Starting phenix.real_space_refine on Mon Sep 14 00:01:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ri9_4886/09_2026/6ri9_4886.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ri9_4886/09_2026/6ri9_4886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ri9_4886/09_2026/6ri9_4886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ri9_4886/09_2026/6ri9_4886.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ri9_4886/09_2026/6ri9_4886.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ri9_4886/09_2026/6ri9_4886.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ri9_4886/09_2026/6ri9_4886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ri9_4886/09_2026/6ri9_4886.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.102 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 16251 2.51 5 N 4648 2.21 5 O 5193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.20s 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: 26264 Number of models: 1 Model: "" Number of chains: 9 Chain: "N" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 449 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "T" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "B" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1772 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} Chain: "C" Number of atoms: 10407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10407 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1263} Chain breaks: 1 Chain: "D" Number of atoms: 10397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10397 Classifications: {'peptide': 1336} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1281} Chain breaks: 2 Chain: "E" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "R" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 273 Classifications: {'RNAv2': 13} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 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 15472 SG CYS D 72 108.701 49.617 71.756 1.00149.74 S ATOM 15580 SG CYS D 85 110.183 52.106 69.815 1.00149.71 S ATOM 15604 SG CYS D 88 106.745 52.973 69.946 1.00154.89 S ATOM 21292 SG CYS D 814 87.014 118.152 77.656 1.00 98.23 S ATOM 21857 SG CYS D 888 86.227 114.813 76.900 1.00 98.99 S ATOM 21908 SG CYS D 895 86.794 115.833 80.077 1.00 90.14 S ATOM 21929 SG CYS D 898 83.987 117.434 79.268 1.00 92.60 S Time building chain proxies: 5.00, per 1000 atoms: 0.19 Number of scatterers: 26264 At special positions: 0 Unit cell: (129.107, 158.983, 167.519, 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 5193 8.00 N 4648 7.00 C 16251 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: 1.94 Conformation dependent library (CDL) restraints added in 992.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 6 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5880 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 52 sheets defined 39.6% alpha, 14.7% beta 30 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.912A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 234 removed outlier: 4.267A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.639A pdb=" N ILE B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 160' Processing helix chain 'B' and resid 212 through 230 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 28 through 39 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 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 318 through 327 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 387 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 455 through 481 removed outlier: 4.160A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.516A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.617A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 529 removed outlier: 3.647A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.892A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.651A pdb=" N GLU C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 607 through 614' Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 738 through 741 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 942 through 980 Processing helix chain 'C' and resid 986 through 991 Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.574A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.846A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.816A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.536A pdb=" N PHE C1164 " --> pdb=" O LEU C1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1177 removed outlier: 3.514A pdb=" N ARG C1171 " --> pdb=" O GLU C1167 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU C1172 " --> pdb=" O GLU C1168 " (cutoff:3.500A) Processing helix chain 'C' and resid 1185 through 1189 removed outlier: 3.598A