Starting phenix.real_space_refine on Mon Sep 14 10:44:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vvz_21408/09_2026/6vvz_21408.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vvz_21408/09_2026/6vvz_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_21408/09_2026/6vvz_21408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vvz_21408/09_2026/6vvz_21408.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vvz_21408/09_2026/6vvz_21408.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vvz_21408/09_2026/6vvz_21408.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vvz_21408/09_2026/6vvz_21408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vvz_21408/09_2026/6vvz_21408.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} 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: {'ASN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 2} 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: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} 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: {'ARG:plan': 1, 'ASP:plan': 4, 'GLU:plan': 2, 'GLN:plan1': 1} 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: 5.90, per 1000 atoms: 0.20 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: 2.45 Conformation dependent library (CDL) restraints added in 1.3 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: 4.68 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: 8.59 Time building geometry restraints manager: 3.32 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: 41833 4.38 - 8.75: 184 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=" O4' DA P 120 " pdb=" C1' DA P 120 " pdb=" N9 DA P 120 " ideal model delta sigma weight residual 108.00 112.50 -4.50 7.00e-01 2.04e+00 4.14e+01 angle pdb=" O4' DT O 20 " pdb=" C1' DT O 20 " pdb=" N1 DT O 20 " ideal model delta sigma weight residual 108.00 112.12 -4.12 7.00e-01 2.04e+00 3.46e+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 ... (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: 3795 0.065 - 0.130: 911 0.130 - 0.195: 73 0.195 - 0.260: 9 0.260 - 0.325: 8 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 36.470 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 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= 0.547 Angle : 0.973 21.885 42040 Z= 0.588 Chirality : 0.055 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.009 0.001 ARG D 206 TYR 0.019 0.002 TYR B 96 PHE 0.021 0.002 PHE D 811 TRP 0.017 0.003 TRP D 723 HIS 0.008 0.002 HIS D 525 Details of bonding type rmsd/Z covalent geometry : bond 0.01000 / 0.54 (30628) covalent geometry : angle 0.96627 / 0.59 (42034) hydrogen bonds : bond 0.17060 / 11.74 ( 1366) hydrogen bonds : angle 7.14035 / 4.94 ( 3770) metal coordination : bond 0.14078 / 7.02 ( 7) metal coordination : angle 9.52310 / 3.59 ( 6) *********************** 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 : 1.150 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 244 LEU cc_start: 0.9769 (tt) cc_final: 0.9488 (mt) REVERT: D 342 ASP cc_start: 0.9396 (OUTLIER) cc_final: 0.8886 (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: 0.9333 (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: 0.9321 (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: 0.7544 (tt0) 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: 0.9167 (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: 0.8523 (t70) outliers start: 185 outliers final: 40 residues processed: 429 average time/residue: 0.1959 time to fit residues: 136.0500 Evaluate side-chains 229 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 166 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 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 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 HIS A 119 HIS A 124 HIS C 81 ASN C 141 ASN C 142 ASN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN C 920 HIS C 941 HIS C1034 HIS C1035 HIS 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 D 852 ASN D1001 GLN D1109 GLN D1145 GLN D1190 ASN E 100 HIS F 234 GLN F 353 GLN F 388 GLN J 28 GLN ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.051642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.035810 restraints weight = 190493.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.036995 restraints weight = 94785.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.037774 restraints weight = 61021.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.038278 restraints weight = 46000.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.038560 restraints weight = 38478.679| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 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 = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30635 Z= 0.162 Angle : 0.704 13.272 42040 Z= 0.370 Chirality : 0.045 0.264 4796 Planarity : 0.005 0.087 5076 Dihedral : 19.715 171.540 5422 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.61 % Allowed : 26.16 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.13), residues: 3488 helix: -0.46 (0.13), residues: 1372 sheet: -2.58 (0.23), residues: 404 loop : -2.04 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 454 TYR 0.022 0.001 TYR B 176 PHE 0.023 0.002 PHE F 335 TRP 0.013 0.002 TRP D 723 HIS 0.013 0.001 HIS E 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (30628) covalent geometry : angle 0.70010 / 0.37 (42034) hydrogen bonds : bond 0.05023 / 3.41 ( 1366) hydrogen bonds : angle 5.69834 / 3.96 ( 3770) metal coordination : bond 0.00869 / 0.46 ( 7) metal coordination : angle 6.21059 / 2.52 ( 6) *********************** 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 334 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 200 time to evaluate : 0.878 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: A 62 GLU cc_start: 0.9075 (tt0) cc_final: 0.8457 (tp30) REVERT: A 173 LYS cc_start: 0.9255 (ttmt) cc_final: 0.8536 (tttp) REVERT: B 95 MET cc_start: 0.8170 (mpp) cc_final: 0.7921 (mpp) REVERT: C 211 TRP cc_start: 0.8959 (m-10) cc_final: 0.8715 (m100) REVERT: C 393 MET cc_start: 0.9648 (mmt) cc_final: 0.9343 (mmm) REVERT: C 396 MET cc_start: 0.9328 (pp-130) cc_final: 0.8659 (pp-130) REVERT: C 429 GLU cc_start: 0.9316 (tp30) cc_final: 0.8780 (tp30) REVERT: C 593 MET cc_start: 0.8723 (mtp) cc_final: 0.8447 (mmm) REVERT: C 607 MET cc_start: 0.8946 (mtt) cc_final: 0.8659 (mtp) REVERT: C 611 MET cc_start: 0.9336 (tpp) cc_final: 0.8897 (mmp) REVERT: C 661 MET cc_start: 0.8543 (tpt) cc_final: 0.8154 (tpt) REVERT: C 672 MET cc_start: 0.9265 (mmm) cc_final: 0.8413 (mmm) REVERT: C 754 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: C 757 ILE cc_start: 0.9651 (OUTLIER) cc_final: 0.9386 (tt) REVERT: C 904 MET cc_start: 0.9074 (tpp) cc_final: 0.8849 (tpp) REVERT: C 1051 MET cc_start: 0.9088 (tpt) cc_final: 0.8425 (tpp) REVERT: C 1087 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8648 (mt-10) REVERT: C 1094 ASP cc_start: 0.8619 (m-30) cc_final: 0.7035 (t0) REVERT: C 1104 GLU cc_start: 0.9504 (tt0) cc_final: 0.9073 (tm-30) REVERT: D 92 MET cc_start: 0.8407 (mtp) cc_final: 0.7534 (mmm) REVERT: D 101 VAL cc_start: 0.9713 (OUTLIER) cc_final: 0.9446 (m) REVERT: D 143 MET cc_start: 0.9439 (ttp) cc_final: 0.9177 (tmm) REVERT: D 329 GLN cc_start: 0.9510 (OUTLIER) cc_final: 0.9265 (pp30) REVERT: D 373 MET cc_start: 0.8923 (mtp) cc_final: 0.8226 (mpp) REVERT: D 404 ASP cc_start: 0.8565 (m-30) cc_final: 0.8357 (m-30) REVERT: D 504 LEU cc_start: 0.9169 (mp) cc_final: 0.8474 (tp) REVERT: D 520 LYS cc_start: 0.8717 (pttt) cc_final: 0.8258 (pttt) REVERT: D 533 ASN cc_start: 0.9421 (t0) cc_final: 0.9112 (t0) REVERT: D 576 MET cc_start: 0.9103 (ttp) cc_final: 0.8504 (ppp) REVERT: D 581 MET cc_start: 0.9374 (mtm) cc_final: 0.8972 (mtm) REVERT: D 582 VAL cc_start: 0.9669 (OUTLIER) cc_final: 0.9403 (m) REVERT: D 667 THR cc_start: 0.9350 (OUTLIER) cc_final: 0.9065 (t) REVERT: D 862 ASP cc_start: 0.9042 (t70) cc_final: 0.8741 (t0) REVERT: D 865 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9161 (pp) REVERT: D 983 MET cc_start: 0.8574 (mmm) cc_final: 0.8300 (tpp) REVERT: E 35 ILE cc_start: 0.9752 (tp) cc_final: 0.9519 (mm) REVERT: E 66 ASP cc_start: 0.9311 (m-30) cc_final: 0.8583 (t0) REVERT: E 89 GLU cc_start: 0.7309 (pm20) cc_final: 0.7063 (pm20) REVERT: F 278 ARG cc_start: 0.9380 (OUTLIER) cc_final: 0.8811 (ttm110) REVERT: F 302 LEU cc_start: 0.9866 (tp) cc_final: 