Starting phenix.real_space_refine on Fri Sep 19 11:11:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u5o_20651/09_2025/6u5o_20651.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u5o_20651/09_2025/6u5o_20651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6u5o_20651/09_2025/6u5o_20651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u5o_20651/09_2025/6u5o_20651.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u5o_20651/09_2025/6u5o_20651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u5o_20651/09_2025/6u5o_20651.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 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 S 72 5.16 5 C 8248 2.51 5 N 2231 2.21 5 O 2426 1.98 5 H 13339 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26316 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 22107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1354, 22107 Classifications: {'peptide': 1354} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1302} Chain breaks: 1 Chain: "P" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1531 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain: "Q" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1022 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "R" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 806 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "S" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 850 Classifications: {'peptide': 53} Link IDs: {'TRANS': 52} Chain breaks: 1 Time building chain proxies: 3.75, per 1000 atoms: 0.14 Number of scatterers: 26316 At special positions: 0 Unit cell: (109.12, 120.28, 101.68, 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 72 16.00 O 2426 8.00 N 2231 7.00 C 8248 6.00 H 13339 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 700.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3090 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 9 sheets defined 58.5% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'L' and resid 24 through 36 removed outlier: 3.951A pdb=" N LEU L 34 " --> pdb=" O ILE L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 52 removed outlier: 3.620A pdb=" N LYS L 47 " --> pdb=" O ASP L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 67 Processing helix chain 'L' and resid 77 through 80 Processing helix chain 'L' and resid 81 through 86 Processing helix chain 'L' and resid 93 through 120 removed outlier: 3.841A pdb=" N TRP L 118 " --> pdb=" O MET L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 139 removed outlier: 3.501A pdb=" N ILE L 139 " --> pdb=" O VAL L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 167 removed outlier: 4.114A pdb=" N ASN L 149 " --> pdb=" O ASN L 145 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE L 166 " --> pdb=" O ARG L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 231 removed outlier: 3.676A pdb=" N CYS L 222 " --> pdb=" O ASN L 218 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE L 223 " --> pdb=" O ALA L 219 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER L 226 " --> pdb=" O CYS L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 261 Processing helix chain 'L' and resid 264 through 270 Processing helix chain 'L' and resid 270 through 285 removed outlier: 4.422A pdb=" N GLY L 274 " --> pdb=" O LYS L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 316 removed outlier: 4.747A pdb=" N ARG L 292 " --> pdb=" O GLN L 288 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN L 299 " --> pdb=" O ASN L 295 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY L 300 " --> pdb=" O THR L 296 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS L 309 " --> pdb=" O LEU L 305 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASN L 310 " --> pdb=" O THR L 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 328 through 347 removed outlier: 3.824A pdb=" N VAL L 332 " --> pdb=" O MET L 328 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE L 347 " --> pdb=" O ILE L 343 " (cutoff:3.500A) Processing helix chain 'L' and resid 352 through 357 Processing helix chain 'L' and resid 359 through 364 removed outlier: 3.910A pdb=" N PHE L 364 " --> pdb=" O ILE L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 383 removed outlier: 3.793A pdb=" N LEU L 380 " --> pdb=" O ASP L 376 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN L 381 " --> pdb=" O ALA L 377 " (cutoff:3.500A) Processing helix chain 'L' and resid 390 through 412 removed outlier: 3.614A pdb=" N ARG L 397 " --> pdb=" O LEU L 393 " (cutoff:3.500A) Processing helix chain 'L' and resid 425 through 435 Processing helix chain 'L' and resid 444 through 452 removed outlier: 3.534A pdb=" N PHE L 448 " --> pdb=" O SER L 444 " (cutoff:3.500A) Processing helix chain 'L' and resid 467 through 472 Processing helix chain 'L' and resid 484 through 488 Processing helix chain 'L' and resid 494 through 505 Processing helix chain 'L' and resid 509 through 514 removed outlier: 3.739A pdb=" N LYS L 513 " --> pdb=" O ASP L 510 " (cutoff:3.500A) Processing helix chain 'L' and resid 516 through 523 Processing helix chain 'L' and resid 530 through 539 removed outlier: 3.773A pdb=" N SER L 534 " --> pdb=" O LYS L 530 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL L 537 " --> pdb=" O LYS L 533 " (cutoff:3.500A) Processing helix chain 'L' and resid 568 through 586 removed outlier: 3.663A pdb=" N ILE L 574 " --> pdb=" O LYS L 570 " (cutoff:3.500A) Processing helix chain 'L' and resid 590 through 595 removed outlier: 4.091A pdb=" N LEU L 594 " --> pdb=" O PHE L 590 " (cutoff:3.500A) Processing helix chain 'L' and resid 599 through 604 removed outlier: 3.731A pdb=" N GLN L 603 " --> pdb=" O ASP L 599 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG L 604 " --> pdb=" O LEU L 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 599 through 604' Processing helix chain 'L' and resid 639 through 643 removed outlier: 3.891A pdb=" N PHE L 643 " --> pdb=" O ASN L 640 " (cutoff:3.500A) Processing helix chain 'L' and resid 644 through 660 removed outlier: 4.989A pdb=" N ILE L 650 " --> pdb=" O GLU L 646 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N CYS L 651 " --> pdb=" O THR L 647 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL L 654 " --> pdb=" O ILE L 650 " (cutoff:3.500A) Processing helix chain 'L' and resid 666 through 671 Processing helix chain 'L' and resid 672 through 