pdb=" N ASP C1188 " --> pdb=" O PRO C1185 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY C1189 " --> pdb=" O VAL C1186 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1185 through 1189' 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 1284 through 1292 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 34 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 263 through 283 Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 4.338A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) 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 484 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 589 through 593 Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 704 Processing helix chain 'D' and resid 720 through 729 removed outlier: 4.065A pdb=" N GLY D 729 " --> pdb=" O MET D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.884A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 895 through 899 Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.283A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1068 through 1072 Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1225 Processing helix chain 'D' and resid 1225 through 1245 Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1315 removed outlier: 4.048A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1325 removed outlier: 4.050A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1346 through 1353 removed outlier: 3.660A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1373 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.606A pdb=" N ALA A 24 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 7.480A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 4.021A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 removed outlier: 3.504A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 19 removed outlier: 6.956A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 4.237A 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: 7.469A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 7.252A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.419A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.419A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.633A pdb=" N ILE C 127 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 143 through 145 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'C' and resid 227 through 230 Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.709A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 302 removed outlier: 7.025A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.451A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (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 716 through 717 removed outlier: 6.597A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.555A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 4.299A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1066 through 1067 Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 840 removed outlier: 3.736A pdb=" N GLN C 834 " --> pdb=" O LEU C1054 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 842 through 843 Processing sheet with id=AD2, first strand: chain 'C' and resid 876 through 877 Processing sheet with id=AD3, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.779A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AD5, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD6, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD7, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 8.195A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD9, first strand: chain 'C' and resid 1336 through 1337 Processing sheet with id=AE1, first strand: chain 'D' and resid 103 through 111 removed outlier: 9.909A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 11.003A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AE3, first strand: chain 'D' and resid 253 through 254 removed outlier: 4.824A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 261 " --> pdb=" O VAL D 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 368 through 369 removed outlier: 6.213A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AE6, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE7, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE8, first strand: chain 'D' and resid 825 through 826 removed outlier: 6.824A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 949 through 952 removed outlier: 4.063A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL D 952 " --> pdb=" O THR D1016 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N THR D1016 " --> pdb=" O VAL D 952 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 957 through 961 removed outlier: 6.611A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AF3, first