Starting phenix.real_space_refine on Sun Jul 5 07:53:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mko_23901/07_2026/7mko_23901.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mko_23901/07_2026/7mko_23901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mko_23901/07_2026/7mko_23901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mko_23901/07_2026/7mko_23901.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7mko_23901/07_2026/7mko_23901.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mko_23901/07_2026/7mko_23901.cif" model { file = "/net/cci-nas-00/data/ceres_data/7mko_23901/07_2026/7mko_23901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mko_23901/07_2026/7mko_23901.cif" } resolution = 3.15 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= -0.000 sd= 0.006 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 63 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16253 2.51 5 N 4652 2.21 5 O 5192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26269 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1794 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain: "B" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "C" Number of atoms: 10414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1320, 10414 Classifications: {'peptide': 1320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1264} Chain breaks: 1 Chain: "D" Number of atoms: 10419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1344, 10419 Classifications: {'peptide': 1344} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 55, 'TRANS': 1288} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 546 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "N" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "R" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 244 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 583 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {' MG': 1, ' ZN': 2, '2TM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14459 SG CYS D 70 18.688 104.023 76.170 1.00 78.71 S ATOM 14473 SG CYS D 72 18.980 106.965 73.987 1.00 79.04 S ATOM 14581 SG CYS D 85 16.360 104.678 73.284 1.00 73.63 S ATOM 14605 SG CYS D 88 19.900 103.740 72.560 1.00 74.07 S ATOM 20293 SG CYS D 814 33.429 37.780 77.850 1.00 41.29 S ATOM 20858 SG CYS D 888 35.339 41.067 77.440 1.00 38.47 S ATOM 20909 SG CYS D 895 34.295 39.745 80.540 1.00 34.69 S ATOM 20930 SG CYS D 898 36.728 38.164 79.128 1.00 35.95 S Time building chain proxies: 4.95, per 1000 atoms: 0.19 Number of scatterers: 26269 At special positions: 0 Unit cell: (125.4, 158.4, 163.68, 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 106 16.00 P 63 15.00 Mg 1 11.99 O 5192 8.00 N 4652 7.00 C 16253 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: 2.21 Conformation dependent library (CDL) restraints added in 963.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 72 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 85 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 88 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 70 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 895 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 898 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 814 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " Number of angles added : 12 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5896 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 40 sheets defined 39.4% alpha, 17.3% beta 22 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 34 through 51 removed outlier: 3.853A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.851A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 212 through 233 removed outlier: 3.952A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.616A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.943A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.874A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.749A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.619A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.817A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.761A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 482 Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.642A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.521A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.606A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.908A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 864 removed outlier: 3.636A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 