675 Processing helix chain 'L' and resid 715 through 734 removed outlier: 4.204A pdb=" N LEU L 727 " --> pdb=" O ALA L 723 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP L 728 " --> pdb=" O ILE L 724 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL L 729 " --> pdb=" O SER L 725 " (cutoff:3.500A) Processing helix chain 'L' and resid 763 through 784 Processing helix chain 'L' and resid 802 through 806 removed outlier: 3.847A pdb=" N LYS L 805 " --> pdb=" O PHE L 802 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL L 806 " --> pdb=" O ILE L 803 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 802 through 806' Processing helix chain 'L' and resid 820 through 824 removed outlier: 4.145A pdb=" N ARG L 823 " --> pdb=" O LYS L 820 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL L 824 " --> pdb=" O VAL L 821 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 820 through 824' Processing helix chain 'L' and resid 834 through 847 Processing helix chain 'L' and resid 847 through 852 Processing helix chain 'L' and resid 855 through 872 removed outlier: 3.932A pdb=" N TRP L 866 " --> pdb=" O LEU L 862 " (cutoff:3.500A) Processing helix chain 'L' and resid 883 through 901 Processing helix chain 'L' and resid 907 through 914 Processing helix chain 'L' and resid 916 through 920 Processing helix chain 'L' and resid 937 through 953 Processing helix chain 'L' and resid 962 through 970 removed outlier: 3.782A pdb=" N LYS L 966 " --> pdb=" O VAL L 962 " (cutoff:3.500A) Processing helix chain 'L' and resid 979 through 985 Processing helix chain 'L' and resid 997 through 1012 removed outlier: 4.318A pdb=" N THR L1004 " --> pdb=" O ASP L1000 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALA L1005 " --> pdb=" O ILE L1001 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU L1012 " --> pdb=" O SER L1008 " (cutoff:3.500A) Processing helix chain 'L' and resid 1015 through 1024 removed outlier: 3.741A pdb=" N HIS L1024 " --> pdb=" O ASP L1020 " (cutoff:3.500A) Processing helix chain 'L' and resid 1024 through 1036 removed outlier: 4.417A pdb=" N GLY L1033 " --> pdb=" O GLU L1029 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE L1034 " --> pdb=" O GLU L1030 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE L1035 " --> pdb=" O GLU L1031 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA L1036 " --> pdb=" O VAL L1032 " (cutoff:3.500A) Processing helix chain 'L' and resid 1043 through 1054 removed outlier: 3.628A pdb=" N LEU L1054 " --> pdb=" O LEU L1050 " (cutoff:3.500A) Processing helix chain 'L' and resid 1055 through 1068 removed outlier: 3.699A pdb=" N ALA L1059 " --> pdb=" O PRO L1055 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY L1068 " --> pdb=" O ASN L1064 " (cutoff:3.500A) Processing helix chain 'L' and resid 1084 through 1099 removed outlier: 3.700A pdb=" N LEU L1098 " --> pdb=" O MET L1094 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY L1099 " --> pdb=" O LEU L1095 " (cutoff:3.500A) Processing helix chain 'L' and resid 1099 through 1105 Processing helix chain 'L' and resid 1124 through 1136 removed outlier: 3.909A pdb=" N THR L1130 " --> pdb=" O GLN L1126 " (cutoff:3.500A) Processing helix chain 'L' and resid 1207 through 1224 Processing helix chain 'L' and resid 1229 through 1242 Processing helix chain 'L' and resid 1249 through 1253 Processing helix chain 'L' and resid 1260 through 1265 Processing helix chain 'L' and resid 1279 through 1284 Processing helix chain 'L' and resid 1290 through 1292 No H-bonds generated for 'chain 'L' and resid 1290 through 1292' Processing helix chain 'L' and resid 1293 through 1301 Processing helix chain 'L' and resid 1309 through 1328 Processing helix chain 'L' and resid 1359 through 1368 removed outlier: 3.984A pdb=" N LYS L1363 " --> pdb=" O LYS L1359 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 193 removed outlier: 3.771A pdb=" N GLU P 177 " --> pdb=" O GLU P 173 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU P 181 " --> pdb=" O GLU P 177 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR P 192 " --> pdb=" O GLY P 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 214 through 226 Processing helix chain 'P' and resid 227 through 238 removed outlier: 3.747A pdb=" N ALA P 231 " --> pdb=" O LYS P 227 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU P 232 " --> pdb=" O GLY P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 254 through 264 removed outlier: 4.277A pdb=" N LEU P 258 " --> pdb=" O LYS P 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 197 removed outlier: 3.879A pdb=" N GLU Q 177 " --> pdb=" O GLU Q 173 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER Q 178 " --> pdb=" O ALA Q 174 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE Q 179 " --> pdb=" O ARG Q 175 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE Q 186 " --> pdb=" O LYS Q 182 " (cutoff:3.500A) Processing helix chain 'Q' and resid 199 through 204 Processing helix chain 'Q' and resid 207 through 213 Processing helix chain 'Q' and resid 217 through 232 Processing helix chain 'Q' and resid 233 through 236 removed outlier: 3.873A pdb=" N GLU Q 236 " --> pdb=" O MET Q 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 233 through 236' Processing helix chain 'R' and resid 173 through 191 Processing helix chain 'R' and resid 200 through 205 removed outlier: 4.257A pdb=" N ASP R 205 " --> pdb=" O THR R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 218 removed outlier: 4.365A pdb=" N ASP R 209 " --> pdb=" O ASP R 205 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA R 210 " --> pdb=" O GLY R 206 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG R 215 " --> pdb=" O MET R 211 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU R 218 " --> pdb=" O ILE R 214 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 191 removed outlier: 4.130A pdb=" N LEU S 176 " --> pdb=" O ILE S 172 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLU S 177 " --> pdb=" O GLU S 173 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER S 178 " --> pdb=" O ALA S 174 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER S 184 " --> pdb=" O GLU S 180 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET S 185 " --> pdb=" O GLU S 181 " (cutoff:3.500A) Processing helix chain 'S' and resid 205 through 231 removed outlier: 3.777A pdb=" N ASP S 209 " --> pdb=" O ASP S 205 