Starting phenix.real_space_refine on Thu Mar 14 20:43:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwo_16292/03_2024/8bwo_16292_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwo_16292/03_2024/8bwo_16292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwo_16292/03_2024/8bwo_16292.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwo_16292/03_2024/8bwo_16292.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwo_16292/03_2024/8bwo_16292_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bwo_16292/03_2024/8bwo_16292_updated.pdb" } resolution = 3.2 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= -0.000 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 6279 2.51 5 N 1636 2.21 5 O 1747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9712 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1211, 9648 Classifications: {'peptide': 1211} Link IDs: {'PTRANS': 36, 'TRANS': 1174} Chain breaks: 3 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.43, per 1000 atoms: 0.56 Number of scatterers: 9712 At special positions: 0 Unit cell: (75.712, 90.688, 148.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 6 15.00 Mg 2 11.99 O 1747 8.00 N 1636 7.00 C 6279 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: 3.87 Conformation dependent library (CDL) restraints added in 1.8 seconds 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 4 sheets defined 63.3% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 12 through 14 No H-bonds generated for 'chain 'A' and resid 12 through 14' Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 25 through 34 Proline residue: A 29 - end of helix Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 80 through 119 removed outlier: 5.630A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 134 through 149 Processing helix chain 'A' and resid 151 through 180 removed outlier: 3.667A pdb=" N ARG A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'A' and resid 201 through 230 removed outlier: 3.823A pdb=" N VAL A 208 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR A 209 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A 212 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N HIS A 213 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 217 " --> pdb=" O PHE A 214 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY A 218 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 3.506A pdb=" N VAL A 225 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 226 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 229 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 281 removed outlier: 3.536A pdb=" N MET A 241 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU A 248 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.552A pdb=" N PHE A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 259 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 261 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 264 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 266 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 270 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR A 281 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 289 Processing helix chain 'A' and resid 291 through 340 removed outlier: 3.525A pdb=" N SER A 296 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 299 " --> pdb=" O SER A 296 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 303 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 308 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 310 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 312 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 313 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 321 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 325 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA A 327 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N SER A 328 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 332 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR A 335 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 337 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR A 338 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 340 " --> pdb=" O THR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 366 removed outlier: 4.928A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 390 removed outlier: 3.677A pdb=" N VAL A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 537 through 551 removed outlier: 3.664A pdb=" N ARG A 542 " --> pdb=" O GLY A 538 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 576 Processing helix chain 'A' and resid 578 through 581 No H-bonds generated for 'chain 'A' and resid 578 through 581' Processing helix chain 'A' and resid 594 through 599 removed outlier: 3.967A pdb=" N LYS A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ALA A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 594 through 599' Processing helix