981 removed outlier: 3.590A pdb=" N GLN C 955 " --> pdb=" O MET C 951 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.566A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 998 removed outlier: 4.015A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.710A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.688A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 Processing helix chain 'C' and resid 1137 through 1151 Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.699A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1333 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 113 through 119 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.641A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 3.891A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 309 removed outlier: 3.506A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 370 through 388 Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 504 through 515 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 636 Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.719A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.744A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.715A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 935 removed outlier: 3.671A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Proline residue: D 926 - end of helix removed outlier: 3.501A pdb=" N THR D 931 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1147 removed outlier: 3.864A pdb=" N ARG D1140 " --> pdb=" O GLY D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.633A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.573A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.364A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1293 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.653A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1373 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.518A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 70 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 8.731A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.511A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLY A 151 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 105 Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.564A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 17 removed outlier: 3.888A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 8.164A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.869A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.182A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.182A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.493A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB8, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.241A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.721A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.817A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'C' and resid 623 through 624 removed outlier: 4.307A pdb=" N HIS C 628 " --> pdb=" O ASP C 624 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.533A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.046A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.355A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.862A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.257A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD3, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.548A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.468A pdb=" N GLN D 158 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD6, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AD7, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD8, first strand: chain 'D' and resid 957 through 961 removed outlier: 4.003A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 966 through 967 removed outlier: 4.050A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 1035 through 1038 Processing sheet with id=AE2, first strand: chain 'D' and resid 1059 through 1061 removed outlier: 3.896A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1163 through 1165 removed outlier: 4.475A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1277 through 1279 1087 hydrogen bonds defined for protein. 