0.9487 (mt) REVERT: F 325 ASN cc_start: 0.9359 (m-40) cc_final: 0.9102 (m110) REVERT: F 438 PHE cc_start: 0.9061 (m-80) cc_final: 0.8749 (m-80) REVERT: F 511 MET cc_start: 0.9564 (mmm) cc_final: 0.9129 (mmm) REVERT: F 514 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9470 (mt) REVERT: J 64 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8873 (tt) REVERT: M 25 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8713 (ttp80) REVERT: M 55 TYR cc_start: 0.8897 (m-10) cc_final: 0.8607 (m-10) REVERT: M 72 GLN cc_start: 0.9436 (tt0) cc_final: 0.9066 (tm-30) REVERT: M 116 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.9074 (mt0) outliers start: 134 outliers final: 45 residues processed: 323 average time/residue: 0.1900 time to fit residues: 99.4929 Evaluate side-chains 228 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 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 79 ASP Chi-restraints excluded: chain C residue 241 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 636 ILE Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 757 ILE 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 936 LEU Chi-restraints excluded: chain C residue 997 ASP 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 7 PHE Chi-restraints excluded: chain D residue 101 VAL 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 418 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1060 ARG Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1117 ASP Chi-restraints excluded: chain D residue 1122 LEU Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain F residue 278 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 35 ASP Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 116 GLN 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: 0.9990 chunk 332 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 305 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 222 optimal weight: 0.7980 chunk 267 optimal weight: 0.9980 chunk 341 optimal weight: 5.9990 chunk 344 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 ASN ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN F 425 GLN F 459 GLN ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.051262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.035485 restraints weight = 193786.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.036651 restraints weight = 95827.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.037434 restraints weight = 61787.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.037933 restraints weight = 46697.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.038231 restraints weight = 39162.294| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30635 Z= 0.178 Angle : 0.668 12.991 42040 Z= 0.351 Chirality : 0.044 0.297 4796 Planarity : 0.005 0.082 5076 Dihedral : 19.465 173.920 5351 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.23 % Allowed : 26.13 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.14), residues: 3488 helix: 0.31 (0.14), residues: 1372 sheet: -2.32 (0.24), residues: 407 loop : -1.79 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 88 TYR 0.029 0.001 TYR B 32 PHE 0.013 0.001 PHE D 6 TRP 0.029 0.002 TRP D 223 HIS 0.009 0.001 HIS C 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (30628) covalent geometry : angle 0.66554 / 0.35 (42034) hydrogen bonds : bond 0.04621 / 3.11 ( 1366) hydrogen bonds : angle 5.30873 / 3.70 ( 3770) metal coordination : bond 0.01079 / 0.45 ( 7) metal coordination : angle 5.25221 / 2.37 ( 6) *********************** 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 303 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 180 time to evaluate : 1.128 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 173 LYS cc_start: 0.9273 (ttmt) cc_final: 0.8522 (tptp) REVERT: B 1 MET cc_start: 0.8741 (mmm) cc_final: 0.8451 (ttm) REVERT: B 95 MET cc_start: 0.8240 (mpp) cc_final: 0.8011 (mpp) REVERT: B 141 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: C 103 MET cc_start: 0.9126 (ptt) cc_final: 0.8906 (ppp) REVERT: C 160 MET cc_start: 0.9030 (ttp) cc_final: 0.8620 (ttp) REVERT: C 258 MET cc_start: 0.6315 (ppp) cc_final: 0.6108 (ppp) REVERT: C 393 MET cc_start: 0.9657 (mmt) cc_final: 0.9353 (mmm) REVERT: C 396 MET cc_start: 0.9370 (pp-130) cc_final: 0.8747 (pp-130) REVERT: C 429 GLU cc_start: 0.9273 (tp30) cc_final: 0.8775 (tp30) REVERT: C 586 MET cc_start: 0.9379 (ppp) cc_final: 0.7792 (ppp) REVERT: C 607 MET cc_start: 0.8916 (mtt) cc_final: 0.8684 (mtp) REVERT: C 611 MET cc_start: 0.9330 (mpp) cc_final: 0.8949 (mmp) REVERT: C 661 MET cc_start: 0.8148 (tpt) cc_final: 0.7657 (tpt) REVERT: C 904 MET cc_start: 0.9018 (tpp) cc_final: 0.8783 (tpp) REVERT: C 1028 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8702 (tpp) REVERT: C 1051 MET cc_start: 0.9055 (tpt) cc_final: 0.8461 (tpp) REVERT: C 1087 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8495 (mt-10) REVERT: C 1088 LEU cc_start: 0.9633 (mt) cc_final: 0.9388 (mt) REVERT: C 1104 GLU cc_start: 0.9504 (tt0) cc_final: 0.9158 (tm-30) REVERT: D 143 MET cc_start: 0.9484 (ttp) cc_final: 0.9272 (tmm) REVERT: D 329 GLN cc_start: 0.9599 (OUTLIER) cc_final: 0.9267 (pp30) REVERT: D 373 MET cc_start: 0.8907 (mtp) cc_final: 0.8307 (mtp) REVERT: D 404 ASP cc_start: 0.8581 (m-30) cc_final: 0.8369 (m-30) REVERT: D 504 LEU cc_start: 0.9177 (mp) cc_final: 0.8484 (tp) REVERT: D 520 LYS cc_start: 0.8788 (pttt) cc_final: 0.8417 (pttt) REVERT: D 533 ASN cc_start: 0.9404 (t0) cc_final: 0.9120 (t0) REVERT: D 581 MET cc_start: 0.9387 (mtm) cc_final: 0.8967 (mtm) REVERT: D 640 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8801 (mt) REVERT: D 667 THR cc_start: 0.9359 (OUTLIER) cc_final: 0.9093 (t) REVERT: D 817 LEU cc_start: 0.9599 (mt) cc_final: 0.9377 (mt) REVERT: D 862 ASP cc_start: 0.9021 (t70) cc_final: 0.8724 (t0) REVERT: D 865 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9098 (pp) REVERT: D 1161 MET cc_start: 0.9042 (mtp) cc_final: 0.8792 (mmt) REVERT: D 1208 MET cc_start: 0.8199 (pmm) cc_final: 0.7227 (ptt) REVERT: D 1250 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8155 (pm20) REVERT: E 35 ILE cc_start: 0.9759 (tp) cc_final: 0.9555 (tp) REVERT: E 66 ASP cc_start: 0.9330 (m-30) cc_final: 0.8811 (t0) REVERT: F 278 ARG cc_start: 0.9371 (OUTLIER) cc_final: 0.8864 (ttm110) REVERT: F 309 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8171 (tpm170) REVERT: F 323 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8527 (mm-30) REVERT: F 325 ASN cc_start: 0.9357 (m-40) cc_final: 0.9089 (m110) REVERT: F 377 ASN cc_start: 0.9506 (m-40) cc_final: 0.9302 (t0) REVERT: F 438 PHE cc_start: 0.9076 (m-80) cc_final: 0.8834 (m-80) REVERT: F 511 MET cc_start: 0.9579 (mmm) cc_final: 0.9127 (mmp) REVERT: F 514 LEU cc_start: 0.9722 (OUTLIER) cc_final: 0.9491 (mt) REVERT: J 64 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8842 (tt) REVERT: M 25 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8661 (ttp80) REVERT: M 55 TYR cc_start: 0.8845 (m-10) cc_final: 0.8558 (m-10) REVERT: M 72 GLN cc_start: 0.9406 (tt0) cc_final: 0.9032 (tm-30) outliers start: 123 outliers final: 56 residues processed: 288 average time/residue: 0.1907 time to fit residues: 89.2124 Evaluate side-chains 234 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 165 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 127 THR 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 241 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 737 LEU Chi-restraints excluded: chain C residue 807 THR 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 1028 MET Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1132 CYS Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 70 PHE 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 248 TYR Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 447 MET 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 706 MET 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 1060 ARG Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1133 HIS Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 309 ARG Chi-restraints excluded: chain F residue 344 SER 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 M residue 25 ARG Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 85 TRP 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 244 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 chunk 251 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 332 optimal weight: 0.0870 chunk 260 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 852 ASN ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN M 14 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.051801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.036054 restraints weight = 191183.