Starting phenix.real_space_refine on Tue May 27 22:27:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vvz_21408/05_2025/6vvz_21408.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vvz_21408/05_2025/6vvz_21408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vvz_21408/05_2025/6vvz_21408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vvz_21408/05_2025/6vvz_21408.map" model { file = "/net/cci-nas-00/data/ceres_data/6vvz_21408/05_2025/6vvz_21408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vvz_21408/05_2025/6vvz_21408.cif" } resolution = 3.72 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= 0.004 sd= 0.089 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 127 5.49 5 Mg 1 5.21 5 S 99 5.16 5 C 18328 2.51 5 N 5327 2.21 5 O 5976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29860 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1759 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 8577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8577 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "D" Number of atoms: 9873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 9873 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1205} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 76} Chain: "F" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2503 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 310} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 29 Chain: "J" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 875 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 153} Chain: "P" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1270 Classifications: {'DNA': 62} Link IDs: {'rna3p': 61} Chain breaks: 1 Chain: "O" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1336 Classifications: {'DNA': 65} Link IDs: {'rna3p': 64} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'SRN': 1} Classifications: {'undetermined': 1} 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 19116 SG CYS D 891 112.320 87.855 105.454 1.00176.22 S ATOM 19683 SG CYS D 968 108.714 88.823 104.330 1.00159.66 S ATOM 19725 SG CYS D 975 108.987 86.684 107.379 1.00164.31 S ATOM 19743 SG CYS D 978 110.917 90.554 107.426 1.00167.96 S ATOM 12558 SG CYS D 60 56.811 64.408 74.360 1.00192.32 S ATOM 12576 SG CYS D 62 54.864 64.732 71.352 1.00187.10 S ATOM 12711 SG CYS D 78 58.795 66.927 71.695 1.00186.73 S Time building chain proxies: 16.61, per 1000 atoms: 0.56 Number of scatterers: 29860 At special positions: 0 Unit cell: (139.1, 167.7, 193.7, 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 99 16.00 P 127 15.00 Mg 1 11.99 O 5976 8.00 N 5327 7.00 C 18328 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: 7.35 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " Number of angles added : 6 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 47 sheets defined 42.6% alpha, 14.1% beta 55 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 10.68 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.693A pdb=" N SER A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 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 203 through 224 removed outlier: 4.072A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.690A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (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: 4.013A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.892A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.981A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 233 through 241 removed outlier: 4.239A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 250 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.612A pdb=" N THR C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 407 removed outlier: 4.070A pdb=" N VAL C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.824A 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 432 Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 532 through 538 Processing helix chain 'C' and resid 590 through 594 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 613 removed outlier: 4.184A pdb=" N ARG C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 638 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 779 through 783 removed outlier: 4.285A 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 922 through 926 Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 991 removed outlier: 4.010A pdb=" N CYS C 991 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1079 Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.609A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1108 removed outlier: 3.901A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.505A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.533A pdb=" N SER D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 112 through 118 Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 140 through 186 removed outlier: 4.929A pdb=" N ASN D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.633A pdb=" N ASP D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG D 247 " --> pdb=" O GLU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 252 removed outlier: 3.790A pdb=" N TYR D 251 " --> pdb=" O TYR D 248 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE D 252 " --> pdb=" O GLY D 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 248 through 252' Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.913A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.977A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 340 through 361 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 393 through 397 removed outlier: 3.660A pdb=" N ARG D 397 " --> pdb=" O PRO D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 419 Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.949A 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 492 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 578 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 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 727 removed outlier: 3.874A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 806 removed outlier: 3.835A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.999A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 882 removed outlier: 4.157A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 917 removed outlier: 3.845A pdb=" N ILE D 916 " --> pdb=" O ASP D 913 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU D 917 " --> pdb=" O PRO D 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 913 through 917' Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 removed outlier: 3.796A pdb=" N CYS D 968 " --> pdb=" O VAL D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1006 through 1009 Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1145 removed outlier: 3.690A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Proline residue: D1127 - end of helix removed outlier: 3.614A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 3.875A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 3.502A pdb=" N