3078 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8805 1.34 - 1.47: 5846 1.47 - 1.60: 11876 1.60 - 1.73: 76 1.73 - 1.86: 186 Bond restraints: 26789 Sorted by residual: bond pdb=" C2 2TM D2004 " pdb=" O2 2TM D2004 " ideal model delta sigma weight residual 1.235 1.392 -0.157 2.00e-02 2.50e+03 6.17e+01 bond pdb=" C4 2TM D2004 " pdb=" N4 2TM D2004 " ideal model delta sigma weight residual 1.342 1.452 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C2' 2TM D2004 " pdb=" C3' 2TM D2004 " ideal model delta sigma weight residual 1.543 1.443 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C3' DT T 24 " pdb=" O3' DT T 24 " ideal model delta sigma weight residual 1.435 1.371 0.064 1.30e-02 5.92e+03 2.39e+01 bond pdb=" C1' 2TM D2004 " pdb=" O4' 2TM D2004 " ideal model delta sigma weight residual 1.409 1.501 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 26784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 36012 3.75 - 7.49: 399 7.49 - 11.24: 43 11.24 - 14.98: 4 14.98 - 18.73: 2 Bond angle restraints: 36460 Sorted by residual: angle pdb=" CA PRO D 758 " pdb=" N PRO D 758 " pdb=" CD PRO D 758 " ideal model delta sigma weight residual 112.00 100.93 11.07 1.40e+00 5.10e-01 6.25e+01 angle pdb=" CB ARG B 170 " pdb=" CG ARG B 170 " pdb=" CD ARG B 170 " ideal model delta sigma weight residual 111.30 126.72 -15.42 2.30e+00 1.89e-01 4.49e+01 angle pdb=" N GLU B 226 " pdb=" CA GLU B 226 " pdb=" CB GLU B 226 " ideal model delta sigma weight residual 110.12 119.67 -9.55 1.47e+00 4.63e-01 4.22e+01 angle pdb=" CB ARG C 542 " pdb=" CG ARG C 542 " pdb=" CD ARG C 542 " ideal model delta sigma weight residual 111.30 96.75 14.55 2.30e+00 1.89e-01 4.00e+01 angle pdb=" O4' DG T 12 " pdb=" C4' DG T 12 " pdb=" C3' DG T 12 " ideal model delta sigma weight residual 106.00 102.33 3.67 6.00e-01 2.78e+00 3.74e+01 ... (remaining 36455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 15695 35.26 - 70.52: 584 70.52 - 105.78: 43 105.78 - 141.05: 1 141.05 - 176.31: 1 Dihedral angle restraints: 16324 sinusoidal: 7157 harmonic: 9167 Sorted by residual: dihedral pdb=" CA LYS C 236 " pdb=" C LYS C 236 " pdb=" N LEU C 237 " pdb=" CA LEU C 237 " ideal model delta harmonic sigma weight residual 180.00 139.10 40.90 0 5.00e+00 4.00e-02 6.69e+01 dihedral pdb=" CA THR C 595 " pdb=" C THR C 595 " pdb=" N ASP C 596 " pdb=" CA ASP C 596 " ideal model delta harmonic sigma weight residual -180.00 -142.26 -37.74 0 5.00e+00 4.00e-02 5.70e+01 dihedral pdb=" CA ASP D1184 " pdb=" C ASP D1184 " pdb=" N PRO D1185 " pdb=" CA PRO D1185 " ideal model delta harmonic sigma weight residual -180.00 -145.28 -34.72 0 5.00e+00 4.00e-02 4.82e+01 ... (remaining 16321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3785 0.097 - 0.193: 350 0.193 - 0.290: 26 0.290 - 0.387: 4 0.387 - 0.483: 1 Chirality restraints: 4166 Sorted by residual: chirality pdb=" CB VAL C 913 " pdb=" CA VAL C 913 " pdb=" CG1 VAL C 913 " pdb=" CG2 VAL C 913 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CA ARG B 170 " pdb=" N ARG B 170 " pdb=" C ARG B 170 " pdb=" CB ARG B 170 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CG LEU D 478 " pdb=" CB LEU D 478 " pdb=" CD1 LEU D 478 " pdb=" CD2 LEU D 478 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 4163 not shown) Planarity restraints: 4557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 757 " -0.141 5.00e-02 4.00e+02 2.05e-01 6.71e+01 pdb=" N PRO D 758 " 0.353 5.00e-02 4.00e+02 pdb=" CA PRO D 758 " -0.119 5.00e-02 4.00e+02 pdb=" CD PRO D 758 " -0.094 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 514 " 0.038 2.00e-02 2.50e+03 3.04e-02 1.61e+01 pdb=" CG PHE C 514 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE C 514 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 514 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 514 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 514 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 514 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 287 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO D 288 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO D 288 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 288 " 0.055 5.00e-02 4.00e+02 ... (remaining 4554 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 5 2.00 - 2.72: 1898 2.72 - 3.45: 39372 3.45 - 4.17: 63167 4.17 - 4.90: 111988 Nonbonded interactions: 216430 Sorted by model distance: nonbonded pdb=" ND2 ASN D 910 " pdb=" O ASN E 15 " model vdw 1.275 3.120 nonbonded pdb=" OE1 GLU D 418 " pdb=" CG2 VAL E 48 " model vdw 1.523 3.460 nonbonded pdb=" ND2 ASN D 910 " pdb=" C ASN E 15 " model vdw 1.632 3.350 nonbonded pdb=" ND2 ASN D 910 " pdb=" OD1 ASN E 15 " model vdw 1.740 3.120 nonbonded pdb=" ND2 ASN D 910 " pdb=" CA ASN E 15 " model vdw 1.800 3.550 ... (remaining 216425 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 