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.037232 restraints weight = 94654.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.038002 restraints weight = 60995.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.038499 restraints weight = 46210.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.038811 restraints weight = 38818.542| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30635 Z= 0.146 Angle : 0.633 12.451 42040 Z= 0.331 Chirality : 0.043 0.302 4796 Planarity : 0.004 0.077 5076 Dihedral : 19.343 173.206 5344 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.16 % Allowed : 26.57 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.14), residues: 3488 helix: 0.64 (0.14), residues: 1376 sheet: -2.08 (0.24), residues: 397 loop : -1.66 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1085 TYR 0.028 0.001 TYR B 32 PHE 0.013 0.001 PHE D 6 TRP 0.013 0.001 TRP M 112 HIS 0.005 0.001 HIS C1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (30628) covalent geometry : angle 0.63061 / 0.33 (42034) hydrogen bonds : bond 0.04197 / 2.84 ( 1366) hydrogen bonds : angle 5.07320 / 3.54 ( 3770) metal coordination : bond 0.00468 / 0.21 ( 7) metal coordination : angle 4.53891 / 2.12 ( 6) *********************** 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 297 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 176 time to evaluate : 1.047 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: A 62 GLU cc_start: 0.9032 (tt0) cc_final: 0.8319 (tm-30) REVERT: A 173 LYS cc_start: 0.9250 (ttmt) cc_final: 0.8817 (ttpt) REVERT: B 1 MET cc_start: 0.8720 (mmm) cc_final: 0.8483 (mtm) REVERT: B 95 MET cc_start: 0.8237 (mpp) cc_final: 0.7955 (mpp) REVERT: B 141 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: C 127 MET cc_start: 0.8806 (ptp) cc_final: 0.8181 (pmm) REVERT: C 160 MET cc_start: 0.9052 (ttp) cc_final: 0.8607 (ttp) REVERT: C 258 MET cc_start: 0.6215 (ppp) cc_final: 0.5927 (ppp) REVERT: C 393 MET cc_start: 0.9655 (mmt) cc_final: 0.9352 (mmm) REVERT: C 396 MET cc_start: 0.9345 (pp-130) cc_final: 0.8714 (pp-130) REVERT: C 429 GLU cc_start: 0.9283 (tp30) cc_final: 0.8792 (tp30) REVERT: C 586 MET cc_start: 0.9418 (ppp) cc_final: 0.7879 (ppp) REVERT: C 607 MET cc_start: 0.8837 (mtt) cc_final: 0.8560 (mtp) REVERT: C 611 MET cc_start: 0.9296 (mpp) cc_final: 0.8869 (mmp) REVERT: C 661 MET cc_start: 0.8259 (tpt) cc_final: 0.7810 (tpt) REVERT: C 754 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8504 (tm-30) REVERT: C 1028 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8720 (tpp) REVERT: C 1051 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8399 (tpp) REVERT: C 1071 MET cc_start: 0.9651 (mpp) cc_final: 0.8716 (mpp) REVERT: C 1074 TRP cc_start: 0.9150 (m-10) cc_final: 0.7990 (m-90) REVERT: C 1087 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8570 (mt-10) REVERT: C 1088 LEU cc_start: 0.9604 (mt) cc_final: 0.9355 (mt) REVERT: C 1104 GLU cc_start: 0.9493 (tt0) cc_final: 0.9162 (tm-30) REVERT: D 329 GLN cc_start: 0.9633 (OUTLIER) cc_final: 0.9337 (pp30) REVERT: D 373 MET cc_start: 0.8905 (mtp) cc_final: 0.8289 (mtp) REVERT: D 404 ASP cc_start: 0.8591 (m-30) cc_final: 0.8366 (m-30) REVERT: D 474 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8310 (mtm110) REVERT: D 504 LEU cc_start: 0.9170 (mp) cc_final: 0.8472 (tp) REVERT: D 520 LYS cc_start: 0.8805 (pttt) cc_final: 0.8414 (pttt) REVERT: D 533 ASN cc_start: 0.9369 (t0) cc_final: 0.9084 (t0) REVERT: D 581 MET cc_start: 0.9385 (mtm) cc_final: 0.8947 (mtm) REVERT: D 640 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8801 (mt) REVERT: D 667 THR cc_start: 0.9411 (OUTLIER) cc_final: 0.9174 (t) REVERT: D 862 ASP cc_start: 0.9036 (t70) cc_final: 0.8760 (t0) REVERT: D 865 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9066 (pp) REVERT: D 943 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8372 (t70) REVERT: D 983 MET cc_start: 0.8377 (mmm) cc_final: 0.7837 (tpp) REVERT: D 1161 MET cc_start: 0.9117 (mtp) cc_final: 0.8674 (mmt) REVERT: D 1208 MET cc_start: 0.8301 (pmm) cc_final: 0.7231 (ptt) REVERT: D 1250 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: E 35 ILE cc_start: 0.9704 (tp) cc_final: 0.9491 (mm) REVERT: E 66 ASP cc_start: 0.9324 (m-30) cc_final: 0.8903 (t0) REVERT: F 302 LEU cc_start: 0.9862 (tp) cc_final: 0.9471 (mt) REVERT: F 323 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8531 (mm-30) REVERT: F 325 ASN cc_start: 0.9325 (m-40) cc_final: 0.8999 (m-40) REVERT: F 438 PHE cc_start: 0.9032 (m-80) cc_final: 0.8778 (m-80) REVERT: F 511 MET cc_start: 0.9563 (mmm) cc_final: 0.9081 (mmp) REVERT: J 64 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8802 (tt) REVERT: M 25 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8697 (ttp80) REVERT: M 55 TYR cc_start: 0.8856 (m-10) cc_final: 0.8552 (m-10) REVERT: M 72 GLN cc_start: 0.9352 (tt0) cc_final: 0.8982 (tm-30) outliers start: 121 outliers final: 67 residues processed: 285 average time/residue: 0.1872 time to fit residues: 87.2036 Evaluate side-chains 245 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 164 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 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 125 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 175 THR 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 140 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 356 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 754 GLU Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 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 1051 MET Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1063 PHE 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 1102 VAL Chi-restraints excluded: chain D residue 37 ARG 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 329 GLN Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 474 ARG 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 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 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 1165 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 E residue 64 ILE Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 488 THR 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 M residue 25 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 128 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 342 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 316 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 40 optimal weight: 0.1980 chunk 310 optimal weight: 0.9980 chunk 338 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 275 optimal weight: 2.9990 chunk 312 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** 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 499 ASN ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.051594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.035818 restraints weight = 193309.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.036986 restraints weight = 95946.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.037760 restraints weight = 61914.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.038259 restraints weight = 46850.