strand: chain 'D' and resid 1033 through 1034 Processing sheet with id=AF4, first strand: chain 'D' and resid 1042 through 1043 removed outlier: 8.348A pdb=" N GLY D1043 " --> pdb=" O ARG D1048 " (cutoff:3.500A) removed outlier: 9.642A pdb=" N THR D1050 " --> pdb=" O GLY D1043 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1077 through 1079 Processing sheet with id=AF6, first strand: chain 'D' and resid 1176 through 1178 Processing sheet with id=AF7, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.538A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 2970 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 6.17 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6173 1.32 - 1.44: 5210 1.44 - 1.56: 15097 1.56 - 1.68: 124 1.68 - 1.81: 184 Bond restraints: 26788 Sorted by residual: bond pdb=" C SER B 178 " pdb=" N PRO B 179 " ideal model delta sigma weight residual 1.337 1.261 0.076 1.11e-02 8.12e+03 4.66e+01 bond pdb=" CA GLN C 659 " pdb=" C GLN C 659 " ideal model delta sigma weight residual 1.524 1.393 0.131 2.25e-02 1.98e+03 3.38e+01 bond pdb=" C VAL C 690 " pdb=" N PRO C 691 " ideal model delta sigma weight residual 1.332 1.280 0.052 1.12e-02 7.97e+03 2.18e+01 bond pdb=" C VAL D 501 " pdb=" N PRO D 502 " ideal model delta sigma weight residual 1.331 1.282 0.050 1.21e-02 6.83e+03 1.69e+01 bond pdb=" N1 DC T 14 " pdb=" C6 DC T 14 " ideal model delta sigma weight residual 1.367 1.342 0.025 6.00e-03 2.78e+04 1.69e+01 ... (remaining 26783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.41: 36292 5.41 - 10.82: 150 10.82 - 16.23: 14 16.23 - 21.64: 0 21.64 - 27.05: 3 Bond angle restraints: 36459 Sorted by residual: angle pdb=" O3' DG T 24 " pdb=" P DG T 25 " pdb=" OP1 DG T 25 " ideal model delta sigma weight residual 108.00 80.95 27.05 3.00e+00 1.11e-01 8.13e+01 angle pdb=" O3' DG T 24 " pdb=" P DG T 25 " pdb=" OP2 DG T 25 " ideal model delta sigma weight residual 108.00 83.99 24.01 3.00e+00 1.11e-01 6.40e+01 angle pdb=" C LYS D 321 " pdb=" N ARG D 322 " pdb=" CA ARG D 322 " ideal model delta sigma weight residual 122.38 100.26 22.12 2.90e+00 1.19e-01 5.82e+01 angle pdb=" C HIS D 897 " pdb=" N CYS D 898 " pdb=" CA CYS D 898 " ideal model delta sigma weight residual 122.56 110.63 11.93 1.72e+00 3.38e-01 4.81e+01 angle pdb=" CA CYS D 898 " pdb=" C CYS D 898 " pdb=" N TYR D 899 " ideal model delta sigma weight residual 118.13 125.86 -7.73 1.28e+00 6.10e-01 3.65e+01 ... (remaining 36454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.68: 15796 26.68 - 53.36: 435 53.36 - 80.04: 74 80.04 - 106.72: 4 106.72 - 133.40: 1 Dihedral angle restraints: 16310 sinusoidal: 7168 harmonic: 9142 Sorted by residual: dihedral pdb=" O5' U R 1 " pdb=" C5' U R 1 " pdb=" C4' U R 1 " pdb=" C3' U R 1 " ideal model delta sinusoidal sigma weight residual 60.00 0.53 59.47 3 6.40e+00 2.44e-02 5.21e+01 dihedral pdb=" O5' C R 2 " pdb=" C5' C R 2 " pdb=" C4' C R 2 " pdb=" C3' C R 2 " ideal model delta sinusoidal sigma weight residual 60.00 7.83 52.17 3 6.40e+00 2.44e-02 4.99e+01 dihedral pdb=" O5' G R 10 " pdb=" C5' G R 10 " pdb=" C4' G R 10 " pdb=" C3' G R 10 " ideal model delta sinusoidal sigma weight residual 60.00 109.83 -49.83 3 6.40e+00 2.44e-02 4.85e+01 ... (remaining 16307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.382: 4168 0.382 - 0.764: 0 0.764 - 1.146: 0 1.146 - 1.528: 0 1.528 - 1.909: 1 Chirality restraints: 4169 Sorted by residual: chirality pdb=" P DG T 25 " pdb=" OP1 DG T 25 " pdb=" OP2 DG T 25 " pdb=" O5' DG T 25 " both_signs ideal model delta sigma weight residual True 2.34 0.43 1.91 2.00e-01 2.50e+01 9.12e+01 chirality pdb=" CA GLN C 659 " pdb=" N GLN C 659 " pdb=" C GLN C 659 " pdb=" CB GLN C 659 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" P U R 11 " pdb=" OP1 U R 11 " pdb=" OP2 U R 11 " pdb=" O5' U R 11 " both_signs ideal model delta sigma weight residual True 2.17 -2.44 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 4166 not shown) Planarity restraints: 4551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 204 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.47e+00 pdb=" N PRO C 205 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 205 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 205 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 250 " -0.041 5.00e-02 4.00e+02 6.26e-02 6.28e+00 pdb=" N PRO D 251 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 251 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 251 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C1080 " -0.039 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO C1081 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO C1081 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C1081 " -0.032 