7 through 235) selection = (chain 'B' and resid 7 through 235) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 26.390 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.008 0.372 26797 Z= 0.374 Angle : 1.068 18.727 36472 Z= 0.606 Chirality : 0.059 0.483 4166 Planarity : 0.007 0.205 4557 Dihedral : 17.113 176.306 10428 Min Nonbonded Distance : 1.275 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.93 % Favored : 91.60 % Rotamer: Outliers : 1.22 % Allowed : 1.29 % Favored : 97.49 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.13 % 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: -2.39 (0.13), residues: 3178 helix: -0.54 (0.14), residues: 1119 sheet: -1.03 (0.24), residues: 393 loop : -2.55 (0.12), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 170 TYR 0.041 0.003 TYR D 555 PHE 0.069 0.003 PHE C 514 TRP 0.026 0.003 TRP D1020 HIS 0.017 0.002 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.36 (26789) covalent geometry : angle 1.06754 / 0.61 (36460) hydrogen bonds : bond 0.13601 / 9.39 ( 1128) hydrogen bonds : angle 6.67559 / 4.68 ( 3190) metal coordination : bond 0.17571 / 8.03 ( 8) metal coordination : angle 1.34292 / 0.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 396 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 CYS cc_start: 0.7461 (m) cc_final: 0.7106 (m) REVERT: B 142 MET cc_start: 0.7960 (ptp) cc_final: 0.7672 (ptp) REVERT: C 104 ILE cc_start: 0.6244 (OUTLIER) cc_final: 0.5613 (mt) REVERT: C 1119 MET cc_start: 0.8525 (tpt) cc_final: 0.8310 (tpt) REVERT: D 604 MET cc_start: 0.8362 (ttm) cc_final: 0.8153 (ttp) REVERT: D 739 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7973 (mm-40) REVERT: D 1175 LEU cc_start: 0.6593 (mt) cc_final: 0.6161 (tt) outliers start: 33 outliers final: 2 residues processed: 417 average time/residue: 0.1725 time to fit residues: 111.3875 Evaluate side-chains 278 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 275 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain D residue 1301 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 462 ASN C 659 GLN C 677 ASN C 761 GLN C 808 ASN C 932 GLN C1023 HIS ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN C1313 HIS D 157 GLN D 276 ASN D 458 ASN D 488 ASN D 861 ASN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1108 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.187053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.144192 restraints weight = 34431.722| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.12 r_work: 0.3508 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26797 Z= 0.183 Angle : 0.763 12.519 36472 Z= 0.394 Chirality : 0.046 0.323 4166 Planarity : 0.006 0.090 4557 Dihedral : 13.807 156.012 4207 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.76 % Favored : 94.15 % Rotamer: Outliers : 1.22 % Allowed : 10.44 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.20 (0.14), residues: 3178 helix: 0.73 (0.15), residues: 1132 sheet: -0.63 (0.24), residues: 395 loop : -2.02 (0.13), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 88 TYR 0.027 0.002 TYR C 62 PHE 0.023 0.002 PHE C 514 TRP 0.013 0.002 TRP D 580 HIS 0.011 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (26789) covalent geometry : angle 0.76122 / 0.39 (36460) hydrogen bonds : bond 0.04977 / 3.40 ( 1128) hydrogen bonds : angle 5.26845 / 3.69 ( 3190) metal coordination : bond 0.00941 / 0.43 ( 8) metal coordination : angle 3.13644 / 1.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 314 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 CYS cc_start: 0.8162 (m) cc_final: 0.7786 (m) REVERT: B 193 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: B 199 ASP cc_start: 0.6863 (p0) cc_final: 0.6454 (p0) REVERT: B 226 GLU cc_start: 0.7609 (pt0) cc_final: 0.7271 (mm-30) REVERT: C 542 ARG cc_start: 0.8053 (tpp-160) cc_final: 0.7822 (mmt180) REVERT: D 475 GLU cc_start: 0.8039 (mp0) cc_final: 0.7765 (mp0) REVERT: D 1040 MET cc_start: 0.2164 (tmm) cc_final: 0.1084 (tmm) REVERT: D 1108 GLN cc_start: 0.2433 (OUTLIER) cc_final: 0.2183 (tp40) REVERT: D 1175 LEU cc_start: 0.6713 (mt) cc_final: 0.6459 (mt) outliers start: 33 outliers final: 21 residues processed: 336 average time/residue: 0.1599 time to fit residues: 84.7252 Evaluate side-chains 289 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 266 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 752 ASN Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1313 HIS Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1108 GLN Chi-restraints excluded: chain D residue 1301 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 72 optimal weight: 9.9990 chunk 271 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 284 optimal weight: 0.0040 chunk 162 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 29 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 overall best weight: 2.