ASN D1190 " --> pdb=" O PHE D1186 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D1191 " --> pdb=" O GLU D1187 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG D1192 " --> pdb=" O ALA D1188 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 removed outlier: 3.675A pdb=" N LEU D1215 " --> pdb=" O THR D1211 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 4.040A pdb=" N SER D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 4.490A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA D1236 " --> pdb=" O VAL D1232 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1254 removed outlier: 3.746A pdb=" N ASN D1251 " --> pdb=" O GLY D1247 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D1253 " --> pdb=" O LYS D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1264 through 1269 removed outlier: 3.884A pdb=" N ASN D1269 " --> pdb=" O ASN D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1280 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.902A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 71 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 210 through 220 Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 266 Processing helix chain 'F' and resid 274 through 308 removed outlier: 3.622A pdb=" N ASP F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 334 Processing helix chain 'F' and resid 342 through 362 removed outlier: 3.913A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 406 through 418 Processing helix chain 'F' and resid 448 through 466 Processing helix chain 'F' and resid 468 through 480 Processing helix chain 'F' and resid 488 through 497 Processing helix chain 'F' and resid 499 through 515 Processing helix chain 'F' and resid 516 through 525 removed outlier: 6.446A pdb=" N VAL F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU F 523 " --> pdb=" O ARG F 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 110 Processing helix chain 'M' and resid 52 through 57 Processing helix chain 'M' and resid 63 through 74 Processing helix chain 'M' and resid 84 through 99 Processing helix chain 'M' and resid 100 through 118 removed outlier: 3.840A pdb=" N GLU M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 143 Processing helix chain 'M' and resid 146 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 9 removed outlier: 6.182A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100 removed outlier: 8.047A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 100 removed outlier: 3.540A pdb=" N SER A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.571A pdb=" N SER A 86 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 117 " --> pdb=" O SER A 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.536A pdb=" N SER B 10 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL B 22 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 100 removed outlier: 3.671A pdb=" N SER B 53 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.419A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.930A pdb=" N GLU C 138 " --> pdb=" O SER C 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 110 through 112 removed outlier: 6.323A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 376 through 379 Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 191 removed outlier: 3.945A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 215 through 216 Processing sheet with id=AB9, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 removed outlier: 6.511A pdb=" N ILE C 512 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU C 531 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR C 514 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL C 529 " --> pdb=" O THR C 514 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N TYR C 516 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU C 527 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LYS C 518 " --> pdb=" O SER C 525 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 505 through 506 removed outlier: 3.703A pdb=" N VAL C 541 " --> pdb=" O ARG C 562 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.968A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 648 through 652 removed outlier: 6.787A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC6, first strand: chain 'C' and resid 717 through 722 removed outlier: 8.590A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 751 through 760 removed outlier: 3.635A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C 845 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC9, first strand: chain 'C' and resid 801 through 803 removed outlier: 7.009A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 906 through 907 Processing sheet with id=AD2, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD3, first strand: chain 'C' and resid 1007 through 1008 Processing sheet with id=AD4, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 6.301A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN D 523 " --> pdb=" O GLY D 442 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.184A 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 1067 removed outlier: 3.820A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AD7, first strand: chain 'D' and resid 93 through 102 removed outlier: 7.274A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 234 through 235 Processing sheet with id=AD9, first strand: chain 'F' and resid 421 through 422 removed outlier: 3.915A pdb=" N GLN D 329 " --> pdb=" O SER J 9 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLU F 440 " --> pdb=" O GLY J 8 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE2, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE3, first strand: chain 'D' and resid 898 through 899 Processing sheet with id=AE4, first strand: chain 'D' and resid 929 through 930 removed outlier: 3.501A pdb=" N VAL D 938 " --> pdb=" O ALA D 929 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1075 through 1081 removed outlier: 5.815A pdb=" N VAL D1076 " --> pdb=" O ILE D1066 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE D1066 " --> pdb=" O VAL D1076 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1085 through 1086 removed outlier: 4.717A pdb=" N ARG D1085 " --> pdb=" O GLU D1113 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1179 through 1182 Processing sheet with id=AE8, first strand: chain 'D' and resid 1271 through 1274 removed outlier: 3.531A pdb=" N ALA D1271 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR E 107 " --> pdb=" O ALA D1271 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 39 through 42 Processing sheet with id=AF1, first strand: chain 'M' and resid 45 through 49 removed outlier: 5.539A pdb=" N TYR M 34 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE M 22 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 26 through 27 1236 hydrogen bonds defined for protein. 3486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 142 hydrogen bonds 284 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 14.90 Time building geometry restraints manager: 8.