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.038569 restraints weight = 39307.116| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 30635 Z= 0.163 Angle : 0.634 11.908 42040 Z= 0.332 Chirality : 0.043 0.307 4796 Planarity : 0.004 0.074 5076 Dihedral : 19.245 173.405 5342 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.16 % Allowed : 26.74 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.14), residues: 3488 helix: 0.81 (0.14), residues: 1382 sheet: -1.92 (0.25), residues: 376 loop : -1.54 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 98 TYR 0.025 0.001 TYR B 32 PHE 0.015 0.001 PHE F 317 TRP 0.019 0.001 TRP M 112 HIS 0.004 0.001 HIS D 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (30628) covalent geometry : angle 0.63255 / 0.33 (42034) hydrogen bonds : bond 0.04162 / 2.81 ( 1366) hydrogen bonds : angle 4.98852 / 3.49 ( 3770) metal coordination : bond 0.00461 / 0.23 ( 7) metal coordination : angle 3.95024 / 1.81 ( 6) *********************** 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 287 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 166 time to evaluate : 1.181 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: A 62 GLU cc_start: 0.9023 (tt0) cc_final: 0.8321 (tm-30) REVERT: B 1 MET cc_start: 0.8698 (mmm) cc_final: 0.8322 (ttm) REVERT: B 95 MET cc_start: 0.8176 (mpp) cc_final: 0.7917 (mpp) REVERT: C 160 MET cc_start: 0.9009 (ttp) cc_final: 0.8535 (ttp) REVERT: C 258 MET cc_start: 0.6238 (ppp) cc_final: 0.5976 (ppp) REVERT: C 393 MET cc_start: 0.9656 (mmt) cc_final: 0.9235 (mmm) REVERT: C 396 MET cc_start: 0.9348 (pp-130) cc_final: 0.8568 (pp-130) REVERT: C 429 GLU cc_start: 0.9261 (tp30) cc_final: 0.8766 (tp30) REVERT: C 440 MET cc_start: 0.7710 (ttt) cc_final: 0.7444 (ttt) REVERT: C 586 MET cc_start: 0.9440 (ppp) cc_final: 0.7861 (ppp) REVERT: C 607 MET cc_start: 0.8850 (mtt) cc_final: 0.8575 (mtp) REVERT: C 611 MET cc_start: 0.9325 (mpp) cc_final: 0.8943 (mmp) REVERT: C 661 MET cc_start: 0.8116 (tpt) cc_final: 0.7756 (tpt) REVERT: C 754 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8511 (tm-30) REVERT: C 1028 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8714 (tpp) REVERT: C 1051 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8456 (tpp) REVERT: C 1071 MET cc_start: 0.9553 (mpp) cc_final: 0.9332 (mpp) REVERT: C 1088 LEU cc_start: 0.9623 (mt) cc_final: 0.9377 (mt) REVERT: C 1104 GLU cc_start: 0.9489 (tt0) cc_final: 0.9185 (tm-30) REVERT: D 312 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8851 (mpp) REVERT: D 373 MET cc_start: 0.8881 (mtp) cc_final: 0.8266 (mtp) REVERT: D 404 ASP cc_start: 0.8588 (m-30) cc_final: 0.8375 (m-30) REVERT: D 474 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8013 (mtm110) REVERT: D 504 LEU cc_start: 0.9127 (mp) cc_final: 0.8463 (tp) REVERT: D 520 LYS cc_start: 0.8838 (pttt) cc_final: 0.8451 (pttt) REVERT: D 533 ASN cc_start: 0.9366 (t0) cc_final: 0.9091 (t0) REVERT: D 581 MET cc_start: 0.9412 (mtm) cc_final: 0.8997 (mtm) REVERT: D 640 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8816 (mt) REVERT: D 667 THR cc_start: 0.9445 (OUTLIER) cc_final: 0.9164 (t) REVERT: D 862 ASP cc_start: 0.8949 (t70) cc_final: 0.8671 (t0) REVERT: D 865 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9041 (pp) REVERT: D 943 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8383 (t70) REVERT: D 983 MET cc_start: 0.8428 (mmm) cc_final: 0.7897 (tpp) REVERT: D 1208 MET cc_start: 0.8357 (pmm) cc_final: 0.7969 (ptm) REVERT: D 1250 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8072 (pm20) REVERT: E 35 ILE cc_start: 0.9710 (tp) cc_final: 0.9489 (mm) REVERT: E 66 ASP cc_start: 0.9322 (m-30) cc_final: 0.8910 (t0) REVERT: F 278 ARG cc_start: 0.9353 (OUTLIER) cc_final: 0.8815 (ttp-110) REVERT: F 325 ASN cc_start: 0.9444 (m-40) cc_final: 0.9057 (m110) REVERT: F 438 PHE cc_start: 0.9038 (m-80) cc_final: 0.8794 (m-80) REVERT: F 509 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9156 (tppt) REVERT: F 511 MET cc_start: 0.9529 (mmm) cc_final: 0.9101 (mmp) REVERT: J 64 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8807 (tt) REVERT: M 25 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8665 (ttp80) REVERT: M 55 TYR cc_start: 0.8853 (m-10) cc_final: 0.8544 (m-10) REVERT: M 72 GLN cc_start: 0.9287 (tt0) cc_final: 0.8880 (tm-30) REVERT: M 102 ASN cc_start: 0.9215 (OUTLIER) cc_final: 0.8421 (m-40) outliers start: 121 outliers final: 77 residues processed: 271 average time/residue: 0.1958 time to fit residues: 87.1167 Evaluate side-chains 246 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 154 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 74 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 167 ILE 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 175 THR 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 140 ILE 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 288 THR Chi-restraints excluded: chain C residue 353 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 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 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 1051 MET Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 70 PHE 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 312 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 474 ARG Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 693 GLN 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 865 LEU Chi-restraints excluded: chain D residue 943 ASP 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 1133 HIS Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 509 LYS 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 M residue 25 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 102 ASN Chi-restraints excluded: chain M residue 103 LYS 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 155 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 293 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 288 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 290 optimal weight: 9.9990 chunk 321 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** 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 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.050639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.034821 restraints weight = 195005.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.035958 restraints weight = 97572.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.036719 restraints weight = 63362.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.037181 restraints weight = 48134.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.037427 restraints weight = 40794.732| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 30635 Z= 0.248 Angle : 0.684 12.258 42040 Z= 0.357 Chirality : 0.044 0.302 4796 Planarity : 0.005 0.076 5076 Dihedral : 19.264 174.124 5339 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.33 % Allowed : 27.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.14), residues: 3488 helix: 0.87 (0.14), residues: 1383 sheet: -1.94 (0.25), residues: 374 loop : -1.45 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1014 TYR 0.021 0.001 TYR B 32 PHE 0.019 0.002 PHE F 317 TRP 0.022 0.002 TRP C 211 HIS 0.005 0.001 HIS C 662 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.25 (30628) covalent geometry : angle 0.68237 / 0.36 (42034) hydrogen bonds : bond 0.04571 / 3.07 ( 1366) hydrogen bonds : angle 5.07968 / 3.55 ( 3770) metal coordination : bond 0.00918 / 0.48 ( 7) metal coordination : angle 4.24889 / 1.99 ( 6) *********************** 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 278 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 152 time to evaluate : 1.170 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: A 62 GLU cc_start: 0.8987 (tt0) cc_final: 0.8286 (tm-30) REVERT: B 1 MET cc_start: 0.8785 (mmm) cc_final: 0.8369 (mtm) REVERT: B 95 MET cc_start: 0.8186 (mpp) cc_final: 0.7973 (mpp) REVERT: B 141 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: C 103 MET cc_start: 0.9014 (ptt) cc_final: 0.8681 (ppp) REVERT: C 127 MET cc_start: 0.8754 (ptp) cc_final: 0.8525 (ptp) REVERT: C 160 MET cc_start: 0.9063 (ttp) cc_final: 0.8602 (ttp) REVERT: C 258 MET cc_start: 0.6298 (ppp) cc_final: 0.5983 (ppp) REVERT: C 393 MET cc_start: 0.9649 (mmt) cc_final: 0.9341 (mmm) REVERT: C 396 MET cc_start: 0.9380 (pp-130) cc_final: 0.8726 (pp-130) REVERT: C 404 MET cc_start: 0.8852 (mtp) cc_final: 0.8375 (mtp) REVERT: C 429 GLU cc_start: 0.9264 (tp30) cc_final: 0.8803 (tp30) REVERT: C 440 MET cc_start: 0.7976 (ttt) cc_final: 0.7686 (ttt) REVERT: C 586 MET cc_start: 0.9486 (ppp) cc_final: 0.7961 (ppp) REVERT: C 593 MET cc_start: 0.8905 (tpp) cc_final: 0.8658 (tpp) REVERT: C 607 MET cc_start: 0.8849 (mtt) cc_final: 0.8599 (mtp) REVERT: C 611 MET cc_start: 0.9321 (mpp) cc_final: 0.8966 (mmp) REVERT: C 661 MET cc_start: 0.8080 (tpt) cc_final: 0.7705 (tpt) REVERT: C 754 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8570 (pp20) REVERT: C 1028 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8700 (tpp) REVERT: C 1051 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8415 (tpp) REVERT: C 1071 MET cc_start: 0.9576 (mpp) cc_final: 0.8897 (mpp) REVERT: C 