5.00e-02 4.00e+02 ... (remaining 4548 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 237 2.48 - 3.08: 21518 3.08 - 3.69: 38581 3.69 - 4.29: 54267 4.29 - 4.90: 85981 Nonbonded interactions: 200584 Sorted by model distance: nonbonded pdb=" OP1 U R 11 " pdb="MG MG D1503 " model vdw 1.871 2.170 nonbonded pdb=" O3' G R 10 " pdb="MG MG D1503 " model vdw 1.895 2.170 nonbonded pdb=" O2 DC N 39 " pdb=" N2 DG T 1 " model vdw 2.021 2.496 nonbonded pdb=" O MET D 29 " pdb=" OG SER D 32 " model vdw 2.072 3.040 nonbonded pdb=" OG1 THR C 164 " pdb=" O LYS C 169 " model vdw 2.081 3.040 ... (remaining 200579 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 232) selection = (chain 'B' and resid 7 through 232) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 27.940 Find NCS groups from input model: 0.240 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 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 : 0.012 0.199 26795 Z= 0.616 Angle : 1.181 44.681 36465 Z= 0.633 Chirality : 0.063 1.909 4169 Planarity : 0.006 0.064 4551 Dihedral : 12.296 133.404 10430 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.75 % Favored : 84.13 % Rotamer: Outliers : 0.07 % Allowed : 1.44 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.89 (0.11), residues: 3169 helix: -2.76 (0.11), residues: 1143 sheet: -2.81 (0.24), residues: 355 loop : -3.82 (0.12), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 10 TYR 0.036 0.004 TYR D 382 PHE 0.028 0.003 PHE D 227 TRP 0.022 0.003 TRP D 409 HIS 0.009 0.002 HIS D 897 Details of bonding type rmsd/Z covalent geometry : bond 0.01221 / 0.61 (26788) covalent geometry : angle 1.14765 / 0.63 (36459) hydrogen bonds : bond 0.11991 / 13.33 ( 1145) hydrogen bonds : angle 7.25147 / 7.82 ( 3096) metal coordination : bond 0.14007 / 13.72 ( 7) metal coordination : angle 21.59466 / 51.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 0.841 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: A 174 ASP cc_start: 0.8173 (m-30) cc_final: 0.7548 (p0) REVERT: B 145 LYS cc_start: 0.9163 (tttt) cc_final: 0.8883 (tttt) REVERT: C 681 MET cc_start: 0.8107 (mtp) cc_final: 0.7675 (mtt) REVERT: C 696 ASP cc_start: 0.7623 (t0) cc_final: 0.7332 (t0) REVERT: C 1315 MET cc_start: 0.7912 (ptm) cc_final: 0.7615 (ptm) REVERT: E 8 ASP cc_start: 0.8900 (m-30) cc_final: 0.8501 (m-30) REVERT: E 15 ASN cc_start: 0.7913 (t0) cc_final: 0.7129 (t0) outliers start: 2 outliers final: 0 residues processed: 286 average time/residue: 0.2086 time to fit residues: 89.2278 Evaluate side-chains 142 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 0.0070 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 2.9990 overall best weight: 1.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN C 65 ASN C 69 GLN C 150 HIS C 330 HIS C 513 GLN C 832 HIS ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1146 GLN C1256 GLN C1268 GLN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN D 865 HIS D1049 GLN D1195 GLN D1326 GLN E 31 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.067290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.048872 restraints weight = 109075.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.050451 restraints weight = 54657.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.051476 restraints weight = 35493.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.052122 restraints weight = 27165.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.052452 restraints weight = 23123.246| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26795 Z= 0.166 Angle : 0.764 27.302 36465 Z= 0.391 Chirality : 0.055 1.850 4169 Planarity : 0.005 0.060 4551 Dihedral : 13.569 138.663 4196 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.07 % Allowed : 6.56 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.95 (0.13), residues: 3169 helix: -0.64 (0.14), residues: 1139 sheet: -2.23 (0.25), residues: 366 loop : -2.95 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 247 TYR 0.026 0.002 TYR C1229 PHE 0.020 0.002 PHE C 514 TRP 0.012 0.001 TRP D 409 HIS 0.015 0.002 HIS C 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (26788) covalent geometry : angle 0.76176 / 0.39 (36459) hydrogen bonds : bond 0.06251 / 6.93 ( 1145) hydrogen bonds : angle 5.32930 / 5.73 ( 3096) metal coordination : bond 0.00865 / 0.83 ( 7) metal coordination : angle 4.76892 / 8.