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG S 215 " --> pdb=" O MET S 211 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU S 217 " --> pdb=" O GLY S 213 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE S 219 " --> pdb=" O ARG S 215 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA S 220 " --> pdb=" O GLU S 216 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS S 224 " --> pdb=" O ALA S 220 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS S 229 " --> pdb=" O GLU S 225 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AA2, first strand: chain 'L' and resid 172 through 174 removed outlier: 3.649A pdb=" N ARG L 197 " --> pdb=" O SER L 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 387 through 389 Processing sheet with id=AA4, first strand: chain 'L' and resid 550 through 551 Processing sheet with id=AA5, first strand: chain 'L' and resid 737 through 741 Processing sheet with id=AA6, first strand: chain 'L' and resid 807 through 809 removed outlier: 3.671A pdb=" N ILE L 807 " --> pdb=" O HIS L 814 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 1154 through 1157 Processing sheet with id=AA8, first strand: chain 'L' and resid 1196 through 1197 removed outlier: 3.651A pdb=" N LEU L1197 " --> pdb=" O ARG L1255 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG L1255 " --> pdb=" O LEU L1197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'P' and resid 199 through 200 621 hydrogen bonds defined for protein. 1791 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: 6.13 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13318 1.03 - 1.23: 25 1.23 - 1.42: 5266 1.42 - 1.62: 7792 1.62 - 1.81: 123 Bond restraints: 26524 Sorted by residual: bond pdb=" CB VAL P 262 " pdb=" CG1 VAL P 262 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.88e+00 bond pdb=" CG GLU P 263 " pdb=" CD GLU P 263 " ideal model delta sigma weight residual 1.516 1.553 -0.037 2.50e-02 1.60e+03 2.15e+00 bond pdb=" CB ILE L 363 " pdb=" CG2 ILE L 363 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.60e+00 bond pdb=" CG PRO L1041 " pdb=" CD PRO L1041 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.59e+00 bond pdb=" C ASP L 762 " pdb=" N GLU L 763 " ideal model delta sigma weight residual 1.324 1.354 -0.030 2.56e-02 1.53e+03 1.39e+00 ... (remaining 26519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 46907 1.84 - 3.68: 1138 3.68 - 5.52: 82 5.52 - 7.36: 9 7.36 - 9.21: 2 Bond angle restraints: 48138 Sorted by residual: angle pdb=" C PHE L1171 " pdb=" CA PHE L1171 " pdb=" CB PHE L1171 " ideal model delta sigma weight residual 109.55 102.40 7.15 2.03e+00 2.43e-01 1.24e+01 angle pdb=" CA THR L1192 " pdb=" CB THR L1192 " pdb=" CG2 THR L1192 " ideal model delta sigma weight residual 110.50 116.00 -5.50 1.70e+00 3.46e-01 1.05e+01 angle pdb=" C ASN L1138 " pdb=" N MET L1139 " pdb=" CA MET L1139 " ideal model delta sigma weight residual 122.54 127.86 -5.32 1.65e+00 3.67e-01 1.04e+01 angle pdb=" C VAL L 75 " pdb=" N VAL L 76 " pdb=" CA VAL L 76 " ideal model delta sigma weight residual 121.71 126.45 -4.74 1.50e+00 4.44e-01 1.00e+01 angle pdb=" C VAL L 672 " pdb=" CA VAL L 672 " pdb=" CB VAL L 672 " ideal model delta sigma weight residual 114.00 110.39 3.61 1.31e+00 5.83e-01 7.59e+00 ... (remaining 48133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 10803 17.70 - 35.40: 1198 35.40 - 53.10: 229 53.10 - 70.80: 63 70.80 - 88.50: 7 Dihedral angle restraints: 12300 sinusoidal: 6907 harmonic: 5393 Sorted by residual: dihedral pdb=" CA ILE L 130 " pdb=" C ILE L 130 " pdb=" N LEU L 131 " pdb=" CA LEU L 131 " ideal model delta harmonic sigma weight residual 180.00 -152.82 -27.18 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ARG L1264 " pdb=" C ARG L1264 " pdb=" N LEU L1265 " pdb=" CA LEU L1265 " ideal model delta harmonic sigma weight residual -180.00 -153.75 -26.25 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ASN L 204 " pdb=" C ASN L 204 " pdb=" N GLN L 205 " pdb=" CA GLN L 205 " ideal model delta harmonic sigma weight residual 180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 12297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1589 0.049 - 0.097: 359 0.097 - 0.146: 98 0.146 - 0.194: 7 0.194 - 0.243: 2 Chirality restraints: 2055 Sorted by residual: chirality pdb=" CA TRP L1136 " pdb=" N TRP L1136 " pdb=" C TRP L1136 " pdb=" CB TRP L1136 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ASN L1137 " pdb=" N ASN L1137 " pdb=" C ASN L1137 " pdb=" CB ASN L1137 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CA ILE L 182 " pdb=" N ILE L 182 " pdb=" C ILE L 182 " pdb=" CB ILE L 182 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.96e-01 ... (remaining 2052 not shown) Planarity restraints: 3810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN L 890 " 0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C ASN L 890 " -0.079 2.00e-02 2.50e+03 pdb=" O ASN L 890 " 0.029 2.00e-02 2.50e+03 pdb=" N LYS L 891 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER Q 178 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C SER Q 178 " -0.070 2.00e-02 2.50e+03 pdb=" O SER Q 178 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE Q 179 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP L 209 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C TRP L 209 " -0.059 2.00e-02 2.50e+03 pdb=" O TRP L 209 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS L 210 " 0.020 2.00e-02 2.50e+03 ... (remaining 3807 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 2095 2.22 - 2.81: 58288 2.81 - 3.41: 69002 3.41 - 4.00: 92038 4.00 - 4.60: 145820 Nonbonded interactions: 367243 Sorted by model distance: nonbonded pdb=" OE2 GLU L 279 " pdb=" HZ2 LYS L 344 " model vdw 1.621 2.450 nonbonded pdb=" H LYS L 790 " pdb=" OE2 GLU L 793 " model vdw 1.678 2.450 nonbonded pdb=" O GLU L1133 " pdb=" H ASN L1138 " model vdw 1.680 2.450 nonbonded pdb="HH21 ARG L 294 " pdb=" OD1 ASN P 259 " model vdw 1.680 2.450 nonbonded pdb=" O THR L1130 " pdb=" HG1 THR L1134 " model vdw 1.686 2.450 ... (remaining 367238 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.020 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: 0.100 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 23.930 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 0.056 13185 Z= 0.213 Angle : 0.782 9.206 17778 Z= 0.442 Chirality : 0.045 0.243 2055 Planarity : 0.006 0.067 