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 490 GLN ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 ASN C 834 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS D 157 GLN D 424 ASN D 861 ASN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1108 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.182317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139620 restraints weight = 34446.616| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.09 r_work: 0.3426 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 26797 Z= 0.242 Angle : 0.737 12.936 36472 Z= 0.383 Chirality : 0.046 0.381 4166 Planarity : 0.006 0.060 4557 Dihedral : 13.602 139.823 4205 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.39 % Favored : 93.46 % Rotamer: Outliers : 2.40 % Allowed : 13.38 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.97 (0.14), residues: 3178 helix: 0.79 (0.15), residues: 1150 sheet: -0.51 (0.24), residues: 385 loop : -1.79 (0.14), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 557 TYR 0.020 0.002 TYR D 46 PHE 0.031 0.002 PHE C 514 TRP 0.011 0.002 TRP D 236 HIS 0.015 0.002 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.24 (26789) covalent geometry : angle 0.73523 / 0.38 (36460) hydrogen bonds : bond 0.04996 / 3.43 ( 1128) hydrogen bonds : angle 5.03088 / 3.53 ( 3190) metal coordination : bond 0.01073 / 0.54 ( 8) metal coordination : angle 2.59086 / 1.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 303 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7757 (m110) REVERT: A 231 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.6555 (t80) REVERT: B 54 CYS cc_start: 0.8137 (m) cc_final: 0.7767 (m) REVERT: B 142 MET cc_start: 0.8487 (ptp) cc_final: 0.8066 (ptp) REVERT: B 152 TYR cc_start: 0.8782 (t80) cc_final: 0.8446 (t80) REVERT: B 193 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6696 (mp0) REVERT: B 199 ASP cc_start: 0.7057 (p0) cc_final: 0.6557 (p0) REVERT: B 226 GLU cc_start: 0.7781 (pt0) cc_final: 0.7475 (mm-30) REVERT: C 121 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6169 (pp20) REVERT: C 239 MET cc_start: 0.6731 (ttp) cc_final: 0.6528 (ttp) REVERT: C 353 VAL cc_start: 0.8627 (t) cc_final: 0.8426 (p) REVERT: C 514 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7997 (m-10) REVERT: C 542 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7735 (mmt-90) REVERT: C 738 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: C 779 ARG cc_start: 0.8239 (ttt90) cc_final: 0.7956 (ttt-90) REVERT: C 834 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7554 (mp-120) REVERT: C 947 GLU cc_start: 0.4462 (OUTLIER) cc_final: 0.3482 (tt0) REVERT: D 214 ARG cc_start: 0.7671 (ttm110) cc_final: 0.7423 (ttm110) REVERT: D 475 GLU cc_start: 0.8196 (mp0) cc_final: 0.7762 (mp0) REVERT: D 905 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.6147 (ptm160) REVERT: D 1040 MET cc_start: 0.2125 (tmm) cc_final: 0.1325 (tmm) REVERT: D 1173 ARG cc_start: 0.6136 (tmm-80) cc_final: 0.4568 (ptp-110) REVERT: D 1325 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.6466 (p90) outliers start: 65 outliers final: 32 residues processed: 351 average time/residue: 0.1640 time to fit residues: 89.5846 Evaluate side-chains 310 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 267 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 752 ASN Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1313 HIS Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1325 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 96 optimal weight: 0.9980 chunk 212 optimal weight: 0.9990 chunk 266 optimal weight: 4.9990 chunk 322 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 194 GLN B 41 ASN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN C 437 ASN C 618 GLN C 834 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1108 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.184811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.143623 restraints weight = 34452.352| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.10 r_work: 0.3471 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 26797 Z= 0.153 Angle : 0.652 12.870 36472 Z= 0.339 Chirality : 0.043 