1074 TRP cc_start: 0.9141 (m-10) cc_final: 0.8016 (m-90) REVERT: C 1076 MET cc_start: 0.9034 (ttt) cc_final: 0.8815 (tpp) REVERT: C 1087 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8611 (mt-10) REVERT: C 1104 GLU cc_start: 0.9490 (tt0) cc_final: 0.9189 (tm-30) REVERT: D 256 MET cc_start: 0.7995 (ttm) cc_final: 0.7719 (ttm) REVERT: D 312 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8778 (mpp) REVERT: D 373 MET cc_start: 0.8823 (mtp) cc_final: 0.8226 (mtp) REVERT: D 404 ASP cc_start: 0.8558 (m-30) cc_final: 0.8344 (m-30) REVERT: D 474 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8171 (mtm-85) REVERT: D 504 LEU cc_start: 0.9129 (mp) cc_final: 0.8830 (mt) REVERT: D 520 LYS cc_start: 0.8841 (pttt) cc_final: 0.8419 (pttt) REVERT: D 533 ASN cc_start: 0.9383 (t0) cc_final: 0.9125 (t0) REVERT: D 581 MET cc_start: 0.9416 (mtm) cc_final: 0.8984 (mtm) REVERT: D 667 THR cc_start: 0.9441 (OUTLIER) cc_final: 0.9162 (t) REVERT: D 820 MET cc_start: 0.8018 (tpp) cc_final: 0.7785 (tpp) REVERT: D 862 ASP cc_start: 0.8990 (t70) cc_final: 0.8715 (t0) REVERT: D 865 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9056 (pp) REVERT: D 983 MET cc_start: 0.8501 (mmm) cc_final: 0.7998 (tpp) REVERT: D 1208 MET cc_start: 0.8324 (pmm) cc_final: 0.7648 (ptm) REVERT: D 1250 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8066 (pm20) REVERT: E 35 ILE cc_start: 0.9736 (tp) cc_final: 0.9512 (mm) REVERT: E 66 ASP cc_start: 0.9293 (m-30) cc_final: 0.8873 (t0) REVERT: F 278 ARG cc_start: 0.9346 (OUTLIER) cc_final: 0.8830 (ttp-110) REVERT: F 325 ASN cc_start: 0.9470 (m-40) cc_final: 0.9043 (m110) REVERT: F 403 MET cc_start: 0.8956 (mmt) cc_final: 0.8688 (mmp) REVERT: F 438 PHE cc_start: 0.9074 (m-80) cc_final: 0.8847 (m-80) REVERT: F 509 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.9176 (tppt) REVERT: F 511 MET cc_start: 0.9556 (mmm) cc_final: 0.9092 (mmp) REVERT: J 64 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8805 (tt) REVERT: J 69 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7966 (tm) REVERT: M 25 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8620 (ttp80) REVERT: M 55 TYR cc_start: 0.8837 (m-10) cc_final: 0.8523 (m-10) REVERT: M 72 GLN cc_start: 0.9309 (tt0) cc_final: 0.8915 (tm-30) outliers start: 126 outliers final: 89 residues processed: 262 average time/residue: 0.1984 time to fit residues: 85.3253 Evaluate side-chains 254 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 150 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 74 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 55 ARG 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 141 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 175 THR 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 140 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 193 LYS 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 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 926 MET Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 60 CYS 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 312 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 474 ARG Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 738 VAL 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 865 LEU 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 1210 ILE Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 509 LYS 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 M residue 25 ARG Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 85 TRP Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 47 optimal weight: 0.9990 chunk 212 optimal weight: 0.0980 chunk 184 optimal weight: 8.9990 chunk 205 optimal weight: 0.7980 chunk 351 optimal weight: 40.0000 chunk 209 optimal weight: 5.9990 chunk 319 optimal weight: 9.9990 chunk 321 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 293 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN C 841 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 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 = 0.3383 r_free = 0.3383 target = 0.051850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.036076 restraints weight = 191306.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.037239 restraints weight = 95125.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.038002 restraints weight = 61380.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.038507 restraints weight = 46478.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.038779 restraints weight = 39052.913| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30635 Z= 0.126 Angle : 0.615 11.657 42040 Z= 0.320 Chirality : 0.043 0.309 4796 Planarity : 0.004 0.071 5076 Dihedral : 19.182 174.018 5337 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.85 % Allowed : 27.60 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3488 helix: 1.07 (0.14), residues: 1380 sheet: -1.75 (0.25), residues: 384 loop : -1.34 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 500 TYR 0.021 0.001 TYR B 176 PHE 0.019 0.001 PHE F 317 TRP 0.023 0.002 TRP C 211 HIS 0.005 0.001 HIS D 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (30628) covalent geometry : angle 0.61407 / 0.32 (42034) hydrogen bonds : bond 0.03857 / 2.60 ( 1366) hydrogen bonds : angle 4.85546 / 3.40 ( 3770) metal coordination : bond 0.00187 / 0.11 ( 7) metal coordination : angle 3.52435 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 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 277 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 165 time to evaluate : 1.218 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: 0.8947 (tt0) cc_final: 0.8221 (tm-30) REVERT: B 95 MET cc_start: 0.8139 (mpp) cc_final: 0.7908 (mpp) REVERT: B 141 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: C 103 MET cc_start: 0.9042 (ptt) cc_final: 0.8816 (ppp) REVERT: C 127 MET cc_start: 0.8710 (ptp) cc_final: 0.8447 (ptp) REVERT: C 160 MET cc_start: 0.8940 (ttp) cc_final: 0.8462 (ttp) REVERT: C 258 MET cc_start: 0.6448 (ppp) cc_final: 0.6110 (ppp) REVERT: C 355 MET cc_start: 0.3971 (OUTLIER) cc_final: 0.3564 (tpp) REVERT: C 393 MET cc_start: 0.9648 (mmt) cc_final: 0.9308 (mmm) REVERT: C 396 MET cc_start: 0.9362 (pp-130) cc_final: 0.8700 (pp-130) REVERT: C 404 MET cc_start: 0.8833 (mtp) cc_final: 0.8522 (mtp) REVERT: C 429 GLU cc_start: 0.9254 (tp30) cc_final: 0.8800 (tp30) REVERT: C 440 MET cc_start: 0.8021 (ttt) cc_final: 0.7748 (ttt) REVERT: C 586 MET cc_start: 0.9461 (ppp) cc_final: 0.7920 (ppp) REVERT: C 593 MET cc_start: 0.8964 (tpp) cc_final: 0.8674 (tpp) REVERT: C 607 MET cc_start: 0.8820 (mtt) cc_final: 0.8544 (mtp) REVERT: C 611 MET cc_start: 0.9267 (mpp) cc_final: 0.8887 (mmp) REVERT: C 661 MET cc_start: 0.8224 (tpt) cc_final: 0.7873 (tpt) REVERT: C 754 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8572 (tm-30) REVERT: C 1028 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8743 (tpp) REVERT: C 1051 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8420 (tpp) REVERT: C 1088 LEU cc_start: 0.9615 (mt) cc_final: 0.9387 (mt) REVERT: C 1104 GLU cc_start: 0.9483 (tt0) cc_final: 0.9171 (tm-30) REVERT: D 158 GLU cc_start: 0.9458 (OUTLIER) cc_final: 0.9148 (mm-30) REVERT: D 312 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8831 (mpp) REVERT: D 327 MET cc_start: 0.9028 (tpp) cc_final: 0.8726 (tpp) REVERT: D 373 MET cc_start: 0.8951 (mtp) cc_final: 0.8322 (mtp) REVERT: D 474 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8150 (mtm-85) REVERT: D 504 LEU cc_start: 0.9018 (mp) cc_final: 0.8301 (tp) REVERT: D 520 LYS cc_start: 0.8862 (pttt) cc_final: 0.8393 (pttt) REVERT: D 533 ASN cc_start: 0.9325 (t0) cc_final: 0.9064 (t0) REVERT: D 581 MET cc_start: 0.9393 (mtm) cc_final: 0.8984 (mtm) REVERT: D 667 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9264 (t) REVERT: D 820 MET cc_start: 0.7832 (tpp) cc_final: 0.7560 (tpp) REVERT: D 865 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9033 (pp) REVERT: D 943 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8379 (t70) REVERT: D 983 MET cc_start: 0.8442 (mmm) cc_final: 0.7936 (tpp) REVERT: D 1100 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8729 (p) REVERT: D 1208 MET cc_start: 0.8136 (pmm) cc_final: 0.7792 (ptm) REVERT: D 1250 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8079 (pm20) REVERT: E 35 ILE cc_start: 0.9712 (tp) cc_final: 0.9488 (mm) REVERT: E 66 ASP