2248 Dihedral : 14.702 88.498 5062 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.22 (0.17), residues: 1609 helix: -2.36 (0.14), residues: 849 sheet: -2.20 (0.54), residues: 80 loop : -3.39 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 282 TYR 0.010 0.002 TYR L 501 PHE 0.035 0.002 PHE L1171 TRP 0.011 0.002 TRP L 428 HIS 0.009 0.001 HIS L1287 Details of bonding type rmsd covalent geometry : bond 0.00492 (13185) covalent geometry : angle 0.78243 (17778) hydrogen bonds : bond 0.08492 ( 621) hydrogen bonds : angle 5.57066 ( 1791) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 98 LYS cc_start: 0.7380 (mttt) cc_final: 0.7098 (mtpt) REVERT: L 345 LEU cc_start: 0.8464 (mt) cc_final: 0.8045 (mt) REVERT: L 349 LYS cc_start: 0.7460 (mmtt) cc_final: 0.6673 (mttt) REVERT: L 576 ILE cc_start: 0.8795 (mm) cc_final: 0.8526 (mm) REVERT: L 687 GLU cc_start: 0.7767 (tp30) cc_final: 0.7548 (tp30) REVERT: L 850 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6695 (mt-10) REVERT: L 1213 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7182 (mm-40) REVERT: L 1235 ASN cc_start: 0.7813 (t0) cc_final: 0.7476 (t0) REVERT: L 1252 LEU cc_start: 0.8100 (mt) cc_final: 0.7865 (mt) REVERT: L 1277 SER cc_start: 0.9285 (t) cc_final: 0.9054 (t) REVERT: L 1286 TYR cc_start: 0.9353 (m-80) cc_final: 0.9042 (m-80) REVERT: L 1321 MET cc_start: 0.7857 (mmm) cc_final: 0.7365 (mtp) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.3229 time to fit residues: 140.3845 Evaluate side-chains 243 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 149 ASN L 420 ASN L 473 ASN L 585 ASN ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1097 ASN L1119 ASN L1260 ASN L1303 ASN P 240 GLN P 259 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.155816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.141554 restraints weight = 44111.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.142781 restraints weight = 37804.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.146250 restraints weight = 27410.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.146720 restraints weight = 16648.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.146731 restraints weight = 12900.956| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13185 Z= 0.237 Angle : 0.645 5.923 17778 Z= 0.351 Chirality : 0.042 0.167 2055 Planarity : 0.005 0.081 2248 Dihedral : 5.293 19.964 1758 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.59 % Favored : 93.35 % Rotamer: Outliers : 0.89 % Allowed : 10.61 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.55 (0.19), residues: 1609 helix: -0.86 (0.17), residues: 859 sheet: -2.37 (0.50), residues: 86 loop : -2.69 (0.21), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 482 TYR 0.019 0.002 TYR L 706 PHE 0.017 0.002 PHE L 639 TRP 0.012 0.002 TRP L 415 HIS 0.006 0.001 HIS L 659 Details of bonding type rmsd covalent geometry : bond 0.00545 (13185) covalent geometry : angle 0.64459 (17778) hydrogen bonds : bond 0.04600 ( 621) hydrogen bonds : angle 4.57409 ( 1791) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 278 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 TYR cc_start: 0.8761 (m-80) cc_final: 0.8501 (m-80) REVERT: L 349 LYS cc_start: 0.7460 (mmtt) cc_final: 0.6893 (mttt) REVERT: L 638 LYS cc_start: 0.8654 (mtmt) cc_final: 0.7982 (mttp) REVERT: L 657 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7498 (mt-10) REVERT: L 733 LYS cc_start: 0.7656 (mttt) cc_final: 0.7355 (mtpt) REVERT: L 738 MET cc_start: 0.7491 (mtt) cc_final: 0.7269 (mtt) REVERT: L 765 LYS cc_start: 0.6822 (ttmt) cc_final: 0.6592 (tppt) REVERT: L 796 ILE cc_start: 0.8580 (tp) cc_final: 0.8319 (pt) REVERT: L 1094 MET cc_start: 0.8029 (ptp) cc_final: 0.7726 (ptm) REVERT: L 1103 ARG cc_start: 0.8392 (ttm110) cc_final: 0.8100 (ttp-110) REVERT: L 1141 ILE cc_start: 0.8587 (mm) cc_final: 0.8220 (mt) REVERT: L 1220 MET cc_start: 0.8185 (tpp) cc_final: 0.7567 (ttm) REVERT: L 1255 ARG cc_start: 0.7700 (mtm-85) cc_final: 0.7491 (ttm-80) outliers start: 13 outliers final: 9 residues processed: 283 average time/residue: 0.2922 time to fit residues: 115.6222 Evaluate side-chains 249 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 240 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 473 ASN Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 562 ARG Chi-restraints excluded: chain L residue 1009 ILE Chi-restraints excluded: chain L residue 1202 ASN Chi-restraints excluded: chain L residue 1283 THR Chi-restraints excluded: chain L residue 1372 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 34 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 153 optimal weight: 0.3980 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 ASN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 152 ASN L 348 ASN L 420 ASN L 683 HIS ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1119 ASN P 240 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.153433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.139369 restraints weight = 44239.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.141102 restraints weight = 31920.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.143044 restraints weight = 25229.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.143354 restraints weight = 18136.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.143422 restraints weight = 14850.612| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13185 Z= 0.181 Angle : 0.572 5.448 17778 Z= 0.309 Chirality : 0.040 0.163 2055 Planarity : 0.004 0.054 2248 Dihedral : 5.068 21.153 1758 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.68 % Allowed : 13.69 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.20), residues: 1609 helix: -0.21 (0.17), residues: 854 sheet: -2.23 (0.49), residues: 86 loop : -2.41 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L1103 TYR 0.021 0.002 TYR L 795 PHE 0.013 0.001 PHE L 275 TRP 0.011 0.001 TRP L 428 HIS 0.006 0.001 HIS L1162 Details of bonding type rmsd covalent geometry : bond 0.00430 (13185) covalent geometry : angle 0.57195 (17778) hydrogen bonds : bond 0.04108 ( 621) hydrogen bonds : angle 4.28539 ( 1791) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 257 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 TYR cc_start: 0.8826 (m-80) cc_final: 0.8586 (m-80) REVERT: L 42 ASN cc_start: 0.7163 (OUTLIER) cc_final: 0.6893 (t0) REVERT: L 349 LYS