chain 'A' and resid 617 through 620 No H-bonds generated for 'chain 'A' and resid 617 through 620' Processing helix chain 'A' and resid 698 through 708 Processing helix chain 'A' and resid 711 through 742 removed outlier: 3.742A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 removed outlier: 3.685A pdb=" N GLY A 753 " --> pdb=" O ASN A 750 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN A 754 " --> pdb=" O GLY A 751 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 755 " --> pdb=" O GLY A 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 750 through 755' Processing helix chain 'A' and resid 761 through 806 Processing helix chain 'A' and resid 810 through 815 Processing helix chain 'A' and resid 818 through 859 removed outlier: 3.964A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE A 829 " --> pdb=" O PHE A 825 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Proline residue: A 837 - end of helix Processing helix chain 'A' and resid 862 through 909 Proline residue: A 867 - end of helix Proline residue: A 870 - end of helix removed outlier: 3.574A pdb=" N LEU A 878 " --> pdb=" O PHE A 875 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A 884 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ARG A 887 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 893 " --> pdb=" O LYS A 890 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 894 " --> pdb=" O ARG A 891 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 896 " --> pdb=" O GLU A 893 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A 897 " --> pdb=" O SER A 894 " (cutoff:3.500A) Proline residue: A 899 - end of helix removed outlier: 3.634A pdb=" N HIS A 903 " --> pdb=" O VAL A 900 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 904 " --> pdb=" O PHE A 901 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 905 " --> pdb=" O SER A 902 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 908 " --> pdb=" O SER A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 Processing helix chain 'A' and resid 920 through 969 removed outlier: 3.919A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 969 " --> pdb=" O PHE A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 973 No H-bonds generated for 'chain 'A' and resid 971 through 973' Processing helix chain 'A' and resid 976 through 980 Processing helix chain 'A' and resid 984 through 1017 removed outlier: 3.949A pdb=" N MET A 990 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE A 993 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS A 996 " --> pdb=" O PHE A 993 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG A 998 " --> pdb=" O TRP A 995 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A1000 " --> pdb=" O VAL A 997 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A1003 " --> pdb=" O SER A1000 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET A1007 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A1012 " --> pdb=" O SER A1009 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A1015 " --> pdb=" O ARG A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1088 removed outlier: 4.003A pdb=" N ILE A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A1086 " --> pdb=" O SER A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1116 removed outlier: 4.073A pdb=" N LYS A1116 " --> pdb=" O ASP A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1135 Processing helix chain 'A' and resid 1143 through 1152 Processing helix chain 'A' and resid 1156 through 1161 removed outlier: 3.573A pdb=" N ASP A1161 " --> pdb=" O GLU A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1172 through 1174 No H-bonds generated for 'chain 'A' and resid 1172 through 1174' Processing helix chain 'A' and resid 1179 through 1193 removed outlier: 3.597A pdb=" N CYS A1186 " --> pdb=" O ARG A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1222 removed outlier: 3.964A pdb=" N LEU A1214 " --> pdb=" O ARG A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1238 No H-bonds generated for 'chain 'A' and resid 1235 through 1238' Processing helix chain 'A' and resid 1258 through 1262 Processing helix chain 'A' and resid 1268 through 1276 Processing helix chain 'A' and resid 1278 through 1292 Processing sheet with id= A, first strand: chain 'A' and resid 433 through 436 Processing sheet with id= B, first strand: chain 'A' and resid 610 through 615 removed outlier: 6.899A pdb=" N ILE A 605 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS A 614 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE A 603 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 3.603A pdb=" N LYS A1097 " --> pdb=" O ASP A1044 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1252 through 1256 removed outlier: 6.788A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A1243 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL A1228 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE A1073 " --> pdb=" O VAL A1228 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR A1230 " --> pdb=" O ILE A1073 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1167 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: 3.25 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3058 1.34 - 1.46: 1356 1.46 - 1.57: 5430 1.57 - 1.69: 4 1.69 - 1.81: 68 Bond restraints: 9916 Sorted by residual: bond pdb=" C5' ATP A1401 " pdb=" O5' ATP A1401 " ideal model delta sigma weight residual 1.443 1.221 0.222 1.00e-02 1.00e+04 4.95e+02 bond pdb=" C5' ATP A1402 " pdb=" O5' ATP A1402 " ideal model delta sigma weight residual 1.443 1.221 0.222 1.00e-02 1.00e+04 4.92e+02 bond pdb=" C4' ATP A1401 " pdb=" O4' ATP A1401 " ideal model delta sigma weight residual 1.444 1.397 0.047 1.10e-02 8.26e+03 1.80e+01 bond pdb=" C1' ATP A1402 " pdb=" O4' ATP A1402 " ideal model delta sigma weight residual 1.416 1.364 0.052 1.30e-02 5.92e+03 1.59e+01 bond pdb=" C4' ATP A1402 " pdb=" O4' ATP A1402 " ideal model delta sigma weight residual 1.444 1.401 0.043 1.10e-02 8.26e+03 1.54e+01 ... (remaining 9911 not shown) Histogram of bond angle deviations from ideal: 83.42 - 98.42: 9 98.42 - 113.41: 5715 113.41 - 128.41: 7633 128.41 - 143.40: 91 143.40 - 158.39: 2 Bond angle restraints: 13450 Sorted by residual: angle pdb=" C5' ATP A1402 " pdb=" O5' ATP A1402 " pdb=" PA ATP A1402 " ideal model delta sigma weight residual 121.27 158.39 -37.12 1.00e+00 1.00e+00 1.38e+03 angle pdb=" C5' ATP A1401 " pdb=" O5' ATP A1401 " pdb=" PA ATP A1401 " ideal model delta sigma weight residual 121.27 157.40 -36.13 1.00e+00 1.00e+00 1.31e+03 angle pdb=" C3' ATP A1402 " pdb=" C4' ATP A1402 " pdb=" C5' ATP A1402 " ideal model delta sigma weight residual 115.19 83.42 31.77 1.76e+00 3.23e-01 3.26e+02 angle pdb=" C3' ATP A1401 " pdb=" C4' ATP A1401 " pdb=" C5' ATP A1401 " ideal model delta sigma weight residual 115.19 85.14 30.05 1.76e+00 3.23e-01 2.92e+02 angle pdb=" C4' ATP A1402 " pdb=" C5' ATP A1402 " pdb=" O5' ATP A1402 " ideal model delta sigma weight residual 108.83 137.57 -28.74 2.33e+00 1.85e-01 1.52e+02 ... (remaining 13445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5481 17.98 - 35.96: 371 35.96 - 53.95: 66 53.95 - 71.93: 19 71.93 - 89.91: 12 Dihedral angle restraints: 5949 sinusoidal: 2418 harmonic: 3531 Sorted by residual: dihedral pdb=" CA CYS A1226 " pdb=" C CYS A1226 " pdb=" N THR A1227 " pdb=" CA THR A1227 " ideal model delta harmonic sigma weight residual 180.00 151.93 28.07 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA MET A 409 " pdb=" C MET A 409 " pdb=" N VAL A 410 " pdb=" CA VAL A 410 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA LEU A 513 " pdb=" C LEU A 513 " pdb=" N LYS A 514 " pdb=" CA LYS A 514 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 5946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1472 0.090 - 0.180: 83 0.180 - 0.270: 4 0.270 - 0.360: 1 0.360 - 0.450: 2 Chirality restraints: 1562 Sorted by residual: chirality pdb=" C4' ATP A1402 " pdb=" C3' ATP A1402 " pdb=" C5' ATP A1402 " pdb=" O4' ATP A1402 " both_signs ideal model delta sigma weight residual False -2.49 -2.94 0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" C4' ATP A1401 " pdb=" C3' ATP A1401 " pdb=" C5' ATP A1401 " pdb=" O4' ATP A1401 " both_signs ideal model delta sigma weight residual False -2.49 -2.94 0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" C3' ATP A1402 " pdb=" C2' ATP A1402 " pdb=" C4' ATP A1402 " pdb=" O3' ATP A1402 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1559 not shown) Planarity restraints: 1660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 157 " 0.002 2.00e-02 2.50e+03 1.72e-02 5.93e+00 pdb=" CG TYR A 157 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 157 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 157 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 157 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 157 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 157 " -0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 157 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 37 " -0.174 9.50e-02 1.11e+02 7.87e-02 4.98e+00 pdb=" NE ARG A 37 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 37 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 37 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 37 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 998 " -0.170 9.50e-02 1.11e+02 7.67e-02 4.89e+00 pdb=" NE ARG A 998 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 998 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A 998 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 998 " 0.000 2.00e-02 2.50e+03 ... (remaining 1657 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 44 2.50 - 3.10: 7565 3.10 - 3.70: 14900 3.70 - 4.30: 22893 4.30 - 4.90: 37522 Nonbonded interactions: 82924 Sorted by model distance: nonbonded pdb=" O3G ATP A1402 " pdb="MG MG A1403 " model vdw 