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4947 1.31 - 1.43: 7936 1.43 - 1.56: 17298 1.56 - 1.68: 269 1.68 - 1.81: 178 Bond restraints: 30628 Sorted by residual: bond pdb=" C9 SRN C1201 " pdb=" O3 SRN C1201 " ideal model delta sigma weight residual 1.429 1.807 -0.378 2.00e-02 2.50e+03 3.56e+02 bond pdb=" C8 SRN C1201 " pdb=" O3 SRN C1201 " ideal model delta sigma weight residual 1.434 1.789 -0.355 2.00e-02 2.50e+03 3.15e+02 bond pdb=" C28 SRN C1201 " pdb=" C29 SRN C1201 " ideal model delta sigma weight residual 1.330 1.607 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" C13 SRN C1201 " pdb=" C14 SRN C1201 " ideal model delta sigma weight residual 1.328 1.599 -0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" C2 SRN C1201 " pdb=" C3 SRN C1201 " ideal model delta sigma weight residual 1.341 1.586 -0.245 2.00e-02 2.50e+03 1.51e+02 ... (remaining 30623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 41842 4.38 - 8.75: 175 8.75 - 13.13: 14 13.13 - 17.51: 2 17.51 - 21.88: 1 Bond angle restraints: 42034 Sorted by residual: angle pdb=" C8 SRN C1201 " pdb=" O3 SRN C1201 " pdb=" C9 SRN C1201 " ideal model delta sigma weight residual 108.56 86.68 21.88 3.00e+00 1.11e-01 5.32e+01 angle pdb=" N VAL F 448 " pdb=" CA VAL F 448 " pdb=" C VAL F 448 " ideal model delta sigma weight residual 112.96 105.98 6.98 1.00e+00 1.00e+00 4.87e+01 angle pdb=" CA ARG C 584 " pdb=" CB ARG C 584 " pdb=" CG ARG C 584 " ideal model delta sigma weight residual 114.10 125.13 -11.03 2.00e+00 2.50e-01 3.04e+01 angle pdb=" C LYS C 229 " pdb=" N ARG C 230 " pdb=" CA ARG C 230 " ideal model delta sigma weight residual 121.54 130.97 -9.43 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C GLU D1059 " pdb=" N ARG D1060 " pdb=" CA ARG D1060 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.27e+01 ... (remaining 42029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 17197 35.46 - 70.91: 1189 70.91 - 106.37: 28 106.37 - 141.82: 3 141.82 - 177.28: 4 Dihedral angle restraints: 18421 sinusoidal: 8373 harmonic: 10048 Sorted by residual: dihedral pdb=" CA ALA D 501 " pdb=" C ALA D 501 " pdb=" N PRO D 502 " pdb=" CA PRO D 502 " ideal model delta harmonic sigma weight residual -180.00 -118.86 -61.14 0 5.00e+00 4.00e-02 1.50e+02 dihedral pdb=" CA ARG C 282 " pdb=" C ARG C 282 " pdb=" N PRO C 283 " pdb=" CA PRO C 283 " ideal model delta harmonic sigma weight residual -180.00 -124.00 -56.00 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA ARG D 578 " pdb=" C ARG D 578 " pdb=" N LEU D 579 " pdb=" CA LEU D 579 " ideal model delta harmonic sigma weight residual -180.00 -144.67 -35.33 0 5.00e+00 4.00e-02 4.99e+01 ... (remaining 18418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3860 0.065 - 0.130: 852 0.130 - 0.195: 68 0.195 - 0.260: 9 0.260 - 0.325: 7 Chirality restraints: 4796 Sorted by residual: chirality pdb=" C35 SRN C1201 " pdb=" C34 SRN C1201 " pdb=" C8 SRN C1201 " pdb=" O8 SRN C1201 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C12 SRN C1201 " pdb=" C10 SRN C1201 " pdb=" C13 SRN C1201 " pdb=" O8 SRN C1201 " both_signs ideal model delta sigma weight residual False 2.40 2.71 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CG LEU C 274 " pdb=" CB LEU C 274 " pdb=" CD1 LEU C 274 " pdb=" CD2 LEU C 274 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 4793 not shown) Planarity restraints: 5076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 501 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO D 502 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO D 502 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 502 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 282 " -0.055 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO C 283 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO C 283 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 283 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 413 " 0.051 5.00e-02 4.00e+02 7.74e-02 9.59e+00 pdb=" N PRO C 414 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 414 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 414 " 0.043 5.00e-02 4.00e+02 ... (remaining 5073 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 1559 2.70 - 3.25: 28465 3.25 - 3.80: 55544 3.80 - 4.35: 62912 4.35 - 4.90: 101696 Nonbonded interactions: 250176 Sorted by model distance: nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 2.145 2.170 nonbonded pdb=" OD2 ASP D 539 " pdb="MG MG D2002 " model vdw 2.168 2.170 nonbonded pdb=" N CYS D 62 " pdb="ZN ZN D2001 " model vdw 2.201 2.310 nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 2.214 2.170 nonbonded pdb=" OD2 ASP D 537 " pdb="MG MG D2002 " model vdw 2.234 2.170 ... (remaining 250171 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 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 or (resid 186 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 2 \ 23 or (resid 224 and (name N or name CA or name C or name O or name CB )) or res \ id 225 through 226)) selection = (chain 'B' and resid 2 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=0.50 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.210 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 79.560 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 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 : 0.010 0.378 30635 Z= 0.479 Angle : 0.947 21.885 42040 Z= 0.512 Chirality : 0.053 0.325 4796 Planarity : 0.007 0.104 5076 Dihedral : 20.484 177.280 11957 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.14 % Favored : 92.80 % Rotamer: Outliers : 6.36 % Allowed : 25.99 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % Twisted General : 0.06 % 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: -3.51 (0.12), residues: 3488 helix: -1.93 (0.11), residues: 1350 sheet: -2.96 (0.21), residues: 397 loop : -2.47 (0.13), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 723 HIS 0.008 0.002 HIS D 525 PHE 0.021 0.002 PHE D 811 TYR 0.019 0.002 TYR B 96 ARG 0.009 0.001 ARG D 206 Details of bonding type rmsd hydrogen bonds : bond 0.17060 ( 1366) hydrogen bonds : angle 7.14035 ( 3770) metal coordination : bond 0.14078 ( 7) metal coordination : angle 9.52310 ( 6) covalent geometry : bond 0.00989 (30628) covalent geometry : angle 0.94013 (42034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 257 time to evaluate : 3.027 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: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.9061 (tt0) cc_final: 0.8693 (tp30) REVERT: B 141 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: B 191 LYS cc_start: 0.9322 (ttpt) cc_final: 0.8874 (ptmm) REVERT: C 126 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8433 (t0) REVERT: C 250 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5873 (pt0) REVERT: C 393 MET cc_start: 0.9670 (mmt) cc_final: 0.9306 (mmm) REVERT: C 396 MET cc_start: 0.9325 (pp-130) cc_final: 0.8663 (pp-130) REVERT: C 404 MET cc_start: 0.9141 (tpp) cc_final: 0.8810 (ttt) REVERT: C 429 GLU cc_start: 0.9164 (tp30) cc_final: 0.8733 (tp30) REVERT: C 456 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8024 (tt) REVERT: C 570 TYR cc_start: 0.9208 (OUTLIER) cc_final: 0.8957 (m-80) REVERT: C 584 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7515 (pmm-80) REVERT: C 593 MET cc_start: 0.8750 (mtp) cc_final: 0.8362 (mmm) REVERT: C 607 MET cc_start: 0.9034 (mtt) cc_final: 0.8578 (mtm) REVERT: C 611 MET cc_start: 0.9374 (tpp) cc_final: 0.8928 (mmp) REVERT: C 661 MET cc_start: 0.8292 (tpt) cc_final: 0.7934 (tpt) REVERT: C 757 ILE cc_start: 0.9654 (OUTLIER) cc_final: 0.9425 (tt) REVERT: C 885 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8560 (mt) REVERT: C 1094 ASP cc_start: 0.8820 (m-30) cc_final: 0.7319 (t0) REVERT: C 1104 GLU cc_start: 0.9509 (tt0) cc_final: 0.9199 (tm-30) REVERT: D 37 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8185 (mtm110) REVERT: D 244 LEU cc_start: 0.9769 (tt) cc_final: 0.9488 (mt) REVERT: D 342 ASP cc_start: 0.9396 (OUTLIER) cc_final: 0.8887 (p0) REVERT: D 373 MET cc_start: 0.8983 (mtp) cc_final: 0.8402 (mtp) REVERT: D 402 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9332 (tt) REVERT: D 404 ASP cc_start: 0.8436 (m-30) cc_final: 0.8184 (m-30) REVERT: D 498 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9302 (mp) REVERT: D 504 LEU cc_start: 0.9163 (mp) cc_final: 0.8500 (tp) REVERT: D 509 ILE cc_start: 0.9371 (mt) cc_final: 0.9101 (tp) REVERT: D 533 ASN cc_start: 0.9422 (t0) cc_final: 0.9124 (t0) REVERT: D 556 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8568 (ttt-90) REVERT: D 576 MET cc_start: 0.9167 (ttp) cc_final: 0.8506 (ppp) REVERT: D 581 MET cc_start: 0.9538 (mtm) cc_final: 0.9162 (mtm) REVERT: D 582 VAL cc_start: 0.9715 (OUTLIER) cc_final: 0.9430 (m) REVERT: D 600 GLN cc_start: 0.9390 (OUTLIER) cc_final: 0.9056 (pm20) REVERT: D 676 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9403 (mp) REVERT: D 862 ASP cc_start: 0.9099 (t70) cc_final: 0.8808 (t0) REVERT: D 865 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9167 (pp) REVERT: E 50 LYS cc_start: 0.9320 (ptpt) cc_final: 0.8942 (mtmm) REVERT: E 66 ASP cc_start: 0.9300 (m-30) cc_final: 0.9075 (p0) REVERT: E 70 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: F 310 TYR cc_start: 0.7877 (m-10) cc_final: 0.7612 (m-80) REVERT: F 325 ASN cc_start: 0.9144 (m-40) cc_final: 0.8765 (m110) REVERT: F 332 VAL cc_start: 0.9712 (OUTLIER) cc_final: 0.9510 (m) REVERT: F 377 ASN cc_start: 0.9462 (m-40) cc_final: 0.9168 (m-40) REVERT: F 438 PHE cc_start: 0.9102 (m-80) cc_final: 0.8695 (m-80) REVERT: F 459 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8788 (tt0) REVERT: F 511 MET cc_start: 0.9569 (mmm) cc_final: 0.9106 (mmm) REVERT: F 514 LEU cc_start: 0.9764 (OUTLIER) cc_final: 0.9467 (mt) REVERT: J 60 MET cc_start: 0.8232 (ptp) cc_final: 0.7886 (ptp) REVERT: J 69 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7832 (tm) REVERT: M 55 TYR cc_start: 0.8988 (m-10) cc_final: 0.8736 (m-10) REVERT: M 65 GLU cc_start: 0.9317 (OUTLIER) cc_final: 0.8966 (pm20) REVERT: M 72 GLN cc_start: 0.9513 (tt0) cc_final: 0.9149 (tm-30) REVERT: M 115 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8522 (t70) outliers start: 185 outliers final: 40 residues processed: 429 average time/residue: 0.4105 time to fit residues: 282.5437 Evaluate side-chains 231 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 167 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 777 SER Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 556 ARG Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 600 GLN Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 730 THR Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1211 THR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 459 GLN Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 65 GLU Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 121 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 302 optimal weight: 4.9990 chunk 271 optimal weight: 20.0000 chunk 150 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 280 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 325 optimal weight: 0.2980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 119 HIS A 124 HIS C 81 ASN C 141 ASN C 298 ASN C 419 ASN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN C 775 ASN C 920 HIS C 941 HIS C1034 HIS C1035 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 ASN D 35 ASN D 239 ASN D 307 ASN D 341 ASN D 368 ASN D 416 ASN D 505 HIS D 544 HIS D 639 GLN ** D 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1001 GLN D1145 GLN D1190 ASN ** F 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN F 388 GLN F 425 GLN ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.051950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.036072 restraints weight = 189537.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.037251 restraints weight = 94652.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.038033 restraints weight = 61153.268| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30635 Z= 0.150 Angle : 0.634 12.658 42040 Z= 0.333 Chirality : 0.042 0.161 4796 Planarity : 0.005 0.087 5076 Dihedral : 19.281 176.479 5426 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.19 % Allowed : 26.23 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.13), residues: 3488 helix: -0.18 (0.13), residues: 1388 sheet: -2.46 (0.23), residues: 395 loop : -2.01 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 723 HIS 0.005 0.001 HIS C1042 PHE 0.012 0.001 PHE C 430 TYR 0.022 0.001 TYR B 176 ARG 0.009 0.000 ARG J 101 Details of bonding type rmsd hydrogen bonds : bond 0.04368 ( 1366) hydrogen bonds : angle 5.29168 ( 3770) metal coordination : bond 0.00844 ( 7) metal coordination : angle 4.84633 ( 6) covalent geometry : bond 0.00323 (30628) covalent geometry : angle 0.63096 (42034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 200 time to evaluate : 3.073 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.9051 (tt0) cc_final: 0.8446 (tp30) REVERT: A 173 LYS cc_start: 0.9259 (ttmt) cc_final: 0.8567 (tttm) REVERT: B 1 MET cc_start: 0.8953 (mmm) cc_final: 0.8677 (mtm) REVERT: B 191 LYS cc_start: 0.9339 (ttpt) cc_final: 0.9139 (ptmm) REVERT: C 258 MET cc_start: 0.6292 (ppp) cc_final: 0.6091 (ppp) REVERT: C 393 MET cc_start: 0.9667 (mmt) cc_final: 0.9379 (mmm) REVERT: C 396 MET cc_start: 0.9360 (pp-130) cc_final: 0.8716 (pp-130) REVERT: C 429 GLU cc_start: 0.9317 (tp30) cc_final: 0.8810 (tp30) REVERT: C 436 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9223 (mm) REVERT: C 438 GLN cc_start: 0.8827 (mt0) cc_final: 0.8622 (mm-40) REVERT: C 593 MET cc_start: 0.8680 (mtp) cc_final: 0.8463 (mmm) REVERT: C 607 MET cc_start: 0.8950 (mtt) cc_final: 0.8674 (mtp) REVERT: C 611 MET cc_start: 0.9330 (mpp) cc_final: 0.8910 (mmp) REVERT: C 661 MET cc_start: 0.8370 (tpt) cc_final: 0.7930 (tpt) REVERT: C 753 GLU cc_start: 0.7955 (tp30) cc_final: 0.7707 (tm-30) REVERT: C 1028 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8730 (tpp) REVERT: C 1051 MET cc_start: 0.9095 (tpt) cc_final: 0.8472 (tpp) REVERT: C 1087 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8543 (mt-10) REVERT: C 1088 LEU cc_start: 0.9592 (mt) cc_final: 0.9356 (mt) REVERT: C 1104 GLU cc_start: 0.9519 (tt0) cc_final: 0.9153 (tm-30) REVERT: D 92 MET cc_start: 0.8476 (mtp) cc_final: 0.8036 (mmm) REVERT: D 312 MET cc_start: 0.9193 (mtp) cc_final: 0.8729 (mtm) REVERT: D 329 GLN cc_start: 0.9629 (OUTLIER) cc_final: 0.9342 (pp30) REVERT: D 373 MET cc_start: 0.8944 (mtp) cc_final: 0.8272 (mpp) REVERT: D 404 ASP cc_start: 0.8641 (m-30) cc_final: 0.8391 (m-30) REVERT: D 504 LEU cc_start: 0.9151 (mp) cc_final: 0.8424 (tp) REVERT: D 520 LYS cc_start: 0.8732 (pttt) cc_final: 0.8315 (pttt) REVERT: D 533 ASN cc_start: 0.9413 (t0) cc_final: 0.9136 (t0) REVERT: D 581 MET cc_start: 0.9374 (mtm) cc_final: 0.8990 (mtm) REVERT: D 640 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8783 (mt) REVERT: D 667 THR cc_start: 0.9410 (OUTLIER) cc_final: 0.9169 (t) REVERT: D 862 ASP cc_start: 0.9052 (t70) cc_final: 0.8743 (t0) REVERT: D 865 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9095 (pp) REVERT: D 1250 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8265 (pm20) REVERT: E 35 ILE cc_start: 0.9750 (tp) cc_final: 0.9465 (mm) REVERT: E 66 ASP cc_start: 0.9331 (m-30) cc_final: 0.9026 (m-30) REVERT: E 70 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7086 (tm-30) REVERT: E 89 GLU cc_start: 0.7192 (pm20) cc_final: 0.6953 (pm20) REVERT: F 278 ARG cc_start: 0.9393 (OUTLIER) cc_final: 0.8844 (ttp-110) REVERT: F 302 LEU cc_start: 0.9866 (tp) cc_final: 0.9495 (mt) REVERT: F 309 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8179 (tpm170) REVERT: F 315 MET cc_start: 0.7212 (mmm) cc_final: 0.6974 (mmm) REVERT: F 317 PHE cc_start: 0.8958 (t80) cc_final: 0.8610 (t80) REVERT: F 323 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8548 (mm-30) REVERT: F 325 ASN cc_start: 0.9343 (m-40) cc_final: 0.9075 (m110) REVERT: F 403 MET cc_start: 0.9008 (mmt) cc_final: 0.8742 (mmm) REVERT: F 438 PHE cc_start: 0.9051 (m-80) cc_final: 0.8769 (m-80) REVERT: F 511 MET cc_start: 0.9572 (mmm) cc_final: 0.9105 (mmp) REVERT: F 514 LEU cc_start: 0.9703 (OUTLIER) cc_final: 0.9478 (mt) REVERT: J 64 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8847 (tt) REVERT: M 25 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8705 (ttp80) REVERT: M 55 TYR cc_start: 0.8873 (m-10) cc_final: 0.8550 (m-10) REVERT: M 72 GLN cc_start: 0.9396 (tt0) cc_final: 0.9023 (tm-30) REVERT: M 115 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8462 (p0) outliers start: 122 outliers final: 38 residues processed: 313 average time/residue: 0.4005 time to fit residues: 200.8798 Evaluate side-chains 232 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 179 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1060 ARG Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 309 ARG Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 176 optimal weight: 1.9990 chunk 162 optimal weight: 0.0000 chunk 341 optimal weight: 1.9990 chunk 346 optimal weight: 20.0000 chunk 312 optimal weight: 20.0000 chunk 306 optimal weight: 0.3980 chunk 339 optimal weight: 6.9990 chunk 293 optimal weight: 3.9990 chunk 243 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 overall best weight: 1.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS ** F 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 GLN ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.052125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.036502 restraints weight = 189773.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.037675 restraints weight = 94456.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.038456 restraints weight = 60819.222| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30635 Z= 0.143 Angle : 0.600 12.195 42040 Z= 0.313 Chirality : 0.041 0.196 4796 Planarity : 0.004 0.079 5076 Dihedral : 18.977 175.865 5350 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.99 % Allowed : 26.61 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3488 helix: 0.66 (0.14), residues: 1371 sheet: -2.22 (0.23), residues: 432 loop : -1.69 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 112 HIS 0.004 0.001 HIS C1042 PHE 0.011 0.001 PHE D 651 TYR 0.022 0.001 TYR B 32 ARG 0.005 0.000 ARG C 77 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 1366) hydrogen bonds : angle 4.89501 ( 3770) metal coordination : bond 0.00558 ( 7) metal coordination : angle 3.61996 ( 6) covalent geometry : bond 0.00309 (30628) covalent geometry : angle 0.59859 (42034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 197 time to evaluate : 3.170 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.9056 (tt0) cc_final: 0.8509 (tp30) REVERT: A 173 LYS cc_start: 0.9217 (ttmt) cc_final: 0.8700 (tmmt) REVERT: B 1 MET cc_start: 0.8881 (mmm) cc_final: 0.8580 (mtm) REVERT: B 123 MET cc_start: 0.9088 (ppp) cc_final: 0.8460 (ptm) REVERT: B 191 LYS cc_start: 0.9350 (ttpt) cc_final: 0.8887 (ttmm) REVERT: C 103 MET cc_start: 0.9182 (ptt) cc_final: 0.8937 (ppp) REVERT: C 127 MET cc_start: 0.8745 (ptp) cc_final: 0.8016 (pmm) REVERT: C 393 MET cc_start: 0.9674 (mmt) cc_final: 0.9396 (mmm) REVERT: C 396 MET cc_start: 0.9359 (pp-130) cc_final: 0.8791 (pp-130) REVERT: C 404 MET cc_start: 0.8539 (mtt) cc_final: 0.8330 (mtt) REVERT: C 429 GLU cc_start: 0.9295 (tp30) cc_final: 0.8803 (tp30) REVERT: C 438 GLN cc_start: 0.8533 (mt0) cc_final: 0.8245 (mm-40) REVERT: C 607 MET cc_start: 0.8844 (mtt) cc_final: 0.8570 (mtp) REVERT: C 611 MET cc_start: 0.9290 (mpp) cc_final: 0.8860 (mmp) REVERT: C 661 MET cc_start: 0.8017 (tpt) cc_final: 0.7517 (tpt) REVERT: C 753 GLU cc_start: 0.8195 (tp30) cc_final: 0.7908 (tp30) REVERT: C 754 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8176 (tm-30) REVERT: C 1028 MET cc_start: 0.9119 (ttm) cc_final: 0.8746 (tpp) REVERT: C 1051 MET cc_start: 0.8992 (tpt) cc_final: 0.8501 (tpp) REVERT: C 1087 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8566 (mt-10) REVERT: C 1088 LEU cc_start: 0.9541 (mt) cc_final: 0.9299 (mt) REVERT: C 1104 GLU cc_start: 0.9522 (tt0) cc_final: 0.9181 (tm-30) REVERT: D 238 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: D 256 MET cc_start: 0.7935 (ttm) cc_final: 0.7683 (ttm) REVERT: D 342 ASP cc_start: 0.9381 (m-30) cc_final: 0.8786 (p0) REVERT: D 373 MET cc_start: 0.8996 (mtp) cc_final: 0.8289 (mpp) REVERT: D 404 ASP cc_start: 0.8662 (m-30) cc_final: 0.8446 (m-30) REVERT: D 504 LEU cc_start: 0.9151 (mp) cc_final: 0.8423 (tp) REVERT: D 520 LYS cc_start: 0.8835 (pttt) cc_final: 0.8419 (pttt) REVERT: D 524 LEU cc_start: 0.9216 (tp) cc_final: 0.8981 (tt) REVERT: D 533 ASN cc_start: 0.9378 (t0) cc_final: 0.9093 (t0) REVERT: D 581 MET cc_start: 0.9441 (mtm) cc_final: 0.9043 (mtm) REVERT: D 667 THR cc_start: 0.9423 (OUTLIER) cc_final: 0.9153 (t) REVERT: D 865 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9069 (pp) REVERT: D 943 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8407 (t70) REVERT: D 1250 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8193 (pm20) REVERT: E 35 ILE cc_start: 0.9714 (tp) cc_final: 0.9500 (mm) REVERT: E 66 ASP cc_start: 0.9323 (m-30) cc_final: 0.9020 (m-30) REVERT: F 278 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.8739 (ttp-110) REVERT: F 302 LEU cc_start: 0.9854 (tp) cc_final: 0.9421 (mt) REVERT: F 315 MET cc_start: 0.7366 (mmm) cc_final: 0.7011 (mmm) REVERT: F 317 PHE cc_start: 0.8943 (t80) cc_final: 0.8586 (t80) REVERT: F 323 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8568 (mm-30) REVERT: F 325 ASN cc_start: 0.9457 (m-40) cc_final: 0.9134 (m110) REVERT: F 437 ASP cc_start: 0.9261 (t0) cc_final: 0.9004 (t0) REVERT: F 438 PHE cc_start: 0.9066 (m-80) cc_final: 0.8780 (m-80) REVERT: F 511 MET cc_start: 0.9533 (mmm) cc_final: 0.9052 (mmp) REVERT: J 64 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8796 (tt) REVERT: M 55 TYR cc_start: 0.8839 (m-10) cc_final: 0.8512 (m-10) REVERT: M 72 GLN cc_start: 0.9386 (tt0) cc_final: 0.9024 (tm-30) REVERT: M 115 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8586 (p0) outliers start: 116 outliers final: 50 residues processed: 303 average time/residue: 0.4113 time to fit residues: 200.5403 Evaluate side-chains 224 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 164 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 1060 ARG Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1133 HIS Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 309 ARG Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 96 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 308 optimal weight: 2.9990 chunk 249 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 348 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 332 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 ASN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1084 GLN D1109 GLN ** F 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.051125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.035219 restraints weight = 194571.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.036378 restraints weight = 96929.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.037155 restraints weight = 62658.439| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 30635 Z= 0.219 Angle : 0.637 12.322 42040 Z= 0.332 Chirality : 0.042 0.199 4796 Planarity : 0.004 0.078 5076 Dihedral : 18.832 176.349 5337 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.37 % Allowed : 26.74 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % 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: -0.91 (0.14), residues: 3488 helix: 0.96 (0.14), residues: 1372 sheet: -2.03 (0.24), residues: 389 loop : -1.57 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 112 HIS 0.004 0.001 HIS C 200 PHE 0.017 0.001 PHE F 479 TYR 0.025 0.001 TYR B 32 ARG 0.007 0.000 ARG D1085 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 1366) hydrogen bonds : angle 4.89382 ( 3770) metal coordination : bond 0.00758 ( 7) metal coordination : angle 3.73183 ( 6) covalent geometry : bond 0.00470 (30628) covalent geometry : angle 0.63567 (42034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 166 time to evaluate : 3.157 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.9058 (tt0) cc_final: 0.8510 (tp30) REVERT: A 133 LYS cc_start: 0.9383 (tttp) cc_final: 0.9160 (ttpp) REVERT: B 191 LYS cc_start: 0.9349 (ttpt) cc_final: 0.8814 (ttmm) REVERT: C 103 MET cc_start: 0.9245 (ptt) cc_final: 0.8952 (ppp) REVERT: C 393 MET cc_start: 0.9658 (mmt) cc_final: 0.9347 (mmm) REVERT: C 396 MET cc_start: 0.9340 (pp-130) cc_final: 0.8692 (pp-130) REVERT: C 429 GLU cc_start: 0.9272 (tp30) cc_final: 0.8824 (tp30) REVERT: C 438 GLN cc_start: 0.8650 (mt0) cc_final: 0.8299 (mm-40) REVERT: C 586 MET cc_start: 0.9501 (ppp) cc_final: 0.8391 (ppp) REVERT: C 607 MET cc_start: 0.8849 (mtt) cc_final: 0.8594 (mtp) REVERT: C 611 MET cc_start: 0.9308 (mpp) cc_final: 0.8918 (mmp) REVERT: C 661 MET cc_start: 0.7930 (tpt) cc_final: 0.7538 (tpt) REVERT: C 754 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8417 (tm-30) REVERT: C 1028 MET cc_start: 0.9203 (ttm) cc_final: 0.8784 (tpp) REVERT: C 1051 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8466 (tpp) REVERT: C 1074 TRP cc_start: 0.9201 (m-10) cc_final: 0.8109 (m-90) REVERT: C 1087 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8658 (mt-10) REVERT: C 1088 LEU cc_start: 0.9639 (mt) cc_final: 0.9407 (mt) REVERT: C 1104 GLU cc_start: 0.9516 (tt0) cc_final: 0.9208 (tm-30) REVERT: D 213 GLN cc_start: 0.9224 (tp-100) cc_final: 0.9022 (tp-100) REVERT: D 312 MET cc_start: 0.9140 (mtp) cc_final: 0.8742 (mtm) REVERT: D 373 MET cc_start: 0.8913 (mtp) cc_final: 0.8299 (mtp) REVERT: D 404 ASP cc_start: 0.8596 (m-30) cc_final: 0.8338 (m-30) REVERT: D 504 LEU cc_start: 0.9165 (mp) cc_final: 0.8505 (tp) REVERT: D 515 MET cc_start: 0.8216 (mtm) cc_final: 0.7823 (mtm) REVERT: D 520 LYS cc_start: 0.8853 (pttt) cc_final: 0.8388 (pttt) REVERT: D 524 LEU cc_start: 0.9232 (tp) cc_final: 0.8991 (tt) REVERT: D 533 ASN cc_start: 0.9389 (t0) cc_final: 0.9128 (t0) REVERT: D 576 MET cc_start: 0.8714 (mtp) cc_final: 0.8462 (mtp) REVERT: D 581 MET cc_start: 0.9409 (mtm) cc_final: 0.9000 (mtm) REVERT: D 640 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8831 (mt) REVERT: D 667 THR cc_start: 0.9432 (OUTLIER) cc_final: 0.9162 (t) REVERT: D 820 MET cc_start: 0.7918 (tpp) cc_final: 0.7699 (tpp) REVERT: D 865 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9077 (pp) REVERT: D 983 MET cc_start: 0.8295 (tpp) cc_final: 0.7933 (tpp) REVERT: D 1250 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7986 (pm20) REVERT: E 35 ILE cc_start: 0.9718 (tp) cc_final: 0.9463 (mm) REVERT: E 66 ASP cc_start: 0.9307 (m-30) cc_final: 0.8967 (m-30) REVERT: F 317 PHE cc_start: 0.8953 (t80) cc_final: 0.8559 (t80) REVERT: F 323 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8620 (mm-30) REVERT: F 325 ASN cc_start: 0.9458 (m-40) cc_final: 0.9214 (m-40) REVERT: F 438 PHE cc_start: 0.9085 (m-80) cc_final: 0.8853 (m-80) REVERT: F 511 MET cc_start: 0.9563 (mmm) cc_final: 0.9055 (mmp) REVERT: F 514 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9497 (mt) REVERT: J 60 MET cc_start: 0.8279 (ptp) cc_final: 0.8063 (ptp) REVERT: J 64 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8824 (tt) REVERT: M 55 TYR cc_start: 0.8848 (m-10) cc_final: 0.8519 (m-10) REVERT: M 72 GLN cc_start: 0.9331 (tt0) cc_final: 0.9070 (tm-30) REVERT: M 115 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8609 (p0) outliers start: 127 outliers final: 80 residues processed: 277 average time/residue: 0.4006 time to fit residues: 180.3678 Evaluate side-chains 248 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 158 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1132 CYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1133 HIS Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 309 ARG Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 331 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 175 optimal weight: 40.0000 chunk 148 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 322 optimal weight: 20.0000 chunk 342 optimal weight: 6.9990 chunk 280 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN ** F 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.050479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.034718 restraints weight = 193242.