cc_start: 0.7307 (mmtt) cc_final: 0.6832 (mttt) REVERT: L 638 LYS cc_start: 0.8665 (mtmt) cc_final: 0.7986 (mttp) REVERT: L 657 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7420 (mt-10) REVERT: L 733 LYS cc_start: 0.7736 (mttt) cc_final: 0.7448 (mtpt) REVERT: L 738 MET cc_start: 0.7434 (mtt) cc_final: 0.7203 (mtt) REVERT: L 765 LYS cc_start: 0.6865 (ttmt) cc_final: 0.6639 (tppt) REVERT: L 874 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7227 (mt-10) REVERT: L 1093 MET cc_start: 0.6693 (ttp) cc_final: 0.6358 (ttt) REVERT: L 1141 ILE cc_start: 0.8411 (mm) cc_final: 0.8146 (mt) REVERT: L 1169 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7136 (mt-10) REVERT: L 1220 MET cc_start: 0.8216 (tpp) cc_final: 0.7563 (ttm) REVERT: L 1255 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7502 (ttm-80) REVERT: L 1342 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6844 (mm-30) outliers start: 10 outliers final: 5 residues processed: 261 average time/residue: 0.2963 time to fit residues: 107.6109 Evaluate side-chains 247 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 241 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 ASN Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 1009 ILE Chi-restraints excluded: chain L residue 1283 THR Chi-restraints excluded: chain L residue 1372 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 110 optimal weight: 9.9990 chunk 159 optimal weight: 30.0000 chunk 127 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 420 ASN ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.146757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.132415 restraints weight = 45374.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.133377 restraints weight = 34291.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.134176 restraints weight = 30134.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.134605 restraints weight = 24208.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.135381 restraints weight = 20791.944| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13185 Z= 0.263 Angle : 0.637 5.879 17778 Z= 0.345 Chirality : 0.043 0.152 2055 Planarity : 0.005 0.087 2248 Dihedral : 5.160 24.276 1758 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.57 % Allowed : 15.95 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.20), residues: 1609 helix: -0.14 (0.17), residues: 853 sheet: -2.09 (0.55), residues: 77 loop : -2.34 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L1103 TYR 0.021 0.002 TYR L 706 PHE 0.016 0.002 PHE L 639 TRP 0.015 0.002 TRP L 415 HIS 0.007 0.001 HIS L1162 Details of bonding type rmsd covalent geometry : bond 0.00627 (13185) covalent geometry : angle 0.63667 (17778) hydrogen bonds : bond 0.04585 ( 621) hydrogen bonds : angle 4.40621 ( 1791) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 261 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 TYR cc_start: 0.8931 (m-80) cc_final: 0.8712 (m-80) REVERT: L 26 GLU cc_start: 0.7555 (tt0) cc_final: 0.6928 (tt0) REVERT: L 141 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8164 (p) REVERT: L 142 TRP cc_start: 0.7480 (p90) cc_final: 0.6914 (p90) REVERT: L 349 LYS cc_start: 0.7383 (mmtt) cc_final: 0.6888 (pttp) REVERT: L 470 MET cc_start: 0.7876 (tmm) cc_final: 0.7537 (tmm) REVERT: L 638 LYS cc_start: 0.8662 (mtmt) cc_final: 0.7965 (mttp) REVERT: L 657 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7511 (mt-10) REVERT: L 733 LYS cc_start: 0.7814 (mttt) cc_final: 0.7515 (mtpt) REVERT: L 738 MET cc_start: 0.7518 (mtt) cc_final: 0.7263 (mtt) REVERT: L 808 GLN cc_start: 0.7946 (mt0) cc_final: 0.7641 (mt0) REVERT: L 1141 ILE cc_start: 0.8489 (mm) cc_final: 0.8187 (mt) REVERT: L 1169 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7168 (mt-10) REVERT: L 1220 MET cc_start: 0.8326 (tpp) cc_final: 0.7837 (ttm) REVERT: L 1255 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.7498 (ttm-80) REVERT: L 1342 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6941 (mm-30) REVERT: L 1375 LYS cc_start: 0.8501 (mttt) cc_final: 0.7968 (mmtt) REVERT: P 253 GLU cc_start: 0.6458 (pt0) cc_final: 0.6224 (mm-30) REVERT: Q 234 MET cc_start: 0.3832 (mtt) cc_final: 0.3139 (tmm) REVERT: S 211 MET cc_start: 0.6718 (mtt) cc_final: 0.6487 (mtt) outliers start: 23 outliers final: 18 residues processed: 274 average time/residue: 0.3032 time to fit residues: 115.4627 Evaluate side-chains 266 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 247 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 118 TRP Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 447 ASP Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 589 PHE Chi-restraints excluded: chain L residue 631 SER Chi-restraints excluded: chain L residue 648 THR Chi-restraints excluded: chain L residue 724 ILE Chi-restraints excluded: chain L residue 806 VAL Chi-restraints excluded: chain L residue 830 THR Chi-restraints excluded: chain L residue 985 ASP Chi-restraints excluded: chain L residue 1009 ILE Chi-restraints excluded: chain L residue 1283 THR Chi-restraints excluded: chain L residue 1372 SER Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 129 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 420 ASN ** L 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1119 ASN L1260 ASN L1312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.147975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.133514 restraints weight = 45023.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.134196 restraints weight = 34368.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.134958 restraints weight = 31458.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.135648 restraints weight = 24374.