1.900 2.170 nonbonded pdb=" O1B ATP A1402 " pdb="MG MG A1403 " model vdw 1.940 2.170 nonbonded pdb=" OG SER A1082 " pdb="MG MG A1404 " model vdw 1.945 2.170 nonbonded pdb=" OE1 GLN A1122 " pdb="MG MG A1404 " model vdw 2.004 2.170 nonbonded pdb=" OH TYR A 92 " pdb=" O THR A 209 " model vdw 2.251 2.440 ... (remaining 82919 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 11.760 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.430 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 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 : 0.005 0.222 9916 Z= 0.367 Angle : 1.109 37.125 13450 Z= 0.718 Chirality : 0.050 0.450 1562 Planarity : 0.008 0.079 1660 Dihedral : 13.918 89.908 3661 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.47 % Allowed : 2.47 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.54 (0.22), residues: 1203 helix: -1.22 (0.16), residues: 761 sheet: -0.58 (0.59), residues: 68 loop : -0.16 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 711 HIS 0.004 0.001 HIS A 172 PHE 0.020 0.002 PHE A 948 TYR 0.026 0.005 TYR A 157 ARG 0.021 0.004 ARG A 782 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 224 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7466 (pt0) cc_final: 0.6664 (pm20) REVERT: A 76 GLN cc_start: 0.5073 (pt0) cc_final: 0.4846 (mt0) REVERT: A 176 ARG cc_start: 0.7245 (ttm170) cc_final: 0.7028 (ttt-90) REVERT: A 264 LYS cc_start: 0.7508 (mttp) cc_final: 0.7197 (mttp) REVERT: A 293 LYS cc_start: 0.7341 (mttt) cc_final: 0.7083 (mmmt) REVERT: A 413 GLN cc_start: 0.7676 (tt0) cc_final: 0.7243 (tp40) REVERT: A 509 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7650 (tttp) REVERT: A 571 ARG cc_start: 0.7027 (ttt180) cc_final: 0.6808 (tmm160) REVERT: A 695 LYS cc_start: 0.7108 (ptpt) cc_final: 0.6088 (tptt) REVERT: A 706 ARG cc_start: 0.7723 (mmm-85) cc_final: 0.6696 (tpt90) REVERT: A 715 ILE cc_start: 0.8179 (mm) cc_final: 0.7977 (mp) REVERT: A 835 LEU cc_start: 0.8349 (tp) cc_final: 0.8111 (tt) REVERT: A 925 GLU cc_start: 0.7874 (tt0) cc_final: 0.7594 (tt0) REVERT: A 1020 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7303 (pm20) REVERT: A 1021 LYS cc_start: 0.8392 (mtpt) cc_final: 0.7960 (mmtm) REVERT: A 1077 THR cc_start: 0.8683 (p) cc_final: 0.8479 (p) REVERT: A 1152 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7748 (mt-10) REVERT: A 1169 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7614 (mm-30) REVERT: A 1201 ASP cc_start: 0.8160 (t0) cc_final: 0.7841 (t0) REVERT: A 1210 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7353 (mtt90) outliers start: 5 outliers final: 1 residues processed: 226 average time/residue: 0.2884 time to fit residues: 84.9128 Evaluate side-chains 142 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 0.0370 chunk 31 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 703 ASN A1047 ASN A1225 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9916 Z= 0.253 Angle : 0.602 7.928 13450 Z= 0.319 Chirality : 0.043 0.170 1562 Planarity : 0.005 0.053 1660 Dihedral : 8.582 72.890 1373 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.61 % Allowed : 7.60 % Favored : 90.79 % 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: -0.46 (0.23), residues: 1203 helix: -0.26 (0.17), residues: 758 sheet: -0.72 (0.56), residues: 69 loop : 0.11 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 763 HIS 0.005 0.001 HIS A 934 PHE 0.013 0.002 PHE A 98 TYR 0.012 0.001 TYR A 737 ARG 0.005 0.001 ARG A1193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7439 (pt0) cc_final: 0.6665 (pm20) REVERT: A 76 GLN cc_start: 0.5227 (pt0) cc_final: 0.4992 (mt0) REVERT: A 77 LYS cc_start: 0.7956 (pptt) cc_final: 0.7613 (mmmt) REVERT: A 89 TRP cc_start: 0.8300 (p-90) cc_final: 0.7963 (p-90) REVERT: A 94 VAL cc_start: 0.8622 (p) cc_final: 0.8410 (m) REVERT: A 176 ARG cc_start: 0.6976 (ttm170) cc_final: 0.6615 (ttt180) REVERT: A 264 LYS cc_start: 0.7106 (mttp) cc_final: 0.6842 (mttp) REVERT: A 413 GLN cc_start: 0.7634 (tt0) cc_final: 0.7196 (tp40) REVERT: A 481 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7872 (mm-40) REVERT: A 509 LYS cc_start: 0.8299 (ttmt) cc_final: 0.7806 (tttp) REVERT: A 571 ARG cc_start: 0.7002 (ttt180) cc_final: 0.6754 (tmm160) REVERT: A 613 GLN cc_start: 0.7457 (mt0) cc_final: 0.7207 (mt0) REVERT: A 695 LYS cc_start: 0.7225 (ptpt) cc_final: 0.6139 (ttmt) REVERT: A 706 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.6543 (tpt90) REVERT: A 744 MET cc_start: 0.4646 (OUTLIER) cc_final: 0.3802 (pp-130) REVERT: A 800 LYS cc_start: 0.6714 (mtmt) cc_final: 0.6385 (mmtm) REVERT: A 835 LEU cc_start: 0.8325 (tp) cc_final: 0.8111 (tt) REVERT: A 925 GLU cc_start: 0.7612 (tt0) cc_final: 0.7205 (mt-10) REVERT: A 1020 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7430 (pm20) REVERT: A 1021 LYS cc_start: 0.8358 (mtpt) cc_final: 0.8022 (mmtm) REVERT: A 1066 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7896 (mtmm) REVERT: A 1176 ASN cc_start: 0.7408 (t0) cc_final: 0.6993 (t0) REVERT: A 1210 ARG cc_start: 0.7890 (mtp85) cc_final: 0.7358 (mtt90) REVERT: A 1253 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8060 (mtmm) REVERT: A 1274 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7809 (tt0) outliers start: 17 outliers final: 8 residues processed: 171 average time/residue: 0.2574 time to fit residues: 59.5191 Evaluate side-chains 155 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 1066 LYS Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1253 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9916 Z= 0.215 Angle : 0.537 6.993 13450 Z= 0.283 Chirality : 0.040 0.161 1562 Planarity : 0.004 0.033 1660 Dihedral : 8.119 79.299 1373 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.80 % Allowed : 9.69 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.09 (0.24), residues: 1203 helix: -0.03 (0.18), residues: 749 sheet: -0.98 (0.54), residues: 76 loop : 0.50 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 763 HIS 0.004 0.001 HIS A 153 PHE 0.012 0.001 PHE A 98 TYR 0.011 0.001 TYR A1259 ARG 0.006 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7480 (pt0) cc_final: 0.6758 (pm20) REVERT: A 77 LYS cc_start: 0.7934 (pptt) cc_final: 0.7607 (mmmt) REVERT: A 89 TRP cc_start: 0.8354 (p-90) cc_final: 0.7990 (p-90) REVERT: A 176 ARG cc_start: 0.6987 (ttm170) cc_final: 0.6562 (ttt180) REVERT: A 264 LYS cc_start: 0.7094 (mttp) cc_final: 0.6830 (mttp) REVERT: A 413 GLN cc_start: 0.7776 (tt0) cc_final: 0.7369 (tp40) REVERT: A 481 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7879 (mm-40) REVERT: A 509 LYS cc_start: 0.8319 (ttmt) cc_final: 0.7830 (tttm) REVERT: A 531 ARG cc_start: 0.8217 (mtm-85) cc_final: 0.8010 (mtm-85) REVERT: A 571 ARG cc_start: 0.7003 (ttt180) cc_final: 0.6746 (tmm160) REVERT: A 613 GLN cc_start: 0.7468 (mt0) cc_final: 0.7239 (mt0) REVERT: A 695 LYS cc_start: 0.7328 (ptpt) cc_final: 0.6162 (tttp) REVERT: A 800 LYS cc_start: 0.6776 (mtmt) cc_final: 0.6349 (mmtm) REVERT: A 925 GLU cc_start: 0.7556 (tt0) cc_final: 0.7184 (mt-10) REVERT: A 1020 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7449 (pm20) REVERT: A 1021 LYS cc_start: 0.8362 (mtpt) cc_final: 0.8005 (mmtm) REVERT: A 1140 GLU cc_start: 0.7986 (tt0) cc_final: 0.7592 (mt-10) REVERT: A 1176 ASN cc_start: 0.7522 (t0) cc_final: 0.7088 (t0) REVERT: A 1210 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7365 (mtt90) REVERT: A 1253 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8084 (mtmm) REVERT: A 1259 TYR cc_start: 0.7882 (t80) cc_final: 0.7543 (t80) REVERT: A 1274 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7816 (tt0) outliers start: 19 outliers final: 9 residues processed: 174 average time/residue: 0.2612 time to fit residues: 61.1482 Evaluate side-chains 159 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1253 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A1216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9916 Z= 0.261 Angle : 0.562 6.849 13450 Z= 0.291 Chirality : 0.041 0.159 1562 Planarity : 0.004 0.032 1660 Dihedral : 8.045 89.290 1373 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.90 % Allowed : 11.21 % Favored : 86.89 % 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: -0.12 (0.24), residues: 1203 helix: -0.03 (0.18), residues: 748 sheet: -0.96 (0.56), residues: 71 loop : 0.40 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 763 HIS 0.005 0.001 HIS A 153 PHE 0.018 0.002 PHE A 352 TYR 0.011 0.001 TYR A 737 ARG 0.005 0.001 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7580 (pt0) cc_final: 0.6823 (pm20) REVERT: A 77 LYS cc_start: 0.7953 (pptt) cc_final: 0.7621 (mmmt) REVERT: A 89 TRP cc_start: 0.8368 (p-90) cc_final: 0.8026 (p-90) REVERT: A 176 ARG cc_start: 0.7066 (ttm170) cc_final: 0.6626 (ttt180) REVERT: A 226 THR cc_start: 0.8568 (t) cc_final: 0.8325 (p) REVERT: A 264 LYS cc_start: 0.7159 (mttp) cc_final: 0.6909 (mttt) REVERT: A 413 GLN cc_start: 0.7766 (tt0) cc_final: 0.7371 (tp40) REVERT: A 474 ARG cc_start: 0.7621 (ptm-80) cc_final: 0.7418 (ptm-80) REVERT: A 481 GLN cc_start: 0.8227 (mm-40) cc_final: 0.8005 (mm-40) REVERT: A 509 LYS cc_start: 0.8381 (ttmt) cc_final: 0.7881 (tttp) REVERT: A 571 ARG cc_start: 0.7054 (ttt180) cc_final: 0.6775 (tmm160) REVERT: A 613 GLN cc_start: 0.7490 (mt0) cc_final: 0.7262 (mt0) REVERT: A 800 LYS cc_start: 0.6770 (mtmt) cc_final: 0.6330 (mmtm) REVERT: A 1020 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7454 (pm20) REVERT: A 1021 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7941 (mmtm) REVERT: A 1140 GLU cc_start: 0.7886 (tt0) cc_final: 0.7572 (mt-10) REVERT: A 1176 ASN cc_start: 0.7605 (t0) cc_final: 0.7189 (t0) REVERT: A 1210 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7216 (mpt180) REVERT: A 1274 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7815 (tt0) outliers start: 20 outliers final: 15 residues processed: 