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.035848 restraints weight = 96604.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.036598 restraints weight = 62488.059| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 30635 Z= 0.252 Angle : 0.666 11.156 42040 Z= 0.346 Chirality : 0.042 0.148 4796 Planarity : 0.005 0.076 5076 Dihedral : 18.819 176.329 5337 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.81 % Allowed : 26.88 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % 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: -0.84 (0.14), residues: 3488 helix: 0.94 (0.14), residues: 1386 sheet: -1.94 (0.25), residues: 381 loop : -1.50 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 112 HIS 0.005 0.001 HIS D 94 PHE 0.018 0.002 PHE C 300 TYR 0.020 0.001 TYR B 32 ARG 0.005 0.000 ARG D 144 Details of bonding type rmsd hydrogen bonds : bond 0.04483 ( 1366) hydrogen bonds : angle 4.98237 ( 3770) metal coordination : bond 0.00893 ( 7) metal coordination : angle 4.02206 ( 6) covalent geometry : bond 0.00540 (30628) covalent geometry : angle 0.66479 (42034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 159 time to evaluate : 3.474 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.9055 (tt0) cc_final: 0.8656 (tm-30) REVERT: B 141 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: B 191 LYS cc_start: 0.9359 (ttpt) cc_final: 0.8993 (ptmm) REVERT: C 127 MET cc_start: 0.8653 (ptp) cc_final: 0.8349 (ptp) REVERT: C 136 THR cc_start: 0.9498 (OUTLIER) cc_final: 0.9171 (p) REVERT: C 211 TRP cc_start: 0.8857 (m-10) cc_final: 0.8654 (m100) REVERT: C 393 MET cc_start: 0.9644 (mmt) cc_final: 0.9266 (mmm) REVERT: C 396 MET cc_start: 0.9333 (pp-130) cc_final: 0.8536 (pp-130) REVERT: C 429 GLU cc_start: 0.9295 (tp30) cc_final: 0.8808 (tp30) REVERT: C 438 GLN cc_start: 0.8744 (mt0) cc_final: 0.8430 (mm-40) REVERT: C 440 MET cc_start: 0.7783 (ttt) cc_final: 0.7523 (ttt) REVERT: C 586 MET cc_start: 0.9518 (ppp) cc_final: 0.8433 (ppp) REVERT: C 607 MET cc_start: 0.8783 (mtt) cc_final: 0.8525 (mtp) REVERT: C 611 MET cc_start: 0.9286 (mpp) cc_final: 0.8960 (mmp) REVERT: C 661 MET cc_start: 0.7941 (tpt) cc_final: 0.7515 (tpt) REVERT: C 753 GLU cc_start: 0.7905 (tp30) cc_final: 0.7670 (tp30) REVERT: C 754 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8276 (tm-30) REVERT: C 926 MET cc_start: 0.8816 (tpp) cc_final: 0.7596 (tpp) REVERT: C 1028 MET cc_start: 0.9160 (ttm) cc_final: 0.8750 (tpp) REVERT: C 1051 MET cc_start: 0.8880 (tpt) cc_final: 0.8422 (tpp) REVERT: C 1087 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8625 (mt-10) REVERT: C 1104 GLU cc_start: 0.9506 (tt0) cc_final: 0.9220 (tm-30) REVERT: D 92 MET cc_start: 0.8956 (mtp) cc_final: 0.8073 (mmm) REVERT: D 213 GLN cc_start: 0.9237 (tp-100) cc_final: 0.9021 (tp-100) REVERT: D 373 MET cc_start: 0.8882 (mtp) cc_final: 0.8283 (mtp) REVERT: D 462 ASP cc_start: 0.9389 (OUTLIER) cc_final: 0.8931 (m-30) REVERT: D 504 LEU cc_start: 0.9058 (mp) cc_final: 0.8802 (mt) REVERT: D 533 ASN cc_start: 0.9386 (t0) cc_final: 0.9138 (t0) REVERT: D 576 MET cc_start: 0.8968 (mtp) cc_final: 0.8728 (mtp) REVERT: D 581 MET cc_start: 0.9415 (mtm) cc_final: 0.9043 (mtm) REVERT: D 640 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8875 (mt) REVERT: D 667 THR cc_start: 0.9462 (OUTLIER) cc_final: 0.9048 (t) REVERT: D 820 MET cc_start: 0.8311 (tpp) cc_final: 0.7893 (tpp) REVERT: D 865 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9072 (pp) REVERT: D 925 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9089 (tp) REVERT: D 983 MET cc_start: 0.8232 (tpp) cc_final: 0.7929 (tpp) REVERT: D 1208 MET cc_start: 0.8207 (pmm) cc_final: 0.7648 (ptm) REVERT: D 1250 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7970 (pm20) REVERT: E 35 ILE cc_start: 0.9750 (tp) cc_final: 0.9533 (mm) REVERT: E 66 ASP cc_start: 0.9341 (m-30) cc_final: 0.9054 (m-30) REVERT: F 317 PHE cc_start: 0.8991 (t80) cc_final: 0.8547 (t80) REVERT: F 323 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8553 (mm-30) REVERT: F 325 ASN cc_start: 0.9463 (m-40) cc_final: 0.9216 (m-40) REVERT: F 403 MET cc_start: 0.8972 (mmt) cc_final: 0.8724 (mmp) REVERT: F 438 PHE cc_start: 0.9100 (m-80) cc_final: 0.8887 (m-80) REVERT: F 511 MET cc_start: 0.9596 (mmm) cc_final: 0.9110 (mmp) REVERT: F 514 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9466 (mt) REVERT: J 64 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8811 (tt) REVERT: M 55 TYR cc_start: 0.8828 (m-10) cc_final: 0.8490 (m-10) REVERT: M 102 ASN cc_start: 0.9422 (OUTLIER) cc_final: 0.8730 (m-40) REVERT: M 115 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8292 (p0) REVERT: M 133 GLN cc_start: 0.9460 (tp-100) cc_final: 0.9158 (tm-30) outliers start: 140 outliers final: 96 residues processed: 287 average time/residue: 0.4153 time to fit residues: 195.2899 Evaluate side-chains 265 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 155 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1052 ILE Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 474 ARG Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 732 SER Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1055 LEU Chi-restraints excluded: chain D residue 1060 ARG Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1117 ASP Chi-restraints excluded: chain D residue 1133 HIS Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 102 ASN Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 314 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 220 optimal weight: 0.9980 chunk 240 optimal weight: 0.0670 chunk 125 optimal weight: 6.9990 chunk 271 optimal weight: 20.0000 chunk 221 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 339 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 218 optimal weight: 8.9990 overall best weight: 3.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1084 GLN ** F 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.050787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.035024 restraints weight = 193574.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.036161 restraints weight = 96474.