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.136614 restraints weight = 20944.923| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13185 Z= 0.180 Angle : 0.569 6.848 17778 Z= 0.304 Chirality : 0.040 0.145 2055 Planarity : 0.004 0.047 2248 Dihedral : 4.951 19.733 1758 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.57 % Allowed : 17.39 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.20), residues: 1609 helix: 0.08 (0.18), residues: 856 sheet: -1.67 (0.49), residues: 92 loop : -2.26 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 538 TYR 0.017 0.002 TYR L 795 PHE 0.012 0.001 PHE L 639 TRP 0.011 0.001 TRP L 428 HIS 0.008 0.001 HIS L1162 Details of bonding type rmsd covalent geometry : bond 0.00430 (13185) covalent geometry : angle 0.56889 (17778) hydrogen bonds : bond 0.04076 ( 621) hydrogen bonds : angle 4.22573 ( 1791) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 141 SER cc_start: 0.8541 (OUTLIER) cc_final: 0.8197 (p) REVERT: L 142 TRP cc_start: 0.7433 (p90) cc_final: 0.7118 (p90) REVERT: L 349 LYS cc_start: 0.7332 (mmtt) cc_final: 0.6883 (pttp) REVERT: L 470 MET cc_start: 0.7827 (tmm) cc_final: 0.7533 (tmm) REVERT: L 638 LYS cc_start: 0.8604 (mtmt) cc_final: 0.7922 (mttp) REVERT: L 733 LYS cc_start: 0.7879 (mttt) cc_final: 0.7382 (mtmt) REVERT: L 738 MET cc_start: 0.7476 (mtt) cc_final: 0.7231 (mtt) REVERT: L 808 GLN cc_start: 0.7917 (mt0) cc_final: 0.7599 (mt0) REVERT: L 1070 LYS cc_start: 0.7851 (ttmt) cc_final: 0.7404 (tttt) REVERT: L 1141 ILE cc_start: 0.8455 (mm) cc_final: 0.8178 (mt) REVERT: L 1169 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7130 (mt-10) REVERT: L 1220 MET cc_start: 0.8371 (tpp) cc_final: 0.7955 (ttm) REVERT: L 1375 LYS cc_start: 0.8527 (mttt) cc_final: 0.7998 (mmtt) REVERT: Q 234 MET cc_start: 0.3823 (mtt) cc_final: 0.3140 (tmm) outliers start: 23 outliers final: 15 residues processed: 262 average time/residue: 0.3105 time to fit residues: 112.3062 Evaluate side-chains 259 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 243 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 118 TRP Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 562 ARG Chi-restraints excluded: chain L residue 589 PHE Chi-restraints excluded: chain L residue 631 SER Chi-restraints excluded: chain L residue 732 VAL Chi-restraints excluded: chain L residue 806 VAL Chi-restraints excluded: chain L residue 1009 ILE Chi-restraints excluded: chain L residue 1283 THR Chi-restraints excluded: chain L residue 1372 SER Chi-restraints excluded: chain L residue 1379 LEU Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 84 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 50 optimal weight: 0.2980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 ASN L 420 ASN L 529 GLN ** L 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.149301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.135022 restraints weight = 44705.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.136551 restraints weight = 32317.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.137177 restraints weight = 26453.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.137593 restraints weight = 20900.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.138072 restraints weight = 18547.269| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13185 Z= 0.129 Angle : 0.520 4.881 17778 Z= 0.276 Chirality : 0.039 0.150 2055 Planarity : 0.004 0.048 2248 Dihedral : 4.742 18.987 1758 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.30 % Allowed : 18.41 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.21), residues: 1609 helix: 0.36 (0.18), residues: 863 sheet: -1.38 (0.50), residues: 92 loop : -2.15 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 538 TYR 0.018 0.001 TYR L 795 PHE 0.012 0.001 PHE L 639 TRP 0.011 0.001 TRP L 428 HIS 0.007 0.001 HIS L1162 Details of bonding type rmsd covalent geometry : bond 0.00305 (13185) covalent geometry : angle 0.51954 (17778) hydrogen bonds : bond 0.03671 ( 621) hydrogen bonds : angle 4.07256 ( 1791) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 141 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8156 (p) REVERT: L 142 TRP cc_start: 0.7372 (p90) cc_final: 0.7169 (p90) REVERT: L 318 SER cc_start: 0.8102 (t) cc_final: 0.7702 (p) REVERT: L 349 LYS cc_start: 0.7144 (mmtt) cc_final: 0.6683 (pttp) REVERT: L 470 MET cc_start: 0.7885 (tmm) cc_final: 0.7579 (tmm) REVERT: L 638 LYS cc_start: 0.8596 (mtmt) cc_final: 0.7901 (mttp) REVERT: L 733 LYS cc_start: 0.7824 (mttt) cc_final: 0.7302 (mtmt) REVERT: L 738 MET cc_start: 0.7429 (mtt) cc_final: 0.7204 (mtt) REVERT: L 808 GLN cc_start: 0.7854 (mt0) cc_final: 0.7538 (mt0) REVERT: L 1141 ILE cc_start: 0.8478 (mm) cc_final: 0.8156 (mt) REVERT: L 1220 MET cc_start: 0.8305 (tpp) cc_final: 0.7935 (ttm) REVERT: L 1375 LYS cc_start: 0.8525 (mttt) cc_final: 0.7987 (mmtt) REVERT: Q 234 MET cc_start: 0.3818 (mtt) cc_final: 0.3141 (tmm) outliers start: 19 outliers final: 11 residues processed: 254 average time/residue: 0.3202 time to fit residues: 110.9443 Evaluate side-chains 249 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 237 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 118 TRP Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 562 ARG Chi-restraints excluded: chain L residue 589 PHE Chi-restraints excluded: chain L residue 631 SER Chi-restraints excluded: chain L residue 1144 VAL Chi-restraints excluded: chain L residue 1283 THR Chi-restraints excluded: chain L residue 1372 SER Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 46 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 420 ASN ** L 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.145201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.130906 restraints weight = 45508.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.131988 restraints weight = 34965.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.132475 restraints weight = 31439.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.133151 restraints weight = 24850.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.133507 restraints weight = 21261.651| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13185 Z= 0.199 Angle : 0.574 5.791 17778 Z= 0.308 Chirality : 0.041 0.174 2055 Planarity : 0.004 0.074 2248 Dihedral : 4.852 19.764 1758 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 1.44 % Allowed : 19.37 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.21), residues: 1609 helix: 0.31 (0.18), residues: 863 sheet: -1.17 (0.52), residues: 92 loop : -2.21 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L1300 TYR 0.017 0.002 TYR L 932 PHE 0.013 0.001 PHE L 639 TRP 0.012 0.002 TRP L 415 HIS 0.008 0.001 HIS L1162 Details of bonding type rmsd covalent geometry : bond 0.00475 (13185) covalent geometry : angle 0.57356 (17778) hydrogen bonds : bond 0.04173 ( 621) hydrogen bonds : angle 4.19761 ( 1791) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 243 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 141 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8363 (p) REVERT: L 