cc_start: 0.9316 (m-30) cc_final: 0.8900 (t0) REVERT: F 281 MET cc_start: 0.8948 (ptm) cc_final: 0.8742 (ppp) REVERT: F 325 ASN cc_start: 0.9464 (m-40) cc_final: 0.8997 (m110) REVERT: F 403 MET cc_start: 0.8946 (mmt) cc_final: 0.8661 (mmp) REVERT: F 438 PHE cc_start: 0.9021 (m-80) cc_final: 0.8773 (m-80) REVERT: F 509 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.9152 (tppt) REVERT: F 511 MET cc_start: 0.9558 (mmm) cc_final: 0.9074 (mmp) REVERT: J 64 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8787 (tt) REVERT: J 69 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7957 (tm) REVERT: M 25 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8677 (ttp80) REVERT: M 55 TYR cc_start: 0.8851 (m-10) cc_final: 0.8523 (m-10) REVERT: M 72 GLN cc_start: 0.9281 (tt0) cc_final: 0.8905 (tm-30) REVERT: M 102 ASN cc_start: 0.9183 (OUTLIER) cc_final: 0.8419 (m-40) REVERT: M 133 GLN cc_start: 0.9408 (tp-100) cc_final: 0.9111 (tm-30) outliers start: 112 outliers final: 72 residues processed: 262 average time/residue: 0.1979 time to fit residues: 84.7760 Evaluate side-chains 244 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 154 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 117 THR 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 B residue 55 ARG 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 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 140 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 355 MET 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 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 869 VAL Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1093 SER 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 135 VAL Chi-restraints excluded: chain D residue 158 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 312 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 474 ARG Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 943 ASP 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 1100 SER 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 1211 THR Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 509 LYS 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 M residue 25 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 102 ASN Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 171 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 220 optimal weight: 0.9990 chunk 233 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** 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 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 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 = 0.3366 r_free = 0.3366 target = 0.051241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.035532 restraints weight = 192927.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.036669 restraints weight = 96258.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.037416 restraints weight = 62404.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.037866 restraints weight = 47421.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.038215 restraints weight = 40176.553| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30635 Z= 0.186 Angle : 0.635 11.628 42040 Z= 0.330 Chirality : 0.043 0.301 4796 Planarity : 0.004 0.071 5076 Dihedral : 19.166 174.883 5337 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.16 % Allowed : 27.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3488 helix: 1.17 (0.14), residues: 1382 sheet: -1.62 (0.26), residues: 362 loop : -1.28 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 278 TYR 0.020 0.001 TYR B 32 PHE 0.015 0.001 PHE F 479 TRP 0.017 0.001 TRP M 112 HIS 0.004 0.001 HIS C 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (30628) covalent geometry : angle 0.63349 / 0.33 (42034) hydrogen bonds : bond 0.04105 / 2.76 ( 1366) hydrogen bonds : angle 4.88262 / 3.42 ( 3770) metal coordination : bond 0.00591 / 0.31 ( 7) metal coordination : angle 3.54413 / 1.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 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 275 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 154 time to evaluate : 1.088 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: A 62 GLU cc_start: 0.8951 (tt0) cc_final: 0.8254 (tm-30) REVERT: B 95 MET cc_start: 0.8081 (mpp) cc_final: 0.7881 (mpp) REVERT: C 103 MET cc_start: 0.9087 (ptt) cc_final: 0.8822 (ppp) REVERT: C 160 MET cc_start: 0.8923 (ttp) cc_final: 0.8426 (ttp) REVERT: C 258 MET cc_start: 0.6371 (ppp) cc_final: 0.5998 (ppp) REVERT: C 355 MET cc_start: 0.4600 (OUTLIER) cc_final: 0.4268 (tpp) REVERT: C 393 MET cc_start: 0.9650 (mmt) cc_final: 0.9330 (mmm) REVERT: C 396 MET cc_start: 0.9358 (pp-130) cc_final: 0.8721 (pp-130) REVERT: C 429 GLU cc_start: 0.9243 (tp30) cc_final: 0.8803 (tp30) REVERT: C 440 MET cc_start: 0.8094 (ttt) cc_final: 0.7826 (ttt) REVERT: C 586 MET cc_start: 0.9482 (ppp) cc_final: 0.7939 (ppp) REVERT: C 593 MET cc_start: 0.9012 (tpp) cc_final: 0.8621 (mmp) REVERT: C 607 MET cc_start: 0.8829 (mtt) cc_final: 0.8567 (mtp) REVERT: C 611 MET cc_start: 0.9266 (mpp) cc_final: 0.8922 (mmp) REVERT: C 661 MET cc_start: 0.8013 (tpt) cc_final: 0.7644 (tpt) REVERT: C 754 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8386 (pp20) REVERT: C 1028 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8730 (tpp) REVERT: C 1051 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8420 (tpp) REVERT: C 1074 TRP cc_start: 0.9020 (m-10) cc_final: 0.7926 (m-90) REVERT: C 1088 LEU cc_start: 0.9556 (mt) cc_final: 0.9347 (mt) REVERT: C 1104 GLU cc_start: 0.9483 (tt0) cc_final: 0.9182 (tm-30) REVERT: D 256 MET cc_start: 0.7953 (ttm) cc_final: 0.7715 (ttm) REVERT: D 312 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8827 (mpp) REVERT: D 373 MET cc_start: 0.8910 (mtp) cc_final: 0.8316 (mtp) REVERT: D 474 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8162 (mtm-85) REVERT: D 504 LEU cc_start: 0.8943 (mp) cc_final: 0.8662 (mt) REVERT: D 533 ASN cc_start: 0.9338 (t0) cc_final: 0.9078 (t0) REVERT: D 581 MET cc_start: 0.9386 (mtm) cc_final: 0.8981 (mtm) REVERT: D 640 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8842 (mt) REVERT: D 820 MET cc_start: 0.8011 (tpp) cc_final: 0.7658 (tpp) REVERT: D 865 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9069 (pp) REVERT: D 943 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8381 (t70) REVERT: D 983 MET cc_start: 0.8492 (mmm) cc_final: 0.8034 (tpp) REVERT: D 1100 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8765 (p) REVERT: D 1208 MET cc_start: 0.8276 (pmm) cc_final: 0.7623 (ptm) REVERT: D 1250 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8010 (pm20) REVERT: E 35 ILE cc_start: 0.9733 (tp) cc_final: 0.9508 (mm) REVERT: E 66 ASP cc_start: 0.9317 (m-30) cc_final: 0.8908 (t0) REVERT: F 278 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.8804 (ttp-110) REVERT: F 325 ASN cc_start: 0.9479 (m-40) cc_final: 0.9019 (m110) REVERT: F 403 MET cc_start: 0.8944 (mmt) cc_final: 0.8662 (mmp) REVERT: F 438 PHE cc_start: 0.9043 (m-80) cc_final: 0.8824 (m-80) REVERT: F 509 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.9158 (tppt) REVERT: F 511 MET cc_start: 0.9526 (mmm) cc_final: 0.9021 (mmp) REVERT: J 64 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8787 (tt) REVERT: J 69 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.8007 (tm) REVERT: M 25 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8590 (ttp80) REVERT: M 55 TYR cc_start: 0.8866 (m-10) cc_final: 0.8539 (m-10) REVERT: M 72 GLN cc_start: 0.9275 (tt0) cc_final: 0.8909 (tm-30) REVERT: M 102 ASN cc_start: 0.9239 (OUTLIER) cc_final: 0.8517 (m-40) REVERT: M 133 GLN cc_start: 0.9413 (tp-100) cc_final: 0.9119 (tm-30) outliers start: 121 outliers final: 87 residues processed: 262 average time/residue: 0.1918 time to fit residues: 81.3100 Evaluate side-chains 254 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 150 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 117 THR 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 15 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 55 ARG 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 141 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 355 MET 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 869 VAL Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 60 CYS 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 