Starting phenix.real_space_refine on Sat May 24 10:08:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fjr_50510/05_2025/9fjr_50510.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fjr_50510/05_2025/9fjr_50510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fjr_50510/05_2025/9fjr_50510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fjr_50510/05_2025/9fjr_50510.map" model { file = "/net/cci-nas-00/data/ceres_data/9fjr_50510/05_2025/9fjr_50510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fjr_50510/05_2025/9fjr_50510.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.027 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 10 5.49 5 Mg 1 5.21 5 S 93 5.16 5 C 15864 2.51 5 N 4525 2.21 5 O 4888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25383 Number of models: 1 Model: "" Number of chains: 8 Chain: "a" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "b" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1765 Classifications: {'peptide': 232} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 217} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8687 Classifications: {'peptide': 1119} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1056} Chain: "d" Number of atoms: 9951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1269, 9951 Classifications: {'peptide': 1269} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1208} Chain breaks: 1 Chain: "e" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 654 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 76} Chain: "f" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2390 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain: "O" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 209 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19232 SG CYS d 891 110.115 63.536 85.513 1.00 61.47 S ATOM 19806 SG CYS d 968 106.412 63.168 87.085 1.00 55.20 S ATOM 19848 SG CYS d 975 106.897 64.864 83.957 1.00 52.92 S ATOM 19866 SG CYS d 978 107.339 61.684 83.926 1.00 46.63 S ATOM 12652 SG CYS d 60 69.421 104.427 118.714 1.00102.18 S ATOM 12670 SG CYS d 62 66.857 105.827 121.713 1.00103.10 S ATOM 12779 SG CYS d 75 70.545 106.296 121.602 1.00100.13 S ATOM 12805 SG CYS d 78 69.277 102.994 121.972 1.00105.56 S Time building chain proxies: 14.21, per 1000 atoms: 0.56 Number of scatterers: 25383 At special positions: 0 Unit cell: (131.886, 143.092, 196.536, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 93 16.00 P 10 15.00 Mg 1 11.99 O 4888 8.00 N 4525 7.00 C 15864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.77 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d1501 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 891 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 978 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 968 " pdb="ZN ZN d1501 " - pdb=" SG CYS d 975 " pdb=" ZN d1502 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 78 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 62 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 60 " pdb="ZN ZN d1502 " - pdb=" SG CYS d 75 " Number of angles added : 12 6430 Ramachandran restraints generated. 3215 Oldfield, 0 Emsley, 3215 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 44 sheets defined 44.2% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.28 Creating SS restraints... Processing helix chain 'a' and resid 30 through 43 Processing helix chain 'a' and resid 72 through 82 removed outlier: 3.837A pdb=" N SER a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 110 No H-bonds generated for 'chain 'a' and resid 108 through 110' Processing helix chain 'a' and resid 148 through 153 Processing helix chain 'a' and resid 203 through 226 removed outlier: 4.308A pdb=" N LEU a 221 " --> pdb=" O GLU a 217 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ALA a 222 " --> pdb=" O LEU a 218 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN a 226 " --> pdb=" O ALA a 222 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 46 removed outlier: 4.145A pdb=" N THR b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER b 37 " --> pdb=" O THR b 33 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE b 46 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 72 through 82 Processing helix chain 'b' and resid 108 through 110 No H-bonds generated for 'chain 'b' and resid 108 through 