Starting phenix.real_space_refine on Fri Dec 8 07:19:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d3r_7793/12_2023/6d3r_7793_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d3r_7793/12_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_7793/12_2023/6d3r_7793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d3r_7793/12_2023/6d3r_7793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d3r_7793/12_2023/6d3r_7793_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d3r_7793/12_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 4.61, per 1000 atoms: 0.61 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: 3.11 Conformation dependent library (CDL) restraints added in 1.5 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: 2.27 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: 2.99 Time building geometry restraints manager: 3.38 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 - 16.80: 4411 16.80 - 33.60: 101 33.60 - 50.39: 30 50.39 - 67.19: 28 67.19 - 83.99: 13 Dihedral angle restraints: 4583 sinusoidal: 1326 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 4580 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.030 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: 13.240 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 25.160 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.750 ------------------------------------------------------------------------------- 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 : 11.893 83.991 2467 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.008 TRP A 362 HIS 0.037 0.004 HIS A 200 PHE 0.089 0.008 PHE A 968 TYR 0.072 0.006 TYR A 381 ARG 0.010 0.001 ARG A1070 *********************** 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 : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1989 time to fit residues: 67.0406 Evaluate side-chains 117 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.837 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1437 ------------------------------------------------------------------------------- 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: 0.7683 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7726 Z= 0.267 Angle : 0.662 7.464 10554 Z= 0.381 Chirality : 0.043 0.241 1302 Planarity : 0.006 0.050 1344 Dihedral : 11.292 74.119 1242 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.79 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % 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: 1.80 (0.24), residues: 1119 helix: 1.58 (0.19), residues: 715 sheet: 1.61 (0.58), residues: 72 loop : 0.43 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 278 HIS 0.006 0.002 HIS A 953 PHE 0.025 0.002 PHE A 491 TYR 0.010 0.001 TYR A 248 ARG 0.006 0.001 ARG A 348 *********************** 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 158 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.877 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1882 time to fit residues: 41.5868 Evaluate side-chains 102 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1792 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 30.0000 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 HIS ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7726 Z= 0.286 Angle : 0.640 7.082 10554 Z= 0.362 Chirality : 0.041 0.157 1302 Planarity : 0.005 0.041 1344 Dihedral : 11.012 70.149 1242 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % 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: 1.63 (0.25), residues: 1119 helix: 1.53 (0.19), residues: 722 sheet: 1.02 (0.57), residues: 69 loop : 0.23 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 362 HIS 0.008 0.002 HIS A 200 PHE 0.014 0.002 PHE A1037 TYR 0.014 0.001 TYR A 276 ARG 0.005 0.001 ARG A 135 *********************** 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 127 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1576 time to fit residues: 29.1230 Evaluate side-chains 92 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1901 ------------------------------------------------------------------------------- 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: 2.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 0.0670 chunk 48 optimal weight: 6.9990 chunk 68 optimal weight: 0.0570 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.2040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7726 Z= 0.189 Angle : 0.537 6.495 10554 Z= 0.304 Chirality : 0.039 0.173 1302 Planarity : 0.004 0.033 1344 Dihedral : 10.468 74.744 1242 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.18 % Allowed : 2.48 % Favored : 97.35 % 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 (0.25), residues: 1119 helix: 1.70 (0.20), residues: 723 sheet: 0.57 (0.59), residues: 68 loop : 0.16 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 362 HIS 0.004 0.001 HIS A 200 PHE 0.012 0.001 PHE A1037 TYR 0.014 0.001 TYR A 90 ARG 0.004 0.000 ARG A 348 *********************** 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 130 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.1417 time to fit residues: 27.6502 Evaluate side-chains 93 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1490 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 92 optimal weight: 30.0000 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7726 Z= 0.200 Angle : 0.537 6.802 10554 Z= 0.301 Chirality : 0.039 0.161 1302 Planarity : 0.004 0.031 1344 Dihedral : 10.161 84.764 1242 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.74 (0.25), residues: 1119 helix: 1.76 (0.20), residues: 724 sheet: 0.48 (0.58), residues: 68 loop : 0.05 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 362 HIS 0.003 0.001 HIS A 200 PHE 0.025 0.001 PHE A 980 TYR 0.021 0.001 TYR A 90 ARG 0.004 0.001 ARG A1162 *********************** 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 127 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1527 time to fit residues: 28.3410 Evaluate side-chains 93 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.859 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1248 ------------------------------------------------------------------------------- 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: 0.9980 