135 VAL 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 312 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 474 ARG Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 614 SER 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 738 VAL Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 943 ASP 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 1100 SER 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 1211 THR Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 509 LYS 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 106 ARG Chi-restraints excluded: chain M residue 25 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 102 ASN Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 286 optimal weight: 0.0370 chunk 266 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 235 optimal weight: 9.9990 chunk 271 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 300 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 229 optimal weight: 0.0170 chunk 256 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** 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 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN ** J 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.052136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.036426 restraints weight = 191717.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.037586 restraints weight = 95614.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.038356 restraints weight = 61727.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.038852 restraints weight = 46737.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.039124 restraints weight = 39233.685| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30635 Z= 0.128 Angle : 0.624 10.399 42040 Z= 0.322 Chirality : 0.043 0.302 4796 Planarity : 0.004 0.068 5076 Dihedral : 19.108 176.345 5337 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.54 % Allowed : 28.19 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3488 helix: 1.22 (0.14), residues: 1385 sheet: -1.51 (0.26), residues: 376 loop : -1.24 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 403 TYR 0.020 0.001 TYR B 176 PHE 0.016 0.001 PHE D 452 TRP 0.014 0.001 TRP M 112 HIS 0.004 0.001 HIS C 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (30628) covalent geometry : angle 0.62299 / 0.32 (42034) hydrogen bonds : bond 0.03790 / 2.55 ( 1366) hydrogen bonds : angle 4.79421 / 3.37 ( 3770) metal coordination : bond 0.00184 / 0.10 ( 7) metal coordination : angle 3.10733 / 1.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 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 261 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 158 time to evaluate : 1.143 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: A 62 GLU cc_start: 0.8935 (tt0) cc_final: 0.8216 (tm-30) REVERT: B 95 MET cc_start: 0.8171 (mpp) cc_final: 0.7950 (mpp) REVERT: B 141 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: C 127 MET cc_start: 0.8693 (ptp) cc_final: 0.8060 (pmm) REVERT: C 160 MET cc_start: 0.8898 (ttp) cc_final: 0.8393 (ttp) REVERT: C 258 MET cc_start: 0.6329 (ppp) cc_final: 0.5976 (ppp) REVERT: C 355 MET cc_start: 0.4705 (OUTLIER) cc_final: 0.4319 (tpp) REVERT: C 393 MET cc_start: 0.9647 (mmt) cc_final: 0.9212 (mmm) REVERT: C 396 MET cc_start: 0.9375 (pp-130) cc_final: 0.8632 (pp-130) REVERT: C 429 GLU cc_start: 0.9277 (tp30) cc_final: 0.8786 (tp30) REVERT: C 440 MET cc_start: 0.7969 (ttt) cc_final: 0.7704 (ttt) REVERT: C 586 MET cc_start: 0.9452 (ppp) cc_final: 0.7894 (ppp) REVERT: C 593 MET cc_start: 0.9031 (tpp) cc_final: 0.8605 (mmp) REVERT: C 607 MET cc_start: 0.8824 (mtt) cc_final: 0.8547 (mtp) REVERT: C 611 MET cc_start: 0.9240 (mpp) cc_final: 0.8897 (mmp) REVERT: C 661 MET cc_start: 0.8170 (tpt) cc_final: 0.7813 (tpt) REVERT: C 754 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8658 (pp20) REVERT: C 1028 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8765 (tpp) REVERT: C 1071 MET cc_start: 0.9491 (mpp) cc_final: 0.9051 (mmm) REVERT: C 1074 TRP cc_start: 0.9056 (m-10) cc_final: 0.7939 (m-90) REVERT: C 1088 LEU cc_start: 0.9571 (mt) cc_final: 0.9346 (mt) REVERT: C 1104 GLU cc_start: 0.9480 (tt0) cc_final: 0.9178 (tm-30) REVERT: D 91 ARG cc_start: 0.8783 (mtt180) cc_final: 0.8576 (mmm-85) REVERT: D 92 MET cc_start: 0.8711 (mtp) cc_final: 0.7766 (mmm) REVERT: D 158 GLU cc_start: 0.9453 (OUTLIER) cc_final: 0.9144 (mm-30) REVERT: D 256 MET cc_start: 0.7883 (ttm) cc_final: 0.7671 (ttm) REVERT: D 312 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8812 (mpp) REVERT: D 327 MET cc_start: 0.9076 (tpp) cc_final: 0.8712 (tpp) REVERT: D 373 MET cc_start: 0.8971 (mtp) cc_final: 0.8363 (mtp) REVERT: D 504 LEU cc_start: 0.8902 (mp) cc_final: 0.8286 (tp) REVERT: D 520 LYS cc_start: 0.8874 (pttt) cc_final: 0.8403 (pttt) REVERT: D 533 ASN cc_start: 0.9303 (t0) cc_final: 0.9037 (t0) REVERT: D 581 MET cc_start: 0.9371 (mtm) cc_final: 0.8973 (mtm) REVERT: D 820 MET cc_start: 0.7917 (tpp) cc_final: 0.7565 (tpp) REVERT: D 865 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9041 (pp) REVERT: D 943 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8403 (t70) REVERT: D 983 MET cc_start: 0.8453 (mmm) cc_final: 0.7949 (tpp) REVERT: D 1100 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8730 (p) REVERT: D 1208 MET cc_start: 0.8156 (pmm) cc_final: 0.7566 (ptm) REVERT: D 1250 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8069 (pm20) REVERT: E 35 ILE cc_start: 0.9720 (tp) cc_final: 0.9487 (mm) REVERT: E 66 ASP cc_start: 0.9307 (m-30) cc_final: 0.8900 (t0) REVERT: F 302 LEU cc_start: 0.9823 (tp) cc_final: 0.9396 (mt) REVERT: F 325 ASN cc_start: 0.9461 (m-40) cc_final: 0.8982 (m110) REVERT: F 403 MET cc_start: 0.8949 (mmt) cc_final: 0.8645 (mmp) REVERT: F 438 PHE cc_start: 0.8991 (m-80) cc_final: 0.8770 (m-80) REVERT: F 511 MET cc_start: 0.9568 (mmm) cc_final: 0.9038 (mmp) REVERT: J 64 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8795 (tt) REVERT: J 69 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7852 (tm) REVERT: M 25 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8576 (ttp80) REVERT: M 55 TYR cc_start: 0.8849 (m-10) cc_final: 0.8509 (m-10) REVERT: M 72 GLN cc_start: 0.9280 (tt0) cc_final: 0.8980 (tm-30) REVERT: M 102 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8898 (p0) outliers start: 103 outliers final: 77 residues processed: 250 average time/residue: 0.1880 time to fit residues: 77.3661 Evaluate side-chains 242 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 151 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 117 THR 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 B residue 34 LEU Chi-restraints excluded: chain B residue 55 ARG 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 165 THR Chi-restraints excluded: chain C residue 176 VAL 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 334 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 529 VAL 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 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 869 VAL Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1093 SER 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 135 VAL Chi-restraints excluded: chain D residue 158 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 312 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 474 ARG Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 943 ASP 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 1100 SER 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 1211 THR Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 488 THR 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 M residue 25 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 102 ASN Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 112 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 275 optimal weight: 6.9990 chunk 319 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 187 optimal weight: 10.0000 chunk 230 optimal weight: 0.8980 chunk 266 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** 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 ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.052395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.036729 restraints weight = 191219.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.037881 restraints weight = 95141.