110' Processing helix chain 'b' and resid 203 through 224 removed outlier: 3.971A pdb=" N LEU b 221 " --> pdb=" O GLU b 217 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA b 222 " --> pdb=" O LEU b 218 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 66 removed outlier: 3.736A pdb=" N SER c 60 " --> pdb=" O VAL c 56 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE c 61 " --> pdb=" O GLN c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 78 Processing helix chain 'c' and resid 84 through 94 removed outlier: 3.561A pdb=" N LEU c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER c 94 " --> pdb=" O LEU c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 118 through 126 Processing helix chain 'c' and resid 234 through 241 Processing helix chain 'c' and resid 244 through 252 Processing helix chain 'c' and resid 256 through 265 Processing helix chain 'c' and resid 269 through 282 Processing helix chain 'c' and resid 288 through 301 Processing helix chain 'c' and resid 309 through 321 Processing helix chain 'c' and resid 334 through 351 Processing helix chain 'c' and resid 380 through 407 removed outlier: 3.504A pdb=" N VAL c 399 " --> pdb=" O ARG c 395 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR c 406 " --> pdb=" O GLU c 402 " (cutoff:3.500A) Processing helix chain 'c' and resid 413 through 418 Processing helix chain 'c' and resid 420 through 434 Processing helix chain 'c' and resid 444 through 453 Processing helix chain 'c' and resid 476 through 480 removed outlier: 4.057A pdb=" N TYR c 480 " --> pdb=" O PRO c 477 " (cutoff:3.500A) Processing helix chain 'c' and resid 532 through 539 Processing helix chain 'c' and resid 582 through 587 removed outlier: 4.496A pdb=" N MET c 586 " --> pdb=" O PRO c 583 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL c 587 " --> pdb=" O ARG c 584 " (cutoff:3.500A) Processing helix chain 'c' and resid 590 through 594 removed outlier: 3.656A pdb=" N ILE c 594 " --> pdb=" O THR c 591 " (cutoff:3.500A) Processing helix chain 'c' and resid 596 through 600 Processing helix chain 'c' and resid 601 through 612 Processing helix chain 'c' and resid 629 through 638 removed outlier: 4.447A pdb=" N ARG c 633 " --> pdb=" O GLY c 629 " (cutoff:3.500A) Processing helix chain 'c' and resid 739 through 744 Processing helix chain 'c' and resid 779 through 783 removed outlier: 4.458A pdb=" N ASP c 783 " --> pdb=" O VAL c 780 " (cutoff:3.500A) Processing helix chain 'c' and resid 815 through 826 Processing helix chain 'c' and resid 856 through 858 No H-bonds generated for 'chain 'c' and resid 856 through 858' Processing helix chain 'c' and resid 920 through 926 removed outlier: 4.312A pdb=" N ARG c 924 " --> pdb=" O HIS c 920 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG c 925 " --> pdb=" O GLY c 921 " (cutoff:3.500A) Processing helix chain 'c' and resid 928 through 943 removed outlier: 3.541A pdb=" N LEU c 932 " --> pdb=" O ILE c 928 " (cutoff:3.500A) Processing helix chain 'c' and resid 953 through 957 Processing helix chain 'c' and resid 960 through 964 removed outlier: 3.789A pdb=" N LEU c 964 " --> pdb=" O ASP c 961 " (cutoff:3.500A) Processing helix chain 'c' and resid 981 through 990 removed outlier: 3.741A pdb=" N SER c 990 " --> pdb=" O GLN c 986 " (cutoff:3.500A) Processing helix chain 'c' and resid 1036 through 1041 removed outlier: 3.795A pdb=" N LYS c1040 " --> pdb=" O LEU c1036 " (cutoff:3.500A) Processing helix chain 'c' and resid 1070 through 1079 removed outlier: 3.586A pdb=" N MET c1076 " --> pdb=" O GLU c1072 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR c1079 " --> pdb=" O ALA c1075 " (cutoff:3.500A) Processing helix chain 'c' and resid 1082 through 1090 removed outlier: 3.556A pdb=" N LEU c1089 " --> pdb=" O LEU c1085 " (cutoff:3.500A) Processing helix chain 'c' and resid 1095 through 1108 removed outlier: 4.210A pdb=" N VAL c1100 " --> pdb=" O THR c1096 " (cutoff:3.500A) Processing helix chain 'c' and resid 1118 through 1131 removed outlier: 3.540A pdb=" N LEU c1124 " --> pdb=" O SER c1120 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER c1130 " --> pdb=" O LYS c1126 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 24 Processing helix chain 'd' and resid 84 through 90 Processing helix chain 'd' and resid 103 through 109 removed outlier: 3.762A pdb=" N PHE d 107 " --> pdb=" O HIS d 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 112 through 119 Processing helix chain 'd' and resid 121 through 130 Processing helix chain 'd' and resid 140 through 147 Processing helix chain 'd' and resid 147 through 188 Processing helix chain 'd' and resid 190 through 228 Processing helix chain 'd' and resid 237 through 248 removed outlier: 3.591A pdb=" N TYR d 241 " --> pdb=" O ASP d 237 " (cutoff:3.500A) Processing helix chain 'd' and resid 257 through 268 Processing helix chain 'd' and resid 269 through 282 removed outlier: 3.591A pdb=" N GLU d 273 " --> pdb=" O ASP d 269 " (cutoff:3.500A) Processing helix chain 'd' and resid 285 through 306 removed outlier: 3.597A pdb=" N LEU d 290 " --> pdb=" O GLY d 286 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ARG d 291 " --> pdb=" O GLN d 287 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER d 305 " --> pdb=" O ALA d 301 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY d 306 " --> pdb=" O PHE d 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 308 through 311 removed outlier: 3.830A pdb=" N GLY d 311 " --> pdb=" O SER d 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 308 through 311' Processing helix chain 'd' and resid 321 through 325 Processing helix chain 'd' and resid 338 through 361 removed outlier: 4.181A pdb=" N ASP d 342 " --> pdb=" O SER d 338 " (cutoff:3.500A) Processing helix chain 'd' and resid 363 through 383 removed outlier: 3.602A pdb=" N VAL d 367 " --> pdb=" O PRO d 363 " (cutoff:3.500A) Processing helix chain 'd' and resid 402 through 406 Processing helix chain 'd' and resid 411 through 418 Processing helix chain 'd' and resid 445 through 452 removed outlier: 3.803A pdb=" N GLU d 450 " --> pdb=" O LEU d 446 " (cutoff:3.500A) Processing helix chain 'd' and resid 452 through 463 Processing helix chain 'd' and resid 468 through 479 Processing helix chain 'd' and resid 482 through 491 removed outlier: 4.243A pdb=" N VAL d 486 " --> pdb=" O GLN d 482 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE d 491 " --> pdb=" O LEU d 487 " (cutoff:3.500A) Processing helix chain 'd' and resid 505 through 507 No H-bonds generated for 'chain 'd' and resid 505 through 507' Processing helix chain 'd' and resid 528 through 533 Processing helix chain 'd' and resid 548 through 558 Processing helix chain 'd' and resid 560 through 564 Processing helix chain 'd' and resid 580 through 590 Processing helix chain 'd' and resid 614 through 625 Processing helix chain 'd' and resid 643 through 651 removed outlier: 3.769A pdb=" N GLU d 649 " --> pdb=" O GLU d 645 " (cutoff:3.500A) Processing helix chain 'd' and resid 668 through 675 Processing helix chain 'd' and resid 689 through 704 Processing helix chain 'd' and resid 705 through 725 removed outlier: 3.845A pdb=" N THR d 725 " --> pdb=" O PHE d 721 " (cutoff:3.500A) Processing helix chain 'd' and resid 726 through 728 No H-bonds generated for 'chain 'd' and resid 726 through 728' Processing helix chain 'd' and resid 741 through 762 removed outlier: 3.642A pdb=" N ILE d 745 " --> pdb=" O ARG d 741 " (cutoff:3.500A) Processing helix chain 'd' and resid 766 through 793 Processing helix chain 'd' and resid 797 through 805 Processing helix chain 'd' and resid 810 through 819 removed outlier: 3.698A pdb=" N THR d 814 " --> pdb=" O ASN d 810 " (cutoff:3.500A) Processing helix chain 'd' and resid 845 through 881 removed outlier: 4.085A pdb=" N HIS d 854 " --> pdb=" O PHE d 850 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY d 855 " --> pdb=" O ILE d 851 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA d 856 " --> pdb=" O ASN d 852 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA d 864 " --> pdb=" O LEU d 860 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU d 865 " --> pdb=" O ALA d 861 " (cutoff:3.500A) Processing helix chain 'd' and resid 915 through 920 Processing helix chain 'd' and resid 945 through 956 Processing helix chain 'd' and resid 964 through 968 Processing helix chain 'd' and resid 975 through 980 Processing helix chain 'd' and resid 995 through 1005 Processing helix chain 'd' and resid 1006 through 1008 No H-bonds generated for 'chain 'd' and resid 1006 through 1008' Processing helix chain 'd' and resid 1027 through 1037 removed outlier: 3.550A pdb=" N VAL d1031 " --> pdb=" O GLY d1027 " (cutoff:3.500A) Processing helix chain 'd' and resid 1117 through 1126 Processing helix chain 'd' and resid 1126 through 1146 removed outlier: 3.559A pdb=" N VAL d1130 " --> pdb=" O GLY d1126 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN d1145 " --> pdb=" O VAL d1141 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY d1146 " --> pdb=" O TYR d1142 " (cutoff:3.500A) Processing helix chain 'd' and resid 1151 through 1162 removed outlier: 4.232A pdb=" N ILE d1157 " --> pdb=" O HIS d1153 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN d1160 " --> pdb=" O VAL d1156 " (cutoff:3.500A) Processing helix chain 'd' and resid 1183 through 1196 removed outlier: 3.787A pdb=" N GLU d1196 " --> pdb=" O ARG d1192 " (cutoff:3.500A) Processing helix chain 'd' and resid 1209 through 1217 Processing helix chain 'd' and resid 1219 through 1227 removed outlier: 3.971A pdb=" N SER d1225 " --> pdb=" O LEU d1221 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE d1226 " --> pdb=" O SER d1222 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN d1227 " --> pdb=" O ALA d1223 " (cutoff:3.500A) Processing helix chain 'd' and resid 1228 through 1240 Processing helix chain 'd' and resid 1247 through 1255 Processing helix chain 'd' and resid 1264 through 1269 Processing helix chain 'd' and resid 1275 through 1283 removed outlier: 4.379A pdb=" N TYR d1283 " --> pdb=" O ARG d1279 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 47 removed outlier: 3.756A pdb=" N ARG e 46 " --> pdb=" O GLU e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 70 removed outlier: 4.030A pdb=" N ILE e 55 " --> pdb=" O TYR e 51 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG e 60 " --> pdb=" O TYR e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 90 through 101 Processing helix chain 'f' and resid 25 through 37 removed outlier: 3.843A pdb=" N VAL f 29 " --> pdb=" O ASP f 25 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR f 30 " --> pdb=" O LEU f 26 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR f 37 " --> pdb=" O GLY f 33 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 63 Processing helix chain 'f' and resid 70 through 103 removed outlier: 3.734A pdb=" N ARG f 74 " --> pdb=" O GLU f 70 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ARG f 96 " --> pdb=" O GLU f 92 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU f 97 " --> pdb=" O ALA f 93 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL f 98 " --> pdb=" O ASN f 94 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 106 No H-bonds generated for 'chain 'f' and resid 104 through 106' Processing helix chain 'f' and resid 111 through 128 Processing helix chain 'f' and resid 137 through 158 removed outlier: 3.655A pdb=" N TYR f 141 " --> pdb=" O LYS f 137 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP f 144 " --> pdb=" O THR f 140 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP f 145 " --> pdb=" O TYR f 141 " (cutoff:3.500A) Processing helix chain 'f' and resid 164 through 186 Processing helix chain 'f' and resid 190 through 199 Processing helix chain 'f' and resid 201 through 212 Processing helix chain 'f' and resid 229 through 234 removed outlier: 3.893A pdb=" N ILE f 234 " --> pdb=" O GLY f 231 " (cutoff:3.500A) Processing helix chain 'f' and resid 244 through 259 Processing helix chain 'f' and resid 263 through 274 Processing helix chain 'f' and resid 283 through 292 Processing helix chain 'f' and resid 294 through 311 removed outlier: 3.834A pdb=" N VAL f 298 " --> pdb=" O SER f 294 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG f 299 " --> pdb=" O ARG f 295 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN f 300 " --> pdb=" O GLU f 296 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE f 301 " --> pdb=" O ARG f 297 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS f 311 " --> pdb=" O SER f 307 " (cutoff:3.500A) Processing helix chain 'f' and resid 312 through 320 removed outlier: 4.418A pdb=" N SER f 320 " --> pdb=" O ASP f 316 " (cutoff:3.500A) Processing helix chain 'f' and resid 321 through 323 No H-bonds generated for 'chain 'f' and resid 321 through 323' Processing sheet with id=AA1, first strand: chain 'a' and resid 8 through 13 removed outlier: 3.502A pdb=" N THR a 8 " --> pdb=" O GLU a 24 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP a 