166 average time/residue: 0.2637 time to fit residues: 59.4375 Evaluate side-chains 163 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1247 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 104 optimal weight: 0.0060 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9916 Z= 0.187 Angle : 0.513 6.859 13450 Z= 0.268 Chirality : 0.039 0.155 1562 Planarity : 0.003 0.031 1660 Dihedral : 7.419 67.408 1373 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.33 % Allowed : 13.30 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.04 (0.24), residues: 1203 helix: 0.15 (0.19), residues: 747 sheet: -0.88 (0.56), residues: 71 loop : 0.32 (0.34), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 230 HIS 0.004 0.001 HIS A 153 PHE 0.012 0.001 PHE A 98 TYR 0.011 0.001 TYR A 737 ARG 0.006 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7566 (pt0) cc_final: 0.6832 (pm20) REVERT: A 77 LYS cc_start: 0.7931 (pptt) cc_final: 0.7595 (mmmt) REVERT: A 89 TRP cc_start: 0.8347 (p-90) cc_final: 0.8019 (p-90) REVERT: A 226 THR cc_start: 0.8548 (t) cc_final: 0.8307 (p) REVERT: A 230 TRP cc_start: 0.7262 (t60) cc_final: 0.6814 (t60) REVERT: A 264 LYS cc_start: 0.7072 (mttp) cc_final: 0.6809 (mttt) REVERT: A 413 GLN cc_start: 0.7749 (tt0) cc_final: 0.7365 (tp40) REVERT: A 481 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7797 (mt0) REVERT: A 509 LYS cc_start: 0.8384 (ttmt) cc_final: 0.7875 (tttp) REVERT: A 571 ARG cc_start: 0.7043 (ttt180) cc_final: 0.6772 (tmm160) REVERT: A 613 GLN cc_start: 0.7549 (mt0) cc_final: 0.7272 (mt0) REVERT: A 715 ILE cc_start: 0.7990 (mp) cc_final: 0.7679 (tp) REVERT: A 800 LYS cc_start: 0.6738 (mtmt) cc_final: 0.6308 (mmtm) REVERT: A 925 GLU cc_start: 0.7648 (tt0) cc_final: 0.7156 (mt-10) REVERT: A 1020 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7429 (pm20) REVERT: A 1021 LYS cc_start: 0.8356 (mtpt) cc_final: 0.7962 (mmtm) REVERT: A 1140 GLU cc_start: 0.7743 (tt0) cc_final: 0.7498 (mt-10) REVERT: A 1176 ASN cc_start: 0.7598 (t0) cc_final: 0.7189 (t0) REVERT: A 1194 LYS cc_start: 0.7243 (mtmm) cc_final: 0.6966 (ptpt) REVERT: A 1210 ARG cc_start: 0.7900 (mtp85) cc_final: 0.7225 (mpt180) REVERT: A 1274 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7743 (tt0) outliers start: 14 outliers final: 10 residues processed: 161 average time/residue: 0.2660 time to fit residues: 58.6430 Evaluate side-chains 152 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1247 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9916 Z= 0.269 Angle : 0.556 10.863 13450 Z= 0.287 Chirality : 0.041 0.154 1562 Planarity : 0.004 0.033 1660 Dihedral : 7.293 56.551 1371 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.90 % Allowed : 13.20 % Favored : 84.90 % 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: -0.12 (0.24), residues: 1203 helix: 0.06 (0.19), residues: 744 sheet: -0.94 (0.58), residues: 66 loop : 0.15 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 763 HIS 0.005 0.001 HIS A 153 PHE 0.021 0.001 PHE A 352 TYR 0.015 0.001 TYR A1259 ARG 0.007 0.001 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7607 (pt0) cc_final: 0.6832 (pm20) REVERT: A 77 LYS cc_start: 0.7904 (pptt) cc_final: 0.7575 (mmmt) REVERT: A 89 TRP cc_start: 0.8355 (p-90) cc_final: 0.8040 (p-90) REVERT: A 230 TRP cc_start: 0.7313 (t60) cc_final: 0.6781 (t60) REVERT: A 264 LYS cc_start: 0.7143 (mttp) cc_final: 0.6899 (mttt) REVERT: A 413 GLN cc_start: 0.7754 (tt0) cc_final: 0.7360 (tp40) REVERT: A 481 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8122 (mm-40) REVERT: A 509 LYS cc_start: 0.8403 (ttmt) cc_final: 0.7911 (tttm) REVERT: A 613 GLN cc_start: 0.7572 (mt0) cc_final: 0.7304 (mt0) REVERT: A 800 LYS cc_start: 0.6731 (mtmt) cc_final: 0.6287 (mmtm) REVERT: A 925 GLU cc_start: 0.7650 (tt0) cc_final: 0.7154 (mt-10) REVERT: A 1020 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7388 (pm20) REVERT: A 1021 LYS cc_start: 0.8411 (mtpt) cc_final: 0.7988 (mmtm) REVERT: A 1130 THR cc_start: 0.8280 (p) cc_final: 0.7924 (t) REVERT: A 1176 ASN cc_start: 0.7661 (t0) cc_final: 0.7229 (t0) REVERT: A 1183 GLN cc_start: 0.7367 (mt0) cc_final: 0.7117 (mt0) REVERT: A 1194 LYS cc_start: 0.7403 (mtmm) cc_final: 0.7092 (ptpt) REVERT: A 1210 ARG cc_start: 0.7904 (mtp85) cc_final: 0.7227 (mpt180) REVERT: A 1259 TYR cc_start: 0.7569 (t80) cc_final: 0.7228 (t80) REVERT: A 1274 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7732 (tt0) outliers start: 20 outliers final: 16 residues processed: 162 average time/residue: 0.2428 time to fit residues: 53.5780 Evaluate side-chains 154 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1111 HIS Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1247 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 69 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 845 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9916 Z= 0.209 Angle : 0.538 10.804 13450 Z= 0.276 Chirality : 0.040 0.155 