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ASP cc_start: 0.8202 (m-30) cc_final: 0.7870 (p0) REVERT: B 41 ASN cc_start: 0.9000 (t0) cc_final: 0.8775 (t0) REVERT: C 239 MET cc_start: 0.7545 (ttm) cc_final: 0.7018 (tmm) REVERT: C 370 MET cc_start: 0.9342 (mmm) cc_final: 0.9137 (mmm) REVERT: C 569 ILE cc_start: 0.9093 (mt) cc_final: 0.8845 (tt) REVERT: C 681 MET cc_start: 0.8037 (mtp) cc_final: 0.7770 (mtt) REVERT: C 696 ASP cc_start: 0.7547 (t0) cc_final: 0.7086 (t0) REVERT: D 130 MET cc_start: 0.8633 (ttm) cc_final: 0.8421 (ttt) REVERT: D 298 MET cc_start: 0.8599 (mmt) cc_final: 0.8218 (mmt) REVERT: D 870 ASP cc_start: 0.8904 (m-30) cc_final: 0.8627 (t0) REVERT: E 30 MET cc_start: 0.8651 (mtm) cc_final: 0.8347 (mtp) REVERT: E 72 GLN cc_start: 0.9039 (tt0) cc_final: 0.8802 (pt0) outliers start: 29 outliers final: 13 residues processed: 193 average time/residue: 0.1759 time to fit residues: 53.9629 Evaluate side-chains 143 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 64 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 87 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 271 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 284 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS B 128 HIS B 160 HIS C 673 HIS C1209 GLN D 910 ASN D1195 GLN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.065145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.046533 restraints weight = 110546.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.048055 restraints weight = 56101.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.049030 restraints weight = 36672.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.049627 restraints weight = 28296.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.050015 restraints weight = 24264.215| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 26795 Z= 0.295 Angle : 0.789 25.829 36465 Z= 0.400 Chirality : 0.055 1.897 4169 Planarity : 0.005 0.057 4551 Dihedral : 13.474 142.354 4196 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 1.92 % Allowed : 8.77 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.35 (0.14), residues: 3169 helix: 0.04 (0.15), residues: 1144 sheet: -1.82 (0.25), residues: 376 loop : -2.78 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 974 TYR 0.020 0.002 TYR D 382 PHE 0.017 0.002 PHE C 514 TRP 0.012 0.002 TRP D 409 HIS 0.007 0.002 HIS C 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.29 (26788) covalent geometry : angle 0.78890 / 0.40 (36459) hydrogen bonds : bond 0.06050 / 6.67 ( 1145) hydrogen bonds : angle 5.22453 / 5.68 ( 3096) metal coordination : bond 0.01579 / 1.69 ( 7) metal coordination : angle 1.97946 / 2.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 134 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9153 (mmm) cc_final: 0.8905 (mmm) REVERT: A 200 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8451 (ttpp) REVERT: B 41 ASN cc_start: 0.9058 (t0) cc_final: 0.8816 (t0) REVERT: C 239 MET cc_start: 0.7905 (ttm) cc_final: 0.7406 (tmm) REVERT: C 488 MET cc_start: 0.8595 (tpp) cc_final: 0.8348 (tpp) REVERT: C 510 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8536 (pt0) REVERT: C 681 MET cc_start: 0.8120 (mtp) cc_final: 0.7707 (mtt) REVERT: C 800 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8197 (mtp) REVERT: C 1290 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8250 (mtp) REVERT: D 117 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9282 (tm) REVERT: D 130 MET cc_start: 0.8703 (ttm) cc_final: 0.8419 (ttt) REVERT: D 870 ASP cc_start: 0.8981 (m-30) cc_final: 0.8721 (t0) REVERT: E 72 GLN cc_start: 0.9097 (tt0) cc_final: 0.8884 (pt0) outliers start: 52 outliers final: 20 residues processed: 173 average time/residue: 0.1610 time to fit residues: 45.9992 Evaluate side-chains 141 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 92 optimal weight: 2.9990 chunk 299 optimal weight: 0.8980 chunk 277 optimal weight: 30.0000 chunk 20 optimal weight: 0.0040 chunk 235 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 266 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN D 488 ASN ** D1249 ASN ** 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 = 0.3428 r_free = 0.3428 target = 0.066831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.048223 restraints weight = 108326.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.049805 restraints weight = 54306.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.050822 restraints weight = 35331.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.051459 restraints weight = 27141.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.051844 restraints weight = 23196.960| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26795 Z= 0.136 Angle : 0.667 26.233 36465 Z= 0.338 Chirality : 0.053 1.877 4169 Planarity : 0.004 0.053 4551 Dihedral : 13.337 144.281 4196 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.77 % Allowed : 9.91 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.75 (0.15), residues: 3169 helix: 0.57 (0.15), residues: 1133 sheet: -1.68 (0.26), residues: 366 loop : -2.38 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 69 TYR 0.014 0.001 TYR D 512 PHE 0.018 0.001 PHE C 514 TRP 0.012 0.001 TRP D 580 HIS 0.008 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (26788) covalent geometry : angle 0.66497 / 0.34 (36459) hydrogen bonds : bond 0.05488 / 6.05 ( 1145) hydrogen bonds : angle 4.76816 / 5.13 ( 3096) metal coordination : bond 0.01390 / 1.34 ( 7) metal coordination : angle 4.34807 / 5.