190 " --> pdb=" O PRO a 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 93 through 100 removed outlier: 7.313A pdb=" N GLU a 135 " --> pdb=" O ILE a 56 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE a 56 " --> pdb=" O GLU a 135 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU a 137 " --> pdb=" O ILE a 54 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE a 54 " --> pdb=" O GLU a 137 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL a 139 " --> pdb=" O THR a 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 85 through 87 removed outlier: 3.553A pdb=" N SER a 86 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR a 117 " --> pdb=" O SER a 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'a' and resid 103 through 106 removed outlier: 3.510A pdb=" N ALA a 126 " --> pdb=" O VAL a 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'b' and resid 8 through 12 removed outlier: 6.545A pdb=" N ASP b 190 " --> pdb=" O PRO b 25 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE b 189 " --> pdb=" O THR b 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 93 through 100 removed outlier: 3.809A pdb=" N LYS b 99 " --> pdb=" O LEU b 134 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU b 134 " --> pdb=" O LYS b 99 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLU b 137 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE b 54 " --> pdb=" O GLU b 137 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL b 139 " --> pdb=" O THR b 52 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU b 141 " --> pdb=" O ALA b 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 93 through 100 removed outlier: 3.809A pdb=" N LYS b 99 " --> pdb=" O LEU b 134 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU b 134 " --> pdb=" O LYS b 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 85 through 86 Processing sheet with id=AB1, first strand: chain 'b' and resid 103 through 106 Processing sheet with id=AB2, first strand: chain 'c' and resid 39 through 40 removed outlier: 6.830A pdb=" N VAL c 39 " --> pdb=" O SER c 973 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'c' and resid 96 through 97 removed outlier: 6.806A pdb=" N PHE c 134 " --> pdb=" O PRO c 110 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N PHE c 112 " --> pdb=" O PRO c 132 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA c 131 " --> pdb=" O ASP c 156 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP c 156 " --> pdb=" O ALA c 131 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU c 133 " --> pdb=" O MET c 154 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN c 150 " --> pdb=" O ALA c 137 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU c 146 " --> pdb=" O ASN c 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'c' and resid 376 through 379 removed outlier: 3.907A pdb=" N SER c 177 " --> pdb=" O ARG c 454 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU c 455 " --> pdb=" O GLY c 498 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 184 through 191 removed outlier: 3.732A pdb=" N LEU c 212 " --> pdb=" O VAL c 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 223 through 224 removed outlier: 3.925A pdb=" N GLN c 232 " --> pdb=" O VAL c 224 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'c' and resid 354 through 355 Processing sheet with id=AB9, first strand: chain 'c' and resid 505 through 506 removed outlier: 4.020A pdb=" N LYS c 518 " --> pdb=" O GLU c 527 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU c 527 " --> pdb=" O LYS c 518 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 505 through 506 Processing sheet with id=AC2, first strand: chain 'c' and resid 558 through 559 Processing sheet with id=AC3, first strand: chain 'c' and resid 667 through 671 removed outlier: 7.034A pdb=" N TYR c 657 " --> pdb=" O VAL c 653 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL c 653 " --> pdb=" O TYR c 657 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR c 659 " --> pdb=" O GLU c 651 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'c' and resid 676 through 677 Processing sheet with id=AC5, first strand: chain 'c' and resid 687 through 688 Processing sheet with id=AC6, first strand: chain 'c' and resid 885 through 887 removed outlier: 4.473A pdb=" N THR c1024 " --> pdb=" O ILE c 723 