1562 Planarity : 0.003 0.032 1660 Dihedral : 7.055 56.477 1371 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.71 % Allowed : 14.15 % Favored : 84.14 % 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: -0.03 (0.24), residues: 1203 helix: 0.17 (0.19), residues: 745 sheet: -0.91 (0.57), residues: 66 loop : 0.11 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 763 HIS 0.005 0.001 HIS A 153 PHE 0.018 0.001 PHE A 352 TYR 0.013 0.001 TYR A 737 ARG 0.007 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7573 (pt0) cc_final: 0.6857 (pm20) REVERT: A 77 LYS cc_start: 0.7911 (pptt) cc_final: 0.7584 (mmmt) REVERT: A 89 TRP cc_start: 0.8376 (p-90) cc_final: 0.8044 (p-90) REVERT: A 230 TRP cc_start: 0.7211 (t60) cc_final: 0.6657 (t60) REVERT: A 264 LYS cc_start: 0.7130 (mttp) cc_final: 0.6891 (mttt) REVERT: A 384 ARG cc_start: 0.7193 (mtm110) cc_final: 0.6958 (mtm-85) REVERT: A 413 GLN cc_start: 0.7736 (tt0) cc_final: 0.7349 (tp40) REVERT: A 481 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8116 (mm-40) REVERT: A 509 LYS cc_start: 0.8392 (ttmt) cc_final: 0.7898 (tttp) REVERT: A 613 GLN cc_start: 0.7570 (mt0) cc_final: 0.7335 (mt0) REVERT: A 715 ILE cc_start: 0.7991 (mp) cc_final: 0.7749 (tp) REVERT: A 800 LYS cc_start: 0.6701 (mtmt) cc_final: 0.6276 (mmtm) REVERT: A 925 GLU cc_start: 0.7645 (tt0) cc_final: 0.7156 (mt-10) REVERT: A 1020 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7368 (pm20) REVERT: A 1021 LYS cc_start: 0.8405 (mtpt) cc_final: 0.7951 (mmtm) REVERT: A 1176 ASN cc_start: 0.7648 (t0) cc_final: 0.7220 (t0) REVERT: A 1194 LYS cc_start: 0.7352 (mtmm) cc_final: 0.7072 (ptpt) REVERT: A 1210 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7191 (mpt180) REVERT: A 1259 TYR cc_start: 0.7656 (t80) cc_final: 0.7350 (t80) REVERT: A 1274 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7708 (tt0) outliers start: 18 outliers final: 16 residues processed: 157 average time/residue: 0.2409 time to fit residues: 53.0959 Evaluate side-chains 151 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1111 HIS Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1247 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 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 183 ASN A 849 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9916 Z= 0.235 Angle : 0.545 10.394 13450 Z= 0.279 Chirality : 0.040 0.155 1562 Planarity : 0.003 0.033 1660 Dihedral : 7.039 57.774 1371 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.80 % Allowed : 14.53 % Favored : 83.67 % 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: -0.09 (0.24), residues: 1203 helix: 0.16 (0.19), residues: 746 sheet: -0.94 (0.56), residues: 66 loop : -0.01 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 763 HIS 0.005 0.001 HIS A 153 PHE 0.013 0.001 PHE A 98 TYR 0.012 0.001 TYR A 737 ARG 0.005 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7587 (pt0) cc_final: 0.6850 (pm20) REVERT: A 77 LYS cc_start: 0.7900 (pptt) cc_final: 0.7580 (mmmt) REVERT: A 89 TRP cc_start: 0.8356 (p-90) cc_final: 0.8037 (p-90) REVERT: A 264 LYS cc_start: 0.7138 (mttp) cc_final: 0.6886 (mttt) REVERT: A 276 MET cc_start: 0.7106 (mmm) cc_final: 0.6764 (mmm) REVERT: A 413 GLN cc_start: 0.7766 (tt0) cc_final: 0.7326 (tp40) REVERT: A 481 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8117 (mm-40) REVERT: A 509 LYS cc_start: 0.8392 (ttmt) cc_final: 0.7893 (tttm) REVERT: A 613 GLN cc_start: 0.7583 (mt0) cc_final: 0.7344 (mt0) REVERT: A 715 ILE cc_start: 0.7952 (mp) cc_final: 0.7700 (tp) REVERT: A 800 LYS cc_start: 0.6719 (mtmt) cc_final: 0.6268 (mmtm) REVERT: A 925 GLU cc_start: 0.7651 (tt0) cc_final: 0.7146 (mt-10) REVERT: A 931 GLN cc_start: 0.7425 (mm-40) cc_final: 0.6914 (mt0) REVERT: A 1020 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7374 (pm20) REVERT: A 1176 ASN cc_start: 0.7669 (t0) cc_final: 0.7226 (t0) REVERT: A 1183 GLN cc_start: 0.7356 (mt0) cc_final: 0.7088 (mt0) REVERT: A 1194 LYS cc_start: 0.7414 (mtmm) cc_final: 0.7131 (ptpt) REVERT: A 1210 ARG cc_start: 0.7862 (mtp85) cc_final: 0.7192 (mpt180) REVERT: A 1259 TYR cc_start: 0.7791 (t80) cc_final: 0.7445 (t80) REVERT: A 1274 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7757 (tt0) outliers start: 19 outliers final: 14 residues processed: 159 average time/residue: 0.2325 time to fit residues: 51.5524 Evaluate side-chains 151 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1111 HIS Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1247 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9916 Z= 0.286 Angle : 0.580 10.546 13450 Z= 0.299 Chirality : 0.041 0.156 1562 Planarity : 0.004 0.034 1660 Dihedral : 7.173 58.184 1371 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.52 % Allowed : 15.29 % Favored : 83.19 % 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: -0.30 (0.24), residues: 1203 helix: 0.03 (0.18), residues: 755 sheet: -0.97 (0.56), residues: 66 loop : -0.19 