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.9027 (t0) cc_final: 0.8738 (t0) REVERT: B 186 ASN cc_start: 0.8561 (m-40) cc_final: 0.8124 (t0) REVERT: B 192 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8509 (m) REVERT: C 239 MET cc_start: 0.8059 (ttm) cc_final: 0.7582 (tmm) REVERT: C 265 LYS cc_start: 0.8304 (mmtt) cc_final: 0.7696 (mmpt) REVERT: C 569 ILE cc_start: 0.9170 (mt) cc_final: 0.8887 (tp) REVERT: C 681 MET cc_start: 0.7989 (mtp) cc_final: 0.7733 (mtt) REVERT: C 742 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: C 1290 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8252 (mtp) REVERT: D 130 MET cc_start: 0.8616 (ttm) cc_final: 0.8409 (ttt) REVERT: D 870 ASP cc_start: 0.8902 (m-30) cc_final: 0.8665 (t0) REVERT: E 55 GLU cc_start: 0.7958 (tt0) cc_final: 0.7539 (tt0) outliers start: 48 outliers final: 23 residues processed: 174 average time/residue: 0.1634 time to fit residues: 47.3402 Evaluate side-chains 147 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 64 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 186 optimal weight: 10.0000 chunk 290 optimal weight: 0.8980 chunk 242 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 16 optimal weight: 0.0170 chunk 73 optimal weight: 7.9990 chunk 299 optimal weight: 0.9980 chunk 196 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** 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 = 0.3419 r_free = 0.3419 target = 0.066485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.047843 restraints weight = 108719.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.049411 restraints weight = 54542.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.050415 restraints weight = 35501.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.051060 restraints weight = 27257.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.051444 restraints weight = 23271.828| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26795 Z= 0.152 Angle : 0.645 26.198 36465 Z= 0.326 Chirality : 0.052 1.871 4169 Planarity : 0.004 0.051 4551 Dihedral : 13.301 144.723 4196 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.73 % Allowed : 10.17 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.45 (0.15), residues: 3169 helix: 0.83 (0.16), residues: 1139 sheet: -1.48 (0.26), residues: 376 loop : -2.22 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 69 TYR 0.014 0.001 TYR D 631 PHE 0.015 0.001 PHE C 514 TRP 0.008 0.001 TRP D 580 HIS 0.006 0.001 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (26788) covalent geometry : angle 0.64397 / 0.33 (36459) hydrogen bonds : bond 0.05305 / 5.86 ( 1145) hydrogen bonds : angle 4.65235 / 5.04 ( 3096) metal coordination : bond 0.00813 / 0.83 ( 7) metal coordination : angle 3.42956 / 3.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.9046 (t0) cc_final: 0.8736 (t0) REVERT: B 186 ASN cc_start: 0.8615 (m-40) cc_final: 0.8192 (t0) REVERT: C 239 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7572 (tmm) REVERT: C 488 MET cc_start: 0.8574 (tpp) cc_final: 0.8317 (tpp) REVERT: C 510 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8545 (pt0) REVERT: C 569 ILE cc_start: 0.9194 (mt) cc_final: 0.8893 (tp) REVERT: C 681 MET cc_start: 0.8020 (mtp) cc_final: 0.7716 (mtt) REVERT: C 800 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8192 (mtp) REVERT: C 1290 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8299 (mtp) REVERT: D 130 MET cc_start: 0.8615 (ttm) cc_final: 0.8395 (ttt) REVERT: D 870 ASP cc_start: 0.8907 (m-30) cc_final: 0.8657 (t0) REVERT: E 3 ARG cc_start: 0.8449 (tpp-160) cc_final: 0.8208 (tpp-160) REVERT: E 56 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8499 (mm-30) outliers start: 47 outliers final: 28 residues processed: 165 average time/residue: 0.1639 time to fit residues: 45.3573 Evaluate side-chains 148 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 256 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 272 optimal weight: 30.0000 chunk 320 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.063329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.044690 restraints weight = 111575.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.046257 restraints weight = 55856.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.047266 restraints weight = 36034.