142 TRP cc_start: 0.7528 (p90) cc_final: 0.7257 (p90) REVERT: L 349 LYS cc_start: 0.7359 (mmtt) cc_final: 0.6937 (pttp) REVERT: L 470 MET cc_start: 0.8011 (tmm) cc_final: 0.7696 (tmm) REVERT: L 638 LYS cc_start: 0.8606 (mtmt) cc_final: 0.7912 (mttp) REVERT: L 733 LYS cc_start: 0.7840 (mttt) cc_final: 0.7331 (mtmt) REVERT: L 738 MET cc_start: 0.7429 (mtt) cc_final: 0.7203 (mtt) REVERT: L 808 GLN cc_start: 0.7893 (mt0) cc_final: 0.7631 (mt0) REVERT: L 1133 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8329 (mm-30) REVERT: L 1141 ILE cc_start: 0.8476 (mm) cc_final: 0.8234 (mt) REVERT: L 1220 MET cc_start: 0.8303 (tpp) cc_final: 0.7993 (ttm) REVERT: L 1375 LYS cc_start: 0.8461 (mttt) cc_final: 0.7993 (mmtt) outliers start: 21 outliers final: 17 residues processed: 257 average time/residue: 0.2927 time to fit residues: 104.9778 Evaluate side-chains 258 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 240 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 118 TRP Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 226 SER Chi-restraints excluded: chain L residue 278 SER Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 589 PHE Chi-restraints excluded: chain L residue 631 SER Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 971 ILE Chi-restraints excluded: chain L residue 1144 VAL Chi-restraints excluded: chain L residue 1283 THR Chi-restraints excluded: chain L residue 1309 VAL Chi-restraints excluded: chain L residue 1372 SER Chi-restraints excluded: chain L residue 1379 LEU Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 146 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 420 ASN ** L 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.144951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.130701 restraints weight = 45456.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.131663 restraints weight = 34446.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.132225 restraints weight = 31292.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.132881 restraints weight = 24496.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.133076 restraints weight = 21095.598| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13185 Z= 0.186 Angle : 0.553 5.020 17778 Z= 0.297 Chirality : 0.040 0.146 2055 Planarity : 0.004 0.051 2248 Dihedral : 4.823 19.611 1758 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 1.98 % Allowed : 19.37 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.21), residues: 1609 helix: 0.31 (0.18), residues: 864 sheet: -1.06 (0.52), residues: 92 loop : -2.22 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L1300 TYR 0.016 0.002 TYR L 706 PHE 0.013 0.001 PHE L 639 TRP 0.011 0.001 TRP L 415 HIS 0.008 0.001 HIS L1162 Details of bonding type rmsd covalent geometry : bond 0.00443 (13185) covalent geometry : angle 0.55330 (17778) hydrogen bonds : bond 0.04067 ( 621) hydrogen bonds : angle 4.19269 ( 1791) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 141 SER cc_start: 0.8607 (OUTLIER) cc_final: 0.8323 (p) REVERT: L 142 TRP cc_start: 0.7503 (p90) cc_final: 0.7269 (p90) REVERT: L 470 MET cc_start: 0.8018 (tmm) cc_final: 0.7682 (tmm) REVERT: L 562 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7105 (ttt180) REVERT: L 638 LYS cc_start: 0.8588 (mtmt) cc_final: 0.7893 (mttp) REVERT: L 733 LYS cc_start: 0.7878 (mttt) cc_final: 0.7369 (mtmt) REVERT: L 738 MET cc_start: 0.7459 (mtt) cc_final: 0.7238 (mtt) REVERT: L 1133 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8364 (mm-30) REVERT: L 1141 ILE cc_start: 0.8492 (mm) cc_final: 0.8257 (mt) REVERT: L 1220 MET cc_start: 0.8310 (tpp) cc_final: 0.7990 (ttm) REVERT: L 1375 LYS cc_start: 0.8560 (mttt) cc_final: 0.8085 (mmtt) REVERT: P 265 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.6224 (mm-30) outliers start: 29 outliers final: 19 residues processed: 258 average time/residue: 0.2990 time to fit residues: 106.9967 Evaluate side-chains 254 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 118 TRP Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 226 SER Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 447 ASP Chi-restraints excluded: chain L residue 562 ARG Chi-restraints excluded: chain L residue 589 PHE Chi-restraints excluded: chain L residue 631 SER Chi-restraints excluded: chain L residue 732 VAL Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 935 THR Chi-restraints excluded: chain L residue 971 ILE Chi-restraints excluded: chain L residue 1144 VAL Chi-restraints excluded: chain L residue 1283 THR Chi-restraints excluded: chain L residue 1309 VAL Chi-restraints excluded: chain L residue 1372 SER Chi-restraints excluded: chain L residue 1379 LEU Chi-restraints excluded: chain P residue 265 GLU Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 96 optimal weight: 0.1980 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 286 HIS L 420 ASN ** L 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.145297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.130585 restraints weight = 45479.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.131323 restraints weight = 35783.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.134145 restraints weight = 30831.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.134554 restraints weight = 20654.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.134701 restraints weight = 16127.206| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13185 Z= 0.164 Angle : 0.544 6.258 17778 Z= 0.290 Chirality : 0.039 0.145 2055 Planarity : 0.004 0.052 2248 Dihedral : 4.771 19.542 1758 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.64 % Allowed : 19.78 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.21), residues: 1609 helix: 0.39 (0.18), residues: 864 sheet: -0.98 (0.53), residues: 90 loop : -2.19 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L1300 TYR 0.015 0.002 TYR L 795 PHE 0.014 0.001 PHE L 639 TRP 0.010 0.001 TRP L 428 HIS 0.008 0.001 HIS L1162 Details of bonding type rmsd covalent geometry : bond 0.00392 (13185) covalent geometry : angle 0.54385 (17778) hydrogen bonds : bond 0.03949 ( 621) hydrogen bonds : angle 4.15456 ( 1791) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 141 SER cc_start: 0.8602 (OUTLIER) cc_final: 0.8337 (p) REVERT: L 470 MET cc_start: 0.8054 (tmm) cc_final: 0.7737 (tmm) REVERT: L 472 LEU cc_start: 0.8426 (mt) cc_final: 0.8198 (mp) REVERT: L 638 