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE c 736 " --> pdb=" O ILE c 916 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU c 737 " --> pdb=" O GLY c 896 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE c 898 " --> pdb=" O LEU c 737 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 885 through 887 Processing sheet with id=AC8, first strand: chain 'c' and resid 749 through 752 removed outlier: 6.436A pdb=" N VAL c 865 " --> pdb=" O ASP c 761 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP c 761 " --> pdb=" O VAL c 865 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU c 867 " --> pdb=" O ALA c 759 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 749 through 752 removed outlier: 3.893A pdb=" N GLY c 849 " --> pdb=" O TYR c 872 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA c 874 " --> pdb=" O VAL c 847 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL c 847 " --> pdb=" O ALA c 874 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'c' and resid 768 through 769 removed outlier: 3.653A pdb=" N THR c 807 " --> pdb=" O ARG c 833 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 801 through 803 removed outlier: 6.913A pdb=" N LEU c 837 " --> pdb=" O LEU c 802 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 1042 through 1044 removed outlier: 3.916A pdb=" N SER d 428 " --> pdb=" O MET d 541 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET d 541 " --> pdb=" O SER d 428 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 1042 through 1044 removed outlier: 7.449A pdb=" N ILE d 522 " --> pdb=" O ARG d 427 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL d 429 " --> pdb=" O ILE d 522 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU d 524 " --> pdb=" O VAL d 429 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL d 431 " --> pdb=" O LEU d 524 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'c' and resid 1066 through 1068 removed outlier: 3.551A pdb=" N GLN c1066 " --> pdb=" O VAL d 422 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'c' and resid 1133 through 1138 removed outlier: 3.587A pdb=" N ARG d 11 " --> pdb=" O GLU c1136 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 26 through 27 removed outlier: 6.682A pdb=" N GLY d 26 " --> pdb=" O HIS d 94 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY d 93 " --> pdb=" O VAL d 319 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'd' and resid 101 through 102 Processing sheet with id=AD9, first strand: chain 'd' and resid 234 through 235 removed outlier: 3.632A pdb=" N TYR d 134 " --> pdb=" O ILE d 235 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 327 through 330 removed outlier: 3.542A pdb=" N ARG d 334 " --> pdb=" O LEU d 330 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'd' and resid 443 through 444 removed outlier: 5.711A pdb=" N LEU d 443 " --> pdb=" O VAL d 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'd' and resid 611 through 612 Processing sheet with id=AE4, first strand: chain 'd' and resid 611 through 612 Processing sheet with id=AE5, first strand: chain 'd' and resid 897 through 900 removed outlier: 3.531A pdb=" N ILE d 897 " --> pdb=" O VAL d 962 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL d 960 " --> pdb=" O VAL d 899 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'd' and resid 1075 through 1080 removed outlier: 3.869A pdb=" N VAL d1075 " --> pdb=" O ILE d1066 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE d1066 " --> pdb=" O VAL d1075 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'd' and resid 1180 through 1182 removed outlier: 4.094A pdb=" N ARG d1164 " --> pdb=" O VAL d1206 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'd' and resid 1270 through 1274 removed outlier: 3.667A pdb=" N GLN d1273 " --> pdb=" O GLU e 105 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU e 105 " --> pdb=" O GLN d1273 " (cutoff:3.500A) 1147 hydrogen bonds defined for protein. 3231 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: 10.45 Time building geometry restraints manager: 7.