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.047916 restraints weight = 27428.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.048255 restraints weight = 23169.766| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 26795 Z= 0.304 Angle : 0.761 26.268 36465 Z= 0.381 Chirality : 0.054 1.863 4169 Planarity : 0.005 0.052 4551 Dihedral : 13.434 143.637 4196 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 2.58 % Allowed : 10.35 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.15), residues: 3169 helix: 0.78 (0.15), residues: 1138 sheet: -1.47 (0.26), residues: 391 loop : -2.21 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 69 TYR 0.018 0.002 TYR D 631 PHE 0.015 0.002 PHE C 514 TRP 0.008 0.002 TRP D 409 HIS 0.009 0.002 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.30 (26788) covalent geometry : angle 0.75982 / 0.38 (36459) hydrogen bonds : bond 0.05682 / 6.26 ( 1145) hydrogen bonds : angle 4.90257 / 5.40 ( 3096) metal coordination : bond 0.01600 / 1.68 ( 7) metal coordination : angle 3.55561 / 4.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 116 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.9108 (t0) cc_final: 0.8826 (t0) REVERT: B 186 ASN cc_start: 0.8642 (m-40) cc_final: 0.8173 (t0) REVERT: B 200 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8792 (tttp) REVERT: C 239 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7463 (tmm) REVERT: C 265 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7571 (mmpt) REVERT: C 488 MET cc_start: 0.8708 (tpp) cc_final: 0.8389 (tpp) REVERT: C 510 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8512 (pt0) REVERT: C 742 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: C 800 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8073 (mtp) REVERT: C 979 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6031 (tp) REVERT: D 130 MET cc_start: 0.8759 (ttm) cc_final: 0.8393 (ttt) REVERT: D 604 MET cc_start: 0.9142 (tmm) cc_final: 0.8894 (tmm) REVERT: D 870 ASP cc_start: 0.9073 (m-30) cc_final: 0.8758 (t0) REVERT: E 56 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8726 (mm-30) REVERT: E 72 GLN cc_start: 0.8880 (pt0) cc_final: 0.8629 (tm-30) outliers start: 70 outliers final: 44 residues processed: 170 average time/residue: 0.1549 time to fit residues: 44.2127 Evaluate side-chains 164 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 114 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 1025 MET Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 297 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 186 optimal weight: 0.3980 chunk 111 optimal weight: 8.9990 chunk 296 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 252 optimal weight: 1.9990 chunk 237 optimal weight: 0.5980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.065028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.046543 restraints weight = 108208.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.048167 restraints weight = 53031.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.049182 restraints weight = 33791.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.049881 restraints weight = 25595.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.050339 restraints weight = 21476.012| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26795 Z= 0.133 Angle : 0.637 25.891 36465 Z= 0.321 Chirality : 0.052 1.871 4169 Planarity : 0.004 0.049 4551 Dihedral : 13.364 143.850 4196 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.95 % Allowed : 11.05 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.16 (0.15), residues: 3169 helix: 1.02 (0.16), residues: 1139 sheet: -1.22 (0.26), residues: 373 loop : -2.04 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 322 TYR 0.014 0.001 TYR D 631 PHE 0.015 0.001 PHE C 514 TRP 0.013 0.001 TRP D 580 HIS 0.004 0.001 HIS D 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (26788) covalent geometry : angle 0.63593 / 0.32 (36459) hydrogen bonds : bond 0.05196 / 5.72 ( 1145) hydrogen bonds : angle 4.58322 / 5.02 ( 3096) metal coordination : bond 0.00607 / 0.60 ( 7) metal coordination : angle 2.74713 / 2.