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 7726 Z= 0.164 Angle : 0.515 6.633 10554 Z= 0.285 Chirality : 0.039 0.160 1302 Planarity : 0.004 0.028 1344 Dihedral : 9.620 86.071 1242 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 1.99 (0.26), residues: 1119 helix: 1.94 (0.20), residues: 726 sheet: 0.56 (0.58), residues: 68 loop : 0.19 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 362 HIS 0.002 0.001 HIS A1039 PHE 0.022 0.001 PHE A 317 TYR 0.019 0.001 TYR A 90 ARG 0.004 0.000 ARG A 154 *********************** 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 134 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1504 time to fit residues: 29.2497 Evaluate side-chains 98 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0623 ------------------------------------------------------------------------------- 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: 0.9980 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 50.0000 chunk 60 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 HIS ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7726 Z= 0.205 Angle : 0.554 7.741 10554 Z= 0.302 Chirality : 0.040 0.159 1302 Planarity : 0.004 0.028 1344 Dihedral : 9.166 87.081 1242 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 1.89 (0.20), residues: 725 sheet: 0.61 (0.58), residues: 68 loop : 0.06 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 240 HIS 0.005 0.001 HIS A1039 PHE 0.022 0.002 PHE A 320 TYR 0.021 0.001 TYR A 90 ARG 0.005 0.001 ARG A 154 *********************** 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 124 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1654 time to fit residues: 30.5108 Evaluate side-chains 91 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2258 ------------------------------------------------------------------------------- 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: 0.4980 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 84 optimal weight: 0.0370 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 7726 Z= 0.154 Angle : 0.545 7.861 10554 Z= 0.289 Chirality : 0.039 0.161 1302 Planarity : 0.003 0.030 1344 Dihedral : 8.476 78.724 1242 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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: 2.00 (0.26), residues: 1119 helix: 1.99 (0.20), residues: 719 sheet: 0.57 (0.59), residues: 68 loop : 0.11 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 240 HIS 0.002 0.001 HIS A1039 PHE 0.015 0.001 PHE A 317 TYR 0.020 0.001 TYR A 90 ARG 0.003 0.000 ARG A 135 *********************** 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 137 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1513 time to fit residues: 30.6895 Evaluate side-chains 100 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2271 ------------------------------------------------------------------------------- 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: 5.9990 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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: 0.7833 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7726 Z= 0.251 Angle : 0.615 8.847 10554 Z= 0.333 Chirality : 0.041 0.159 1302 Planarity : 0.004 0.025 1344 Dihedral : 8.253 71.142 1242 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 1.80 (0.26), residues: 1119 helix: 1.83 (0.20), residues: 724 sheet: 0.77 (0.63), residues: 61 loop : -0.03 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1093 HIS 0.004 0.001 HIS A1039 PHE 0.035 0.002 PHE A1115 TYR 0.022 0.001 TYR A 90 ARG 0.006 0.001 ARG A 135 *********************** 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 124 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1513 time to fit residues: 27.7799 Evaluate side-chains 95 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.813 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0889 ------------------------------------------------------------------------------- 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: 0.0980 chunk 73 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.0570 chunk 54 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- 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: 0.7812 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7726 Z= 0.186 Angle : 0.569 8.637 10554 Z= 0.305 Chirality : 0.040 0.208 1302 Planarity : 0.004 0.028 1344 Dihedral : 7.933 65.587 1242 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 1.85 (0.26), residues: 1119 helix: 1.90 (0.20), residues: 723 sheet: 0.89 (0.65), residues: 61 loop : -0.11 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 240 HIS 0.005 0.001 HIS A 200 PHE 0.029 0.001 PHE A 132 TYR 0.020 0.001 TYR A 90 ARG 0.006 0.000 ARG A 135 ********************** 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 122 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1571 time to fit residues: 27.9193 Evaluate side-chains 97 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9526 ------------------------------------------------------------------------------- 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: 0.9990 chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 91 optimal weight: 50.0000 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3706 r_free = 0.3706 target = 0.095803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.082024 restraints weight = 32228.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.084012 restraints weight = 17962.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.085370 restraints weight = 11746.514| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.6400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7726 Z= 0.162 Angle : 0.561 8.278 10554 Z= 0.293 Chirality : 0.039 0.184 1302 Planarity : 0.003 0.027 1344 Dihedral : 7.413 61.344 1242 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.91 (0.26), residues: 1119 helix: 1.88 (0.20), residues: 737 sheet: 0.93 (0.67), residues: 61 loop : -0.02 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1149 HIS 0.004 0.001 HIS A 200 PHE 0.029 0.001 PHE A 132 TYR 0.019 0.001 TYR A 90 ARG 0.005 0.000 ARG A 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1692.46 seconds wall clock time: 32 minutes 16.40 seconds (1936.40 seconds total)