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.036938 restraints weight = 62420.300| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 30635 Z= 0.207 Angle : 0.634 10.762 42040 Z= 0.327 Chirality : 0.042 0.198 4796 Planarity : 0.004 0.075 5076 Dihedral : 18.755 175.635 5337 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 5.02 % Allowed : 26.85 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % 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: -0.67 (0.14), residues: 3488 helix: 1.07 (0.14), residues: 1384 sheet: -1.81 (0.25), residues: 375 loop : -1.40 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 112 HIS 0.004 0.001 HIS D 854 PHE 0.016 0.001 PHE C 300 TYR 0.020 0.001 TYR B 32 ARG 0.004 0.000 ARG D 144 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 1366) hydrogen bonds : angle 4.86848 ( 3770) metal coordination : bond 0.00657 ( 7) metal coordination : angle 3.60093 ( 6) covalent geometry : bond 0.00447 (30628) covalent geometry : angle 0.63280 (42034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 169 time to evaluate : 3.159 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.9062 (tt0) cc_final: 0.8632 (tm-30) REVERT: A 95 MET cc_start: 0.8915 (ptp) cc_final: 0.8560 (mtm) REVERT: B 123 MET cc_start: 0.9124 (ppp) cc_final: 0.8321 (ptm) REVERT: B 141 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: B 191 LYS cc_start: 0.9343 (ttpt) cc_final: 0.8947 (ptmm) REVERT: C 103 MET cc_start: 0.9273 (pmm) cc_final: 0.8514 (pmm) REVERT: C 211 TRP cc_start: 0.8843 (m-10) cc_final: 0.8638 (m100) REVERT: C 393 MET cc_start: 0.9640 (mmt) cc_final: 0.9335 (mmm) REVERT: C 396 MET cc_start: 0.9331 (pp-130) cc_final: 0.8605 (pp-130) REVERT: C 429 GLU cc_start: 0.9292 (tp30) cc_final: 0.8806 (tp30) REVERT: C 438 GLN cc_start: 0.8746 (mt0) cc_final: 0.8288 (mm-40) REVERT: C 440 MET cc_start: 0.8087 (ttt) cc_final: 0.7754 (ttt) REVERT: C 586 MET cc_start: 0.9475 (ppp) cc_final: 0.8001 (ppp) REVERT: C 607 MET cc_start: 0.8830 (mtt) cc_final: 0.8582 (mtp) REVERT: C 611 MET cc_start: 0.9294 (mpp) cc_final: 0.8974 (mmp) REVERT: C 661 MET cc_start: 0.8029 (tpt) cc_final: 0.7601 (tpt) REVERT: C 753 GLU cc_start: 0.7923 (tp30) cc_final: 0.7655 (tp30) REVERT: C 754 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8257 (tm-30) REVERT: C 926 MET cc_start: 0.8837 (tpp) cc_final: 0.7918 (tpp) REVERT: C 1028 MET cc_start: 0.9121 (ttm) cc_final: 0.8763 (tpp) REVERT: C 1087 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8618 (mt-10) REVERT: C 1104 GLU cc_start: 0.9509 (tt0) cc_final: 0.9217 (tm-30) REVERT: D 213 GLN cc_start: 0.9204 (tp-100) cc_final: 0.8959 (tp-100) REVERT: D 312 MET cc_start: 0.9126 (mtp) cc_final: 0.8798 (mtm) REVERT: D 342 ASP cc_start: 0.9375 (m-30) cc_final: 0.8829 (p0) REVERT: D 373 MET cc_start: 0.8902 (mtp) cc_final: 0.8268 (mtp) REVERT: D 474 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8195 (mtm-85) REVERT: D 504 LEU cc_start: 0.9025 (mp) cc_final: 0.8359 (tp) REVERT: D 520 LYS cc_start: 0.8838 (pttt) cc_final: 0.8262 (pttt) REVERT: D 533 ASN cc_start: 0.9368 (t0) cc_final: 0.9110 (t0) REVERT: D 576 MET cc_start: 0.8941 (mtp) cc_final: 0.8738 (mtp) REVERT: D 581 MET cc_start: 0.9414 (mtm) cc_final: 0.9050 (mtm) REVERT: D 640 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8871 (mt) REVERT: D 667 THR cc_start: 0.9394 (OUTLIER) cc_final: 0.9151 (t) REVERT: D 820 MET cc_start: 0.8315 (tpp) cc_final: 0.7937 (tpp) REVERT: D 865 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9065 (pp) REVERT: D 925 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9088 (tp) REVERT: D 983 MET cc_start: 0.8116 (tpp) cc_final: 0.7777 (tpp) REVERT: D 1208 MET cc_start: 0.8308 (pmm) cc_final: 0.7598 (ptm) REVERT: D 1250 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: E 35 ILE cc_start: 0.9752 (tp) cc_final: 0.9531 (mm) REVERT: E 66 ASP cc_start: 0.9312 (m-30) cc_final: 0.9018 (m-30) REVERT: F 302 LEU cc_start: 0.9836 (tp) cc_final: 0.9412 (mt) REVERT: F 317 PHE cc_start: 0.8923 (t80) cc_final: 0.8466 (t80) REVERT: F 325 ASN cc_start: 0.9469 (m-40) cc_final: 0.9105 (m-40) REVERT: F 403 MET cc_start: 0.8976 (mmt) cc_final: 0.8708 (mmp) REVERT: F 509 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.9145 (tppt) REVERT: F 511 MET cc_start: 0.9587 (mmm) cc_final: 0.9067 (mmm) REVERT: F 514 LEU cc_start: 0.9708 (OUTLIER) cc_final: 0.9491 (mt) REVERT: J 64 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8828 (tt) REVERT: J 69 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7884 (tm) REVERT: M 55 TYR cc_start: 0.8901 (m-10) cc_final: 0.8549 (m-10) REVERT: M 115 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8174 (p0) outliers start: 146 outliers final: 100 residues processed: 301 average time/residue: 0.4166 time to fit residues: 202.2709 Evaluate side-chains 273 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 159 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1132 CYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 474 ARG Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 732 SER Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1060 ARG Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1117 ASP Chi-restraints excluded: chain D residue 1133 HIS Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 509 LYS Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 61.5735 > 50: distance: 2 - 25: 18.749 distance: 9 - 36: 20.857 distance: 15 - 45: 17.911 distance: 20 - 25: 20.936 distance: 21 - 52: 35.054 distance: 25 - 26: 10.910 distance: 26 - 27: 15.241 distance: 27 - 28: 22.244 distance: 27 - 36: 12.867 distance: 29 - 30: 17.136 distance: 30 - 31: 14.896 distance: 30 - 32: 18.048 distance: 31 - 33: 16.437 distance: 32 - 34: 21.857 distance: 33 - 35: 20.970 distance: 34 - 35: 18.346 distance: 36 - 37: 28.493 distance: 37 - 38: 7.069 distance: 37 - 40: 5.463 distance: 38 - 39: 11.023 distance: 38 - 45: 24.798 distance: 40 - 41: 11.832 distance: 41 - 42: 20.455 distance: 42 - 43: 5.199 distance: 42 - 44: 5.915 distance: 45 - 46: 21.149 distance: 46 - 47: 15.285 distance: 46 - 49: 34.723 distance: 47 - 48: 20.530 distance: 47 - 52: 29.926 distance: 49 - 50: 26.238 distance: 49 - 51: 37.747 distance: 52 - 53: 20.777 distance: 53 - 54: 19.313 distance: 53 - 56: 29.941 distance: 54 - 55: 31.097 distance: 54 - 60: 31.193 distance: 56 - 57: 31.752 distance: 57 - 58: 9.878 distance: 57 - 59: 38.297 distance: 60 - 61: 27.406 distance: 61 - 62: 26.740 distance: 61 - 64: 22.066 distance: 62 - 63: 14.896 distance: 62 - 71: 25.608 distance: 64 - 65: 23.193 distance: 65 - 66: 7.887 distance: 66 - 67: 7.932 distance: 67 - 68: 3.946 distance: 68 - 69: 10.709 distance: 68 - 70: 17.814 distance: 71 - 72: 9.327 distance: 72 - 73: 29.124 distance: 72 - 75: 14.302 distance: 73 - 74: 22.716 distance: 73 - 76: 13.573 distance: 76 - 77: 13.710 distance: 76 - 82: 29.071 distance: 77 - 78: 13.747 distance: 77 - 80: 22.536 distance: 78 - 79: 28.282 distance: 78 - 83: 11.961 distance: 80 - 81: 26.958 distance: 81 - 82: 9.134 distance: 83 - 84: 20.689 distance: 84 - 85: 17.075 distance: 84 - 87: 25.774 distance: 85 - 86: 20.895 distance: 85 - 93: 14.877 distance: 87 - 88: 13.089 distance: 88 - 89: 49.360 distance: 88 - 90: 41.589 distance: 89 - 91: 12.131 distance: 90 - 92: 17.798 distance: 91 - 92: 11.096 distance: 93 - 94: 9.310 distance: 94 - 95: 24.021 distance: 94 - 97: 20.278 distance: 95 - 96: 19.483 distance: 95 - 100: 15.748 distance: 97 - 98: 8.487 distance: 97 - 99: 10.432 distance: 100 - 101: 7.493 distance: 101 - 102: 4.211 distance: 101 - 104: 9.157 distance: 104 - 105: 6.174 distance: 105 - 106: 5.509 distance: 106 - 107: 10.139 distance: 106 - 108: 5.127