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 763 HIS 0.006 0.001 HIS A 153 PHE 0.018 0.001 PHE A 352 TYR 0.013 0.001 TYR A 737 ARG 0.007 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7610 (pt0) cc_final: 0.6858 (pm20) REVERT: A 77 LYS cc_start: 0.7939 (pptt) cc_final: 0.7602 (mmmt) REVERT: A 89 TRP cc_start: 0.8364 (p-90) cc_final: 0.8023 (p-90) REVERT: A 264 LYS cc_start: 0.7155 (mttp) cc_final: 0.6929 (mttt) REVERT: A 413 GLN cc_start: 0.7718 (tt0) cc_final: 0.7272 (tp40) REVERT: A 481 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8128 (mm-40) REVERT: A 509 LYS cc_start: 0.8418 (ttmt) cc_final: 0.7917 (tttm) REVERT: A 613 GLN cc_start: 0.7621 (mt0) cc_final: 0.7338 (mt0) REVERT: A 715 ILE cc_start: 0.7973 (mp) cc_final: 0.7704 (tp) REVERT: A 760 ASP cc_start: 0.6965 (t0) cc_final: 0.6372 (t0) REVERT: A 800 LYS cc_start: 0.6720 (mtmt) cc_final: 0.6262 (mmtm) REVERT: A 925 GLU cc_start: 0.7649 (tt0) cc_final: 0.7145 (mt-10) REVERT: A 931 GLN cc_start: 0.7490 (mm-40) cc_final: 0.6930 (mt0) REVERT: A 1020 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7376 (pm20) REVERT: A 1176 ASN cc_start: 0.7704 (t0) cc_final: 0.7257 (t0) REVERT: A 1183 GLN cc_start: 0.7389 (mt0) cc_final: 0.7106 (mt0) REVERT: A 1194 LYS cc_start: 0.7563 (mtmm) cc_final: 0.7237 (ptpt) REVERT: A 1210 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7136 (mpt180) REVERT: A 1274 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7745 (tt0) outliers start: 16 outliers final: 14 residues processed: 150 average time/residue: 0.2482 time to fit residues: 53.0075 Evaluate side-chains 150 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1111 HIS Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 120 optimal weight: 0.0980 chunk 110 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9916 Z= 0.184 Angle : 0.528 10.222 13450 Z= 0.272 Chirality : 0.039 0.155 1562 Planarity : 0.003 0.033 1660 Dihedral : 6.857 59.148 1371 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.33 % Allowed : 15.67 % Favored : 83.00 % 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: -0.07 (0.24), residues: 1203 helix: 0.24 (0.19), residues: 754 sheet: -0.94 (0.56), residues: 66 loop : -0.13 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 763 HIS 0.004 0.001 HIS A 153 PHE 0.010 0.001 PHE A 418 TYR 0.011 0.001 TYR A 737 ARG 0.007 0.000 ARG A 384 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7591 (pt0) cc_final: 0.6876 (pm20) REVERT: A 77 LYS cc_start: 0.7881 (pptt) cc_final: 0.7564 (mmmt) REVERT: A 89 TRP cc_start: 0.8327 (p-90) cc_final: 0.8021 (p-90) REVERT: A 264 LYS cc_start: 0.7103 (mttp) cc_final: 0.6847 (mttt) REVERT: A 413 GLN cc_start: 0.7671 (tt0) cc_final: 0.7279 (tp40) REVERT: A 481 GLN cc_start: 0.8326 (mm-40) cc_final: 0.8106 (mm-40) REVERT: A 509 LYS cc_start: 0.8387 (ttmt) cc_final: 0.7895 (tttp) REVERT: A 613 GLN cc_start: 0.7554 (mt0) cc_final: 0.7282 (mt0) REVERT: A 715 ILE cc_start: 0.7921 (mp) cc_final: 0.7646 (tp) REVERT: A 760 ASP cc_start: 0.6948 (t0) cc_final: 0.6377 (t0) REVERT: A 800 LYS cc_start: 0.6682 (mtmt) cc_final: 0.6254 (mmtm) REVERT: A 925 GLU cc_start: 0.7622 (tt0) cc_final: 0.7141 (mt-10) REVERT: A 931 GLN cc_start: 0.7338 (mm-40) cc_final: 0.6882 (mt0) REVERT: A 1020 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7379 (pm20) REVERT: A 1176 ASN cc_start: 0.7660 (t0) cc_final: 0.7221 (t0) REVERT: A 1194 LYS cc_start: 0.7399 (mtmm) cc_final: 0.7195 (ptpt) REVERT: A 1210 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7161 (mpt180) REVERT: A 1259 TYR cc_start: 0.7644 (t80) cc_final: 0.7359 (t80) REVERT: A 1274 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7735 (tt0) outliers start: 14 outliers final: 12 residues processed: 153 average time/residue: 0.2267 time to fit residues: 48.1110 Evaluate side-chains 150 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1111 HIS Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 0.0770 chunk 40 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.150071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121978 restraints weight = 12393.967| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.16 r_work: 0.3257 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9916 Z= 0.268 Angle : 0.573 10.288 13450 Z= 0.292 Chirality : 0.041 0.156 1562 Planarity : 0.004 0.034 1660 Dihedral : 7.043 59.928 1371 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.33 % Allowed : 15.76 % Favored : 82.91 % 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: -0.25 (0.24), residues: 1203 helix: 0.10 (0.19), residues: 755 sheet: -0.96 (0.56), residues: 66 loop : -0.26 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 863 HIS 0.005 0.001 HIS A 153 PHE 0.025 0.001 PHE A 352 TYR 0.012 0.001 TYR A 737 ARG 0.008 0.000 ARG A 384 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2481.21 seconds wall clock time: 45 minutes 6.02 seconds (2706.02 seconds total)