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5392 1.33 - 1.45: 5424 1.45 - 1.57: 14827 1.57 - 1.69: 19 1.69 - 1.82: 165 Bond restraints: 25827 Sorted by residual: bond pdb=" N VAL d 28 " pdb=" CA VAL d 28 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.10e-02 8.26e+03 1.17e+01 bond pdb=" N LYS d 30 " pdb=" CA LYS d 30 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.18e-02 7.18e+03 1.05e+01 bond pdb=" N ILE d 34 " pdb=" CA ILE d 34 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 1.01e+01 bond pdb=" N LYS d 40 " pdb=" CA LYS d 40 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.18e-02 7.18e+03 9.74e+00 bond pdb=" N VAL d 328 " pdb=" CA VAL d 328 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.14e-02 7.69e+03 9.52e+00 ... (remaining 25822 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 34436 1.78 - 3.57: 474 3.57 - 5.35: 90 5.35 - 7.14: 7 7.14 - 8.92: 1 Bond angle restraints: 35008 Sorted by residual: angle pdb=" N PRO d 326 " pdb=" CA PRO d 326 " pdb=" C PRO d 326 " ideal model delta sigma weight residual 111.19 117.62 -6.43 1.57e+00 4.06e-01 1.68e+01 angle pdb=" CA PHE d 335 " pdb=" C PHE d 335 " pdb=" O PHE d 335 " ideal model delta sigma weight residual 121.56 117.29 4.27 1.09e+00 8.42e-01 1.53e+01 angle pdb=" CA GLY e 109 " pdb=" C GLY e 109 " pdb=" O GLY e 109 " ideal model delta sigma weight residual 122.31 117.07 5.24 1.34e+00 5.57e-01 1.53e+01 angle pdb=" CA LEU d 330 " pdb=" C LEU d 330 " pdb=" O LEU d 330 " ideal model delta sigma weight residual 121.94 117.49 4.45 1.15e+00 7.56e-01 1.50e+01 angle pdb=" CA GLY d 26 " pdb=" C GLY d 26 " pdb=" O GLY d 26 " ideal model delta sigma weight residual 121.37 117.24 4.13 1.09e+00 8.42e-01 1.44e+01 ... (remaining 35003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.10: 15253 30.10 - 60.21: 531 60.21 - 90.31: 40 90.31 - 120.42: 0 120.42 - 150.52: 2 Dihedral angle restraints: 15826 sinusoidal: 6586 harmonic: 9240 Sorted by residual: dihedral pdb=" C4' DT O 56 " pdb=" C3' DT O 56 " pdb=" O3' DT O 56 " pdb=" P DG O 57 " ideal model delta sinusoidal sigma weight residual 220.00 69.48 150.52 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" C4' DG O 55 " pdb=" C3' DG O 55 " pdb=" O3' DG O 55 " pdb=" P DT O 56 " ideal model delta sinusoidal sigma weight residual 220.00 84.93 135.07 1 3.50e+01 8.16e-04 1.34e+01 dihedral pdb=" CA SER d1225 " pdb=" C SER d1225 " pdb=" N PHE d1226 " pdb=" CA PHE d1226 " ideal model delta harmonic sigma weight residual -180.00 -162.51 -17.49 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 15823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2970 0.038 - 0.077: 646 0.077 - 0.115: 287 0.115 - 0.153: 63 0.153 - 0.191: 7 Chirality restraints: 3973 Sorted by residual: chirality pdb=" C3' DT O 56 " pdb=" C4' DT O 56 " pdb=" O3' DT O 56 " pdb=" C2' DT O 56 " both_signs ideal model delta sigma weight residual False -2.66 -2.47 -0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA MET d 327 " pdb=" N MET d 327 " pdb=" C MET d 327 " pdb=" CB MET d 327 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CA ILE d 34 " pdb=" N ILE d 34 " pdb=" C ILE d 34 " pdb=" CB ILE d 34 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.20e-01 ... (remaining 3970 not shown) Planarity restraints: 4590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY d 393 " -0.071 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO d 394 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO d 394 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO d 394 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR d 16 " -0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C THR d 16 " 0.058 2.00e-02 2.50e+03 pdb=" O THR d 16 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA d 17 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE f 234 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C ILE f 234 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE f 234 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU f 235 " 0.016 2.00e-02 2.50e+03 ... (remaining 4587 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 207 2.55 - 3.14: 20970 3.14 - 3.73: 38263 3.73 - 4.31: 51377 4.31 - 4.90: 87827 Nonbonded interactions: 198644 Sorted by model distance: nonbonded pdb=" OG SER d 839 " pdb=" OE1 GLU d 842 " model vdw 1.964 3.040 nonbonded pdb=" OG SER d1170 " pdb=" O PHE d1175 " model vdw 1.995 3.040 nonbonded pdb=" O SER c 182 " pdb=" OH TYR c 186 " model vdw 2.005 3.040 nonbonded pdb=" OD2 ASP c 98 " pdb=" OG SER c 100 " model vdw 2.019 3.040 nonbonded pdb=" O VAL f 258 " pdb=" OG1 THR f 261 " model vdw 2.050 3.040 ... (remaining 198639 