ATP A1502 " pdb=" C2' ATP A1502 " ideal model delta sigma weight residual 1.531 1.607 -0.076 1.20e-02 6.94e+03 4.02e+01 ... (remaining 7721 not shown) Histogram of bond angle deviations from ideal: 91.77 - 100.24: 5 100.24 - 108.70: 840 108.70 - 117.17: 4806 117.17 - 125.63: 4790 125.63 - 134.10: 113 Bond angle restraints: 10554 Sorted by residual: angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 118.15 21.72 1.00e+00 1.00e+00 4.72e+02 angle pdb=" PB ATP A1502 " pdb=" O3B ATP A1502 " pdb=" PG ATP A1502 " ideal model delta sigma weight residual 139.87 124.24 15.63 1.00e+00 1.00e+00 2.44e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 121.81 15.02 1.00e+00 1.00e+00 2.26e+02 angle pdb=" PA ATP A1502 " pdb=" O3A ATP A1502 " pdb=" PB ATP A1502 " ideal model delta sigma weight residual 136.83 123.71 13.12 1.00e+00 1.00e+00 1.72e+02 angle pdb=" C2' ATP A1502 " pdb=" C1' ATP A1502 " pdb=" N9 ATP A1502 " ideal model delta sigma weight residual 114.08 127.10 -13.02 1.53e+00 4.27e-01 7.23e+01 ... (remaining 10549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.16: 4343 14.16 - 28.32: 139 28.32 - 42.48: 20 42.48 - 56.64: 10 56.64 - 70.79: 9 Dihedral angle restraints: 4521 sinusoidal: 1264 harmonic: 3257 Sorted by residual: dihedral pdb=" CA GLY A1129 " pdb=" C GLY A1129 " pdb=" N PRO A1130 " pdb=" CA PRO A1130 " ideal model delta harmonic sigma weight residual -180.00 -159.63 -20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ASN A1264 " pdb=" C ASN A1264 " pdb=" N THR A1265 " pdb=" CA THR A1265 " ideal model delta harmonic sigma weight residual -180.00 -161.08 -18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" C PHE A1120 " pdb=" N PHE A1120 " pdb=" CA PHE A1120 " pdb=" CB PHE A1120 " ideal model delta harmonic sigma weight residual -122.60 -131.97 9.37 0 2.50e+00 1.60e-01 1.41e+01 ... (remaining 4518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 894 0.093 - 0.185: 333 0.185 - 0.278: 61 0.278 - 0.370: 11 0.370 - 0.463: 3 Chirality restraints: 1302 Sorted by residual: chirality pdb=" CA PHE A1120 " pdb=" N PHE A1120 " pdb=" C PHE A1120 " pdb=" CB PHE A1120 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA PHE A 317 " pdb=" N PHE A 317 " pdb=" C PHE A 317 " pdb=" CB PHE A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CB THR A 466 " pdb=" CA THR A 466 " pdb=" OG1 THR A 466 " pdb=" CG2 THR A 466 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 1299 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 968 " 0.089 2.00e-02 2.50e+03 5.50e-02 5.29e+01 pdb=" CG PHE A 968 " -0.086 2.00e-02 2.50e+03 pdb=" CD1 PHE A 968 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 PHE A 968 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE A 968 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE A 968 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 968 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 230 " 0.085 2.00e-02 2.50e+03 5.23e-02 4.79e+01 pdb=" CG PHE A 230 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 PHE A 230 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE A 230 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 PHE A 230 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE A 230 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE A 230 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 381 " 0.072 2.00e-02 2.50e+03 3.68e-02 2.71e+01 pdb=" CG TYR A 381 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 381 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR A 381 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 381 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 381 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 381 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 381 " 0.044 2.00e-02 2.50e+03 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 3224 2.89 - 3.39: 8148 3.39 - 3.89: 11868 3.89 - 4.40: 13838 4.40 - 4.90: 20531 Nonbonded interactions: 57609 Sorted by model distance: nonbonded pdb=" OG SER A 50 " pdb=" OG SER A 159 " model vdw 2.385 2.440 nonbonded pdb=" O TRP A 278 " pdb=" OH TYR A1309 " model vdw 2.441 2.440 nonbonded pdb=" N ASP A 44 " pdb=" OD1 ASP A 44 " model vdw 2.449 2.520 nonbonded pdb=" N ASN A 188 " pdb=" OD1 ASN A 188 " model vdw 2.469 2.520 nonbonded pdb=" N SER A 223 " pdb=" N ALA A 224 " model vdw 2.497 2.560 ... (remaining 57604 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 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: 13.100 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 25.830 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 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 : 0.017 0.146 7726 Z= 1.104 Angle : 1.749 21.719 10554 Z= 1.235 Chirality : 0.098 0.463 1302 Planarity : 0.010 0.100 1344 Dihedral : 9.074 70.794 2405 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.23), residues: 1119 helix: 0.49 (0.17), residues: 724 sheet: 1.24 (0.58), residues: 60 loop : 0.52 (0.33), residues: 335 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2047 time to fit residues: 69.7108 Evaluate side-chains 117 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.858 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7726 Z= 0.260 Angle : 0.656 7.075 10554 Z= 0.375 Chirality : 0.042 0.210 1302 Planarity : 0.006 0.050 1344 Dihedral : 5.298 59.959 1180 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.79 % Favored : 98.12 % Rotamer: Outliers : 0.18 % Allowed : 2.83 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.24), residues: 1119 helix: 1.57 (0.19), residues: 716 sheet: 1.32 (0.55), residues: 79 loop : 0.47 (0.33), residues: 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 0.903 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.1803 time to fit residues: 39.7311 Evaluate side-chains 102 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 101 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 147 HIS ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7726 Z= 0.232 Angle : 0.586 6.230 10554 Z= 0.334 Chirality : 0.040 0.164 1302 Planarity : 0.004 0.038 1344 Dihedral : 5.027 56.153 1180 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.25), residues: 1119 helix: 1.62 (0.19), residues: 722 sheet: 1.17 (0.59), residues: 69 loop : 0.37 (0.34), residues: 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1554 time to fit residues: 30.1754 Evaluate side-chains 93 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.4980 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 108 optimal weight: 40.0000 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 30.0000 chunk 29 optimal weight: 0.0070 chunk 90 optimal weight: 30.0000 overall best weight: 1.