LYS cc_start: 0.8593 (mtmt) cc_final: 0.7870 (mttp) REVERT: L 733 LYS cc_start: 0.7820 (mttt) cc_final: 0.7299 (mtmt) REVERT: L 738 MET cc_start: 0.7456 (mtt) cc_final: 0.7243 (mtt) REVERT: L 1093 MET cc_start: 0.6620 (ttp) cc_final: 0.6215 (ttp) REVERT: L 1095 LEU cc_start: 0.9148 (mm) cc_final: 0.8926 (mm) REVERT: L 1133 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8363 (mm-30) REVERT: L 1141 ILE cc_start: 0.8463 (mm) cc_final: 0.8212 (mt) REVERT: L 1220 MET cc_start: 0.8280 (tpp) cc_final: 0.8034 (ttm) REVERT: L 1263 HIS cc_start: 0.8335 (m90) cc_final: 0.8042 (m90) REVERT: L 1285 ASN cc_start: 0.8425 (t0) cc_final: 0.7814 (t0) REVERT: L 1375 LYS cc_start: 0.8498 (mttt) cc_final: 0.8052 (mmtt) outliers start: 24 outliers final: 20 residues processed: 252 average time/residue: 0.2998 time to fit residues: 104.7132 Evaluate side-chains 251 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 118 TRP Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 226 SER Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 589 PHE Chi-restraints excluded: chain L residue 631 SER Chi-restraints excluded: chain L residue 732 VAL Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 898 ARG Chi-restraints excluded: chain L residue 935 THR Chi-restraints excluded: chain L residue 971 ILE Chi-restraints excluded: chain L residue 1119 ASN Chi-restraints excluded: chain L residue 1144 VAL Chi-restraints excluded: chain L residue 1167 ILE Chi-restraints excluded: chain L residue 1283 THR Chi-restraints excluded: chain L residue 1309 VAL Chi-restraints excluded: chain L residue 1372 SER Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 158 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 707 HIS ** 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 = 0.3466 r_free = 0.3466 target = 0.145568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.131137 restraints weight = 45301.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.132169 restraints weight = 35070.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.132790 restraints weight = 31563.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.133500 restraints weight = 24521.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.133908 restraints weight = 20917.628| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 13185 Z= 0.181 Angle : 0.775 59.182 17778 Z= 0.463 Chirality : 0.039 0.317 2055 Planarity : 0.004 0.050 2248 Dihedral : 4.764 19.547 1758 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.51 % Allowed : 19.78 % Favored : 78.71 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.21), residues: 1609 helix: 0.40 (0.18), residues: 864 sheet: -0.97 (0.53), residues: 90 loop : -2.18 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L1300 TYR 0.015 0.001 TYR L 795 PHE 0.013 0.001 PHE L 639 TRP 0.010 0.001 TRP L 428 HIS 0.008 0.001 HIS L1162 Details of bonding type rmsd covalent geometry : bond 0.00415 (13185) covalent geometry : angle 0.77535 (17778) hydrogen bonds : bond 0.03905 ( 621) hydrogen bonds : angle 4.15097 ( 1791) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 231 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 141 SER cc_start: 0.8595 (OUTLIER) cc_final: 0.8328 (p) REVERT: L 470 MET cc_start: 0.8041 (tmm) cc_final: 0.7737 (tmm) REVERT: L 472 LEU cc_start: 0.8429 (mt) cc_final: 0.8199 (mp) REVERT: L 562 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7102 (ttt180) REVERT: L 638 LYS cc_start: 0.8584 (mtmt) cc_final: 0.7874 (mttp) REVERT: L 733 LYS cc_start: 0.7817 (mttt) cc_final: 0.7309 (mtmt) REVERT: L 738 MET cc_start: 0.7444 (mtt) cc_final: 0.7233 (mtt) REVERT: L 1093 MET cc_start: 0.6558 (ttp) cc_final: 0.6166 (ttp) REVERT: L 1095 LEU cc_start: 0.9141 (mm) cc_final: 0.8920 (mm) REVERT: L 1133 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8366 (mm-30) REVERT: L 1141 ILE cc_start: 0.8448 (mm) cc_final: 0.8218 (mt) REVERT: L 1220 MET cc_start: 0.8340 (tpp) cc_final: 0.8025 (ttm) REVERT: L 1375 LYS cc_start: 0.8487 (mttt) cc_final: 0.8051 (mmtt) outliers start: 22 outliers final: 20 residues processed: 245 average time/residue: 0.2906 time to fit residues: 99.7093 Evaluate side-chains 252 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 118 TRP Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 226 SER Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain L residue 562 ARG Chi-restraints excluded: chain L residue 589 PHE Chi-restraints excluded: chain L residue 631 SER Chi-restraints excluded: chain L residue 640 ASN Chi-restraints excluded: chain L residue 732 VAL Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 898 ARG Chi-restraints excluded: chain L residue 935 THR Chi-restraints excluded: chain L residue 971 ILE Chi-restraints excluded: chain L residue 1144 VAL Chi-restraints excluded: chain L residue 1167 ILE Chi-restraints excluded: chain L residue 1283 THR Chi-restraints excluded: chain L residue 1309 VAL Chi-restraints excluded: chain L residue 1372 SER Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.145568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.131136 restraints weight = 45379.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.132044 restraints weight = 34915.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.132682 restraints weight = 31937.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.133434 restraints weight = 24781.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.133802 restraints weight = 21146.383| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 13185 Z= 0.181 Angle : 0.775 59.200 17778 Z= 0.463 Chirality : 0.039 0.314 2055 Planarity : 0.004 0.050 2248 Dihedral : 4.764 19.547 1758 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.57 % Allowed : 19.71 % Favored : 78.71 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.21), residues: 1609 helix: 0.40 (0.18), residues: 864 sheet: -0.97 (0.53), residues: 90 loop : -2.18 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L1300 TYR 0.015 0.001 TYR L 795 PHE 0.013 0.001 PHE L 639 TRP 0.010 0.001 TRP L 428 HIS 0.008 0.001 HIS L1162 Details of bonding type rmsd covalent geometry : bond 0.00415 (13185) covalent geometry : angle 0.77533 (17778) hydrogen bonds : bond 0.03905 ( 621) hydrogen bonds : angle 4.15096 ( 1791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3525.47 seconds wall clock time: 60 minutes 59.59 seconds (3659.59 seconds total)