0.315 4166 Planarity : 0.005 0.058 4557 Dihedral : 13.509 139.541 4205 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.60 % Favored : 94.27 % Rotamer: Outliers : 2.40 % Allowed : 14.97 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.72 (0.14), residues: 3178 helix: 0.99 (0.15), residues: 1152 sheet: -0.33 (0.25), residues: 384 loop : -1.65 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1223 TYR 0.019 0.002 TYR C 62 PHE 0.025 0.002 PHE C 514 TRP 0.008 0.001 TRP D 580 HIS 0.011 0.001 HIS C1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (26789) covalent geometry : angle 0.65061 / 0.34 (36460) hydrogen bonds : bond 0.04395 / 2.99 ( 1128) hydrogen bonds : angle 4.82676 / 3.39 ( 3190) metal coordination : bond 0.00492 / 0.23 ( 8) metal coordination : angle 2.16719 / 1.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 279 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7815 (mm110) REVERT: A 231 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.6636 (t80) REVERT: B 51 MET cc_start: 0.9131 (mmm) cc_final: 0.8872 (mmm) REVERT: B 54 CYS cc_start: 0.8168 (m) cc_final: 0.7799 (m) REVERT: B 142 MET cc_start: 0.8576 (ptp) cc_final: 0.8180 (ptp) REVERT: B 152 TYR cc_start: 0.8757 (t80) cc_final: 0.8417 (t80) REVERT: B 193 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6609 (tt0) REVERT: B 199 ASP cc_start: 0.7147 (p0) cc_final: 0.6453 (p0) REVERT: B 226 GLU cc_start: 0.8021 (pt0) cc_final: 0.7474 (mm-30) REVERT: C 121 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.5792 (pp20) REVERT: C 490 GLN cc_start: 0.7170 (tt0) cc_final: 0.6659 (tp-100) REVERT: C 514 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8185 (m-10) REVERT: C 542 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7806 (mmt-90) REVERT: C 738 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: C 790 ASP cc_start: 0.7347 (t0) cc_final: 0.7145 (t0) REVERT: C 834 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7492 (mp-120) REVERT: C 947 GLU cc_start: 0.4420 (OUTLIER) cc_final: 0.3426 (tt0) REVERT: D 69 GLU cc_start: 0.7563 (pp20) cc_final: 0.7133 (mt-10) REVERT: D 332 LYS cc_start: 0.8514 (ptmm) cc_final: 0.8129 (pttt) REVERT: D 475 GLU cc_start: 0.8274 (mp0) cc_final: 0.7902 (mp0) REVERT: D 905 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6238 (ptm160) REVERT: D 1040 MET cc_start: 0.2203 (tmm) cc_final: 0.1319 (tmm) REVERT: D 1173 ARG cc_start: 0.6222 (tmm-80) cc_final: 0.4441 (ptp-110) REVERT: D 1325 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.6426 (p90) outliers start: 65 outliers final: 35 residues processed: 330 average time/residue: 0.1622 time to fit residues: 84.5540 Evaluate side-chains 305 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 259 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 752 ASN Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1313 HIS Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1349 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 196 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 94 optimal weight: 0.0870 chunk 1 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 132 optimal weight: 0.1980 chunk 127 optimal weight: 3.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN C 618 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN C1313 HIS D 861 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.186381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.144745 restraints weight = 34340.894| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.04 r_work: 0.3507 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 26797 Z= 0.139 Angle : 0.628 12.979 36472 Z= 0.327 Chirality : 0.043 0.293 4166 Planarity : 0.005 0.090 4557 Dihedral : 13.410 140.464 4205 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.14 % Favored : 93.77 % Rotamer: Outliers : 2.54 % Allowed : 15.56 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.54 (0.14), residues: 3178 helix: 1.15 (0.15), residues: 1145 sheet: -0.23 (0.26), residues: 377 loop : -1.53 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 170 TYR 0.023 0.001 TYR C 62 PHE 0.023 0.001 PHE C 514 TRP 0.007 0.001 TRP D1193 HIS 0.007 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (26789) covalent geometry : angle 0.62672 / 0.33 (36460) hydrogen bonds : bond 0.04167 / 2.83 ( 1128) hydrogen bonds : angle 4.70871 / 3.32 ( 3190) metal coordination : bond 0.00444 / 0.21 ( 8) metal coordination : angle 2.09941 / 1.