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 Found NCS groups: ncs_group { reference = (chain 'a' and (resid 1 through 210 or (resid 211 through 212 and (name N or nam \ e CA or name C or name O )) or resid 213 through 226)) selection = (chain 'b' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.170 Check model and map are aligned: 0.190 Set scattering table: 0.270 Process input model: 61.400 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 : 0.003 0.066 25835 Z= 0.161 Angle : 0.569 21.288 35020 Z= 0.303 Chirality : 0.041 0.191 3973 Planarity : 0.004 0.108 4590 Dihedral : 14.253 150.523 9886 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.18 % Allowed : 7.06 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.16), residues: 3215 helix: 1.81 (0.15), residues: 1256 sheet: -0.39 (0.31), residues: 309 loop : -0.14 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 223 HIS 0.004 0.001 HIS c 200 PHE 0.030 0.001 PHE d1061 TYR 0.017 0.001 TYR c 91 ARG 0.011 0.000 ARG c 833 Details of bonding type rmsd hydrogen bonds : bond 0.17738 ( 1127) hydrogen bonds : angle 6.68901 ( 3231) metal coordination : bond 0.04952 ( 8) metal coordination : angle 10.55695 ( 12) covalent geometry : bond 0.00278 (25827) covalent geometry : angle 0.53456 (35008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6430 Ramachandran restraints generated. 3215 Oldfield, 0 Emsley, 3215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6430 Ramachandran restraints generated. 3215 Oldfield, 0 Emsley, 3215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 219 time to evaluate : 2.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 984 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7861 (mp0) REVERT: d 233 GLN cc_start: 0.7415 (mt0) cc_final: 0.6883 (mt0) REVERT: e 70 GLN cc_start: 0.7298 (mm-40) cc_final: 0.6898 (pp30) outliers start: 5 outliers final: 3 residues processed: 223 average time/residue: 0.3241 time to fit residues: 121.0502 Evaluate side-chains 189 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 186 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 328 VAL Chi-restraints excluded: chain e residue 107 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.1089 > 50: distance: 49 - 56: 28.155 distance: 56 - 57: 45.346 distance: 57 - 58: 20.155 distance: 57 - 60: 44.668 distance: 58 - 59: 36.170 distance: 58 - 64: 41.814 distance: 60 - 61: 35.627 distance: 61 - 62: 38.108 distance: 61 - 63: 41.260 distance: 64 - 65: 60.749 distance: 65 - 66: 34.556 distance: 65 - 68: 17.375 distance: 66 - 67: 54.345 distance: 66 - 71: 37.925 distance: 68 - 69: 51.485 distance: 68 - 70: 44.265 distance: 71 - 72: 40.693 distance: 72 - 73: 3.831 distance: 72 - 75: 40.186 distance: 73 - 74: 24.538 distance: 73 - 80: 31.040 distance: 75 - 76: 41.563 distance: 76 - 77: 13.413 distance: 77 - 78: 13.386 distance: 77 - 79: 20.308 distance: 80 - 81: 20.731 distance: 81 - 82: 14.072 distance: 81 - 84: 34.822 distance: 82 - 83: 53.397 distance: 82 - 85: 18.116 distance: 85 - 86: 13.208 distance: 86 - 87: 45.618 distance: 86 - 89: 39.266 distance: 87 - 88: 48.444 distance: 87 - 93: 33.985 distance: 89 - 90: 45.731 distance: 89 - 91: 56.421 distance: 90 - 92: 25.681 distance: 93 - 94: 22.481 distance: 94 - 95: 69.186 distance: 94 - 97: 28.195 distance: 95 - 96: 41.990 distance: 95 - 100: 40.646 distance: 96 - 123: 51.197 distance: 97 - 98: 26.348 distance: 97 - 99: 33.184 distance: 100 - 101: 18.311 distance: 100 - 106: 39.314 distance: 101 - 102: 13.583 distance: 101 - 104: 47.347 distance: 102 - 103: 35.526 distance: 102 - 107: 26.594 distance: 103 - 131: 21.965 distance: 104 - 105: 47.511 distance: 105 - 106: 24.417 distance: 107 - 108: 50.651 distance: 108 - 109: 33.265 distance: 108 - 111: 17.656 distance: 109 - 110: 23.761 distance: 109 - 116: 24.963 distance: 111 - 112: 29.339 distance: 112 - 113: 12.510 distance: 113 - 114: 21.323 distance: 113 - 115: 40.679 distance: 116 - 117: 28.413 distance: 117 - 118: 14.423 distance: 117 - 120: 26.889 distance: 118 - 119: 26.579 distance: 118 - 123: 30.011 distance: 120 - 121: 34.729 distance: 120 - 122: 33.532 distance: 123 - 124: 44.098 distance: 124 - 125: 46.230 distance: 124 - 127: 31.585 distance: 125 - 126: 31.863 distance: 125 - 131: 27.862 distance: 127 - 128: 27.133 distance: 128 - 129: 21.636 distance: 128 - 130: 23.564