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7726 Z= 0.221 Angle : 0.556 6.942 10554 Z= 0.312 Chirality : 0.040 0.167 1302 Planarity : 0.004 0.034 1344 Dihedral : 4.779 57.832 1180 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.18 % Allowed : 2.65 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.25), residues: 1119 helix: 1.64 (0.19), residues: 728 sheet: 0.58 (0.59), residues: 68 loop : 0.08 (0.34), residues: 323 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.1492 time to fit residues: 26.9591 Evaluate side-chains 93 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 92 optimal weight: 30.0000 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 97 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7726 Z= 0.146 Angle : 0.500 6.525 10554 Z= 0.276 Chirality : 0.039 0.161 1302 Planarity : 0.004 0.031 1344 Dihedral : 4.555 57.163 1180 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.18 % Allowed : 2.30 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.25), residues: 1119 helix: 1.84 (0.20), residues: 722 sheet: 0.66 (0.60), residues: 68 loop : 0.20 (0.35), residues: 329 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.1571 time to fit residues: 30.5997 Evaluate side-chains 101 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.0970 chunk 21 optimal weight: 0.3980 chunk 63 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 0.0270 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7726 Z= 0.145 Angle : 0.499 7.571 10554 Z= 0.270 Chirality : 0.038 0.156 1302 Planarity : 0.003 0.028 1344 Dihedral : 4.397 58.413 1180 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.26), residues: 1119 helix: 2.03 (0.20), residues: 721 sheet: 0.55 (0.59), residues: 68 loop : 0.22 (0.35), residues: 330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1635 time to fit residues: 30.3589 Evaluate side-chains 103 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 0.0270 chunk 43 optimal weight: 0.3980 overall best weight: 1.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7726 Z= 0.165 Angle : 0.517 7.742 10554 Z= 0.282 Chirality : 0.039 0.151 1302 Planarity : 0.003 0.028 1344 Dihedral : 4.386 59.620 1180 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.26), residues: 1119 helix: 2.01 (0.20), residues: 730 sheet: 0.80 (0.60), residues: 66 loop : 0.05 (0.35), residues: 323 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1756 time to fit residues: 31.7654 Evaluate side-chains 94 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 68 optimal weight: 0.0980 chunk 73 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.5776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7726 Z= 0.150 Angle : 0.524 8.030 10554 Z= 0.280 Chirality : 0.039 0.148 1302 Planarity : 0.003 0.027 1344 Dihedral : 4.336 59.864 1180 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.26), residues: 1119 helix: 2.08 (0.20), residues: 720 sheet: 0.70 (0.61), residues: 68 loop : 0.13 (0.35), residues: 331 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1543 time to fit residues: 27.7336 Evaluate side-chains 97 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 0.4980 chunk 106 optimal weight: 5.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7726 Z= 0.305 Angle : 0.630 8.703 10554 Z= 0.345 Chirality : 0.041 0.156 1302 Planarity : 0.004 0.026 1344 Dihedral : 4.649 53.754 1180 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.25), residues: 1119 helix: 1.74 (0.20), residues: 721 sheet: 0.81 (0.62), residues: 66 loop : -0.19 (0.34), residues: 332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1640 time to fit residues: 26.4632 Evaluate side-chains 88 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 50 optimal weight: 0.0870 chunk 73 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 overall best weight: 1.4760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7726 Z= 0.201 Angle : 0.566 8.558 10554 Z= 0.306 Chirality : 0.039 0.147 1302 Planarity : 0.004 0.028 1344 Dihedral : 4.511 53.926 1180 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.26), residues: 1119 helix: 1.78 (0.20), residues: 723 sheet: 0.81 (0.60), residues: 71 loop : -0.13 (0.35), residues: 325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1638 time to fit residues: 28.0859 Evaluate side-chains 94 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.918 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 30.0000 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.093368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.079104 restraints weight = 31286.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.081128 restraints weight = 17238.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.082480 restraints weight = 11165.316| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7726 Z= 0.164 Angle : 0.546 8.462 10554 Z= 0.292 Chirality : 0.039 0.204 1302 Planarity : 0.003 0.025 1344 Dihedral : 4.390 52.801 1180 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.26), residues: 1119 helix: 1.91 (0.20), residues: 732 sheet: 0.72 (0.59), residues: 73 loop : -0.06 (0.36), residues: 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1711.88 seconds wall clock time: 31 minutes 54.02 seconds (1914.02 seconds total)