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 284 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.6653 (t80) REVERT: B 51 MET cc_start: 0.9134 (mmm) cc_final: 0.8889 (mmm) REVERT: B 142 MET cc_start: 0.8561 (ptp) cc_final: 0.8186 (ptp) REVERT: B 152 TYR cc_start: 0.8743 (t80) cc_final: 0.8375 (t80) REVERT: B 185 TYR cc_start: 0.8689 (p90) cc_final: 0.8389 (p90) REVERT: B 193 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6642 (tt0) REVERT: B 199 ASP cc_start: 0.7039 (p0) cc_final: 0.6407 (p0) REVERT: B 226 GLU cc_start: 0.7984 (pt0) cc_final: 0.7401 (mm-30) REVERT: B 231 PHE cc_start: 0.8525 (m-80) cc_final: 0.8240 (m-80) REVERT: C 121 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6102 (pp20) REVERT: C 130 MET cc_start: 0.8936 (ttp) cc_final: 0.8580 (ttp) REVERT: C 490 GLN cc_start: 0.6703 (tt0) cc_final: 0.6285 (tp-100) REVERT: C 514 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8196 (m-10) REVERT: C 542 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7928 (mmt-90) REVERT: C 738 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: C 800 MET cc_start: 0.8485 (mtp) cc_final: 0.8282 (mtp) REVERT: C 947 GLU cc_start: 0.4530 (OUTLIER) cc_final: 0.3549 (tt0) REVERT: C 1296 ASP cc_start: 0.9041 (t0) cc_final: 0.8638 (t0) REVERT: D 69 GLU cc_start: 0.7655 (pp20) cc_final: 0.7088 (mp0) REVERT: D 332 LYS cc_start: 0.8437 (ptmm) cc_final: 0.8076 (pttt) REVERT: D 475 GLU cc_start: 0.8255 (mp0) cc_final: 0.7892 (mp0) REVERT: D 757 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8813 (p) REVERT: D 832 LYS cc_start: 0.7891 (mmtm) cc_final: 0.7508 (mmtm) REVERT: D 905 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6207 (ptm160) REVERT: D 1040 MET cc_start: 0.2227 (tmm) cc_final: 0.1271 (tmm) REVERT: D 1173 ARG cc_start: 0.6229 (tmm-80) cc_final: 0.4540 (ptp-110) REVERT: D 1205 GLU cc_start: 0.6700 (mp0) cc_final: 0.6438 (tp30) REVERT: D 1325 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.6593 (p90) outliers start: 69 outliers final: 42 residues processed: 339 average time/residue: 0.1700 time to fit residues: 90.4686 Evaluate side-chains 312 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 260 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 752 ASN Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1172 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1313 HIS Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1349 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.3153 > 50: distance: 41 - 51: 3.329 distance: 70 - 76: 7.152 distance: 76 - 77: 8.540 distance: 77 - 78: 24.616 distance: 77 - 80: 14.576 distance: 78 - 79: 29.803 distance: 78 - 83: 21.014 distance: 80 - 81: 23.211 distance: 80 - 82: 29.617 distance: 83 - 84: 14.173 distance: 83 - 89: 20.473 distance: 84 - 85: 6.573 distance: 84 - 87: 13.342 distance: 85 - 86: 19.840 distance: 85 - 90: 5.590 distance: 87 - 88: 13.241 distance: 88 - 89: 13.182 distance: 90 - 91: 24.497 distance: 91 - 92: 14.410 distance: 91 - 94: 19.223 distance: 92 - 93: 37.644 distance: 92 - 99: 29.213 distance: 94 - 95: 7.157 distance: 95 - 96: 10.350 distance: 96 - 97: 11.468 distance: 97 - 98: 16.758 distance: 99 - 100: 34.554 distance: 100 - 101: 26.476 distance: 101 - 102: 34.302 distance: 101 - 103: 13.538 distance: 103 - 104: 8.447 distance: 104 - 105: 19.027 distance: 104 - 107: 8.665 distance: 105 - 106: 21.696 distance: 105 - 111: 8.625 distance: 107 - 108: 15.979 distance: 108 - 109: 19.883 distance: 108 - 110: 18.457 distance: 111 - 112: 8.820 distance: 111 - 117: 15.101 distance: 112 - 113: 11.861 distance: 112 - 115: 12.381 distance: 113 - 114: 12.866 distance: 113 - 118: 8.458 distance: 114 - 136: 12.162 distance: 115 - 116: 24.438 distance: 116 - 117: 24.245 distance: 118 - 119: 6.528 distance: 119 - 120: 11.837 distance: 119 - 122: 12.442 distance: 120 - 121: 24.111 distance: 120 - 130: 15.197 distance: 121 - 144: 33.745 distance: 122 - 123: 10.279 distance: 123 - 124: 3.533 distance: 123 - 125: 5.377 distance: 124 - 126: 5.850 distance: 125 - 127: 4.126 distance: 126 - 128: 6.546 distance: 128 - 129: 4.534 distance: 130 - 131: 11.569 distance: 131 - 132: 3.890 distance: 131 - 134: 9.835 distance: 132 - 133: 23.478 distance: 132 - 136: 4.802 distance: 134 - 135: 27.587 distance: 136 - 137: 19.274 distance: 137 - 138: 14.730 distance: 137 - 140: 21.771 distance: 138 - 139: 22.571 distance: 138 - 144: 8.676 distance: 140 - 142: 24.499 distance: 141 - 143: 14.663 distance: 144 - 145: 4.555 distance: 145 - 146: 6.728 distance: 145 - 148: 5.921 distance: 146 - 147: 13.382 distance: 146 - 151: 5.815 distance: 148 - 149: 7.284 distance: 148 - 150: 9.042