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.038657 restraints weight = 61472.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.039146 restraints weight = 46520.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.039465 restraints weight = 39048.260| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3008 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= 0.124 Angle : 0.649 19.841 42040 Z= 0.328 Chirality : 0.043 0.297 4796 Planarity : 0.004 0.068 5076 Dihedral : 19.043 177.879 5337 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.47 % Allowed : 28.29 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 3488 helix: 1.27 (0.14), residues: 1392 sheet: -1.41 (0.26), residues: 389 loop : -1.19 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 500 TYR 0.020 0.001 TYR B 176 PHE 0.014 0.001 PHE D 452 TRP 0.013 0.001 TRP M 112 HIS 0.004 0.001 HIS C 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (30628) covalent geometry : angle 0.64781 / 0.33 (42034) hydrogen bonds : bond 0.03716 / 2.49 ( 1366) hydrogen bonds : angle 4.74821 / 3.34 ( 3770) metal coordination : bond 0.00190 / 0.10 ( 7) metal coordination : angle 2.79721 / 1.25 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 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 259 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 158 time to evaluate : 1.189 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: A 62 GLU cc_start: 0.8922 (tt0) cc_final: 0.8204 (tm-30) REVERT: B 1 MET cc_start: 0.8798 (mmm) cc_final: 0.8339 (ttm) REVERT: B 95 MET cc_start: 0.8152 (mpp) cc_final: 0.7932 (mpp) REVERT: B 141 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: C 127 MET cc_start: 0.8658 (ptp) cc_final: 0.7994 (pmm) REVERT: C 160 MET cc_start: 0.8909 (ttp) cc_final: 0.8401 (ttp) REVERT: C 258 MET cc_start: 0.6344 (ppp) cc_final: 0.5981 (ppp) REVERT: C 355 MET cc_start: 0.4645 (OUTLIER) cc_final: 0.3774 (tpp) REVERT: C 393 MET cc_start: 0.9647 (mmt) cc_final: 0.9215 (mmm) REVERT: C 396 MET cc_start: 0.9353 (pp-130) cc_final: 0.8618 (pp-130) REVERT: C 429 GLU cc_start: 0.9275 (tp30) cc_final: 0.8778 (tp30) REVERT: C 440 MET cc_start: 0.7971 (ttt) cc_final: 0.7736 (ttt) REVERT: C 586 MET cc_start: 0.9450 (ppp) cc_final: 0.7855 (ppp) REVERT: C 593 MET cc_start: 0.9037 (tpp) cc_final: 0.8592 (mmp) REVERT: C 607 MET cc_start: 0.8829 (mtt) cc_final: 0.8551 (mtp) REVERT: C 611 MET cc_start: 0.9214 (mpp) cc_final: 0.8880 (mmp) REVERT: C 661 MET cc_start: 0.8180 (tpt) cc_final: 0.7872 (tpt) REVERT: C 713 MET cc_start: 0.8991 (tpp) cc_final: 0.8759 (tpp) REVERT: C 754 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8431 (pp20) REVERT: C 1028 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8750 (tpp) REVERT: C 1051 MET cc_start: 0.9062 (tpt) cc_final: 0.8375 (tpp) REVERT: C 1071 MET cc_start: 0.9502 (mpp) cc_final: 0.9123 (mmm) REVERT: C 1074 TRP cc_start: 0.9085 (m-10) cc_final: 0.7976 (m-90) REVERT: C 1088 LEU cc_start: 0.9546 (mt) cc_final: 0.9339 (mt) REVERT: C 1104 GLU cc_start: 0.9473 (tt0) cc_final: 0.9173 (tm-30) REVERT: D 92 MET cc_start: 0.8649 (mtp) cc_final: 0.7711 (mmm) REVERT: D 312 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8797 (mpp) REVERT: D 327 MET cc_start: 0.9023 (tpp) cc_final: 0.8702 (tpp) REVERT: D 373 MET cc_start: 0.8981 (mtp) cc_final: 0.8359 (mtp) REVERT: D 520 LYS cc_start: 0.8887 (pttt) cc_final: 0.8392 (pttt) REVERT: D 533 ASN cc_start: 0.9313 (t0) cc_final: 0.9033 (t0) REVERT: D 581 MET cc_start: 0.9369 (mtm) cc_final: 0.8986 (mtm) REVERT: D 820 MET cc_start: 0.7913 (tpp) cc_final: 0.7484 (tpp) REVERT: D 865 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9023 (pp) REVERT: D 943 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8425 (t70) REVERT: D 983 MET cc_start: 0.8490 (mmm) cc_final: 0.8082 (tpp) REVERT: D 1100 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8734 (p) REVERT: D 1208 MET cc_start: 0.8194 (pmm) cc_final: 0.7550 (ptm) REVERT: D 1250 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8094 (pm20) REVERT: E 35 ILE cc_start: 0.9691 (tp) cc_final: 0.9456 (tp) REVERT: E 66 ASP cc_start: 0.9297 (m-30) cc_final: 0.8909 (t0) REVERT: F 302 LEU cc_start: 0.9824 (tp) cc_final: 0.9407 (mt) REVERT: F 325 ASN cc_start: 0.9449 (m-40) cc_final: 0.8961 (m110) REVERT: F 403 MET cc_start: 0.8923 (mmt) cc_final: 0.8610 (mmp) REVERT: F 437 ASP cc_start: 0.9216 (t0) cc_final: 0.9008 (t0) REVERT: F 438 PHE cc_start: 0.8973 (m-80) cc_final: 0.8707 (m-80) REVERT: F 509 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.9150 (tppt) REVERT: F 511 MET cc_start: 0.9558 (mmm) cc_final: 0.9019 (mmp) REVERT: J 64 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8786 (tt) REVERT: M 25 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8569 (ttp80) REVERT: M 55 TYR cc_start: 0.8845 (m-10) cc_final: 0.8550 (m-10) REVERT: M 102 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8320 (m-40) REVERT: M 133 GLN cc_start: 0.9386 (tp-100) cc_final: 0.9083 (tm-30) outliers start: 101 outliers final: 79 residues processed: 246 average time/residue: 0.1859 time to fit residues: 74.2723 Evaluate side-chains 245 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 153 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 55 ARG 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 165 THR Chi-restraints excluded: chain C residue 176 VAL 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 334 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 529 VAL 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 737 LEU Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 820 LEU 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 926 MET Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 60 CYS 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 135 VAL 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 312 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 474 ARG Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 943 ASP 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 1100 SER 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 1248 LEU Chi-restraints excluded: chain D residue 1250 GLU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 509 LYS 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 M residue 25 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 102 ASN Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 314 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 264 optimal weight: 30.0000 chunk 194 optimal weight: 9.9990 chunk 126 optimal weight: 0.5980 chunk 218 optimal weight: 7.9990 chunk 271 optimal weight: 20.0000 chunk 297 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 277 optimal weight: 0.4980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** 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 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.051763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.036120 restraints weight = 192756.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.037271 restraints weight = 96262.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.038038 restraints weight = 62146.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.038527 restraints weight = 47003.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.038794 restraints weight = 39473.228| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30635 Z= 0.151 Angle : 0.653 14.862 42040 Z= 0.332 Chirality : 0.043 0.289 4796 Planarity : 0.004 0.070 5076 Dihedral : 19.018 178.607 5333 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.33 % Allowed : 28.39 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.06 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 3488 helix: 1.28 (0.14), residues: 1394 sheet: -1.39 (0.26), residues: 394 loop : -1.16 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 77 TYR 0.019 0.001 TYR B 176 PHE 0.014 0.001 PHE D 452 TRP 0.014 0.001 TRP M 112 HIS 0.004 0.001 HIS C 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (30628) covalent geometry : angle 0.65259 / 0.33 (42034) hydrogen bonds : bond 0.03798 / 2.55 ( 1366) hydrogen bonds : angle 4.74742 / 3.34 ( 3770) metal coordination : bond 0.00378 / 0.20 ( 7) metal coordination : angle 2.90024 / 1.32 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6176.89 seconds wall clock time: 107 minutes 17.91 seconds (6437.91 seconds total)