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 123 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.9075 (t0) cc_final: 0.8773 (t0) REVERT: B 186 ASN cc_start: 0.8580 (t0) cc_final: 0.8137 (t0) REVERT: B 200 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8531 (tttp) REVERT: C 239 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7682 (tmm) REVERT: C 488 MET cc_start: 0.8689 (tpp) cc_final: 0.8347 (tpp) REVERT: C 569 ILE cc_start: 0.9102 (mt) cc_final: 0.8804 (tp) REVERT: C 742 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: C 800 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8007 (mtp) REVERT: C 979 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.5837 (tp) REVERT: C 1131 MET cc_start: 0.8934 (ttm) cc_final: 0.8733 (ttm) REVERT: D 479 GLU cc_start: 0.8717 (tt0) cc_final: 0.8403 (tt0) REVERT: D 604 MET cc_start: 0.9115 (tmm) cc_final: 0.8834 (tmm) REVERT: D 870 ASP cc_start: 0.9019 (m-30) cc_final: 0.8721 (t0) REVERT: E 56 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8740 (mm-30) REVERT: E 72 GLN cc_start: 0.8704 (pt0) cc_final: 0.8446 (tm-30) outliers start: 53 outliers final: 32 residues processed: 163 average time/residue: 0.1677 time to fit residues: 46.3060 Evaluate side-chains 156 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 233 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 297 optimal weight: 7.9990 chunk 231 optimal weight: 0.7980 chunk 118 optimal weight: 0.0040 chunk 169 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** 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 = 0.3361 r_free = 0.3361 target = 0.065214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.046635 restraints weight = 109524.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.048258 restraints weight = 53824.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.049319 restraints weight = 34423.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.049982 restraints weight = 25981.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.050393 restraints weight = 21908.915| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26795 Z= 0.136 Angle : 0.621 25.993 36465 Z= 0.313 Chirality : 0.051 1.863 4169 Planarity : 0.004 0.048 4551 Dihedral : 13.345 144.768 4196 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.03 % Allowed : 11.34 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.15), residues: 3169 helix: 1.15 (0.16), residues: 1140 sheet: -1.22 (0.26), residues: 378 loop : -1.89 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 764 TYR 0.014 0.001 TYR D 631 PHE 0.012 0.001 PHE C 514 TRP 0.011 0.001 TRP D 580 HIS 0.007 0.001 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (26788) covalent geometry : angle 0.62006 / 0.31 (36459) hydrogen bonds : bond 0.05042 / 5.58 ( 1145) hydrogen bonds : angle 4.47664 / 4.91 ( 3096) metal coordination : bond 0.00607 / 0.61 ( 7) metal coordination : angle 2.70283 / 2.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 126 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.9000 (t0) cc_final: 0.8766 (t0) REVERT: B 75 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8756 (pm20) REVERT: B 186 ASN cc_start: 0.8586 (t0) cc_final: 0.8148 (t0) REVERT: B 200 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8574 (tttp) REVERT: C 239 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7533 (tmm) REVERT: C 265 LYS cc_start: 0.7777 (mmtt) cc_final: 0.7463 (mmpt) REVERT: C 464 PHE cc_start: 0.9237 (t80) cc_final: 0.9003 (t80) REVERT: C 569 ILE cc_start: 0.9101 (mt) cc_final: 0.8838 (tp) REVERT: C 800 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8022 (mtp) REVERT: C 979 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.5837 (tp) REVERT: C 1131 MET cc_start: 0.8948 (ttm) cc_final: 0.8735 (ttm) REVERT: D 130 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8363 (ptm) REVERT: D 479 GLU cc_start: 0.8720 (tt0) cc_final: 0.8254 (tt0) REVERT: D 604 MET cc_start: 0.9124 (tmm) cc_final: 0.8816 (tmm) REVERT: D 802 ASP cc_start: 0.8093 (m-30) cc_final: 0.7871 (t0) REVERT: D 870 ASP cc_start: 0.9026 (m-30) cc_final: 0.8727 (t0) REVERT: D 1040 MET cc_start: 0.5076 (mtp) cc_final: 0.4780 (mtp) REVERT: E 56 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8775 (mm-30) outliers start: 55 outliers final: 33 residues processed: 166 average time/residue: 0.1723 time to fit residues: 47.9980 Evaluate side-chains 161 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 64 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 243 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 208 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 188 optimal weight: 0.6980 chunk 265 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN ** D1249 ASN ** 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 = 0.3353 r_free = 0.3353 target = 0.064866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.046361 restraints weight = 109159.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.047966 restraints weight = 53391.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.049016 restraints weight = 34114.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.049605 restraints weight = 25672.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.050085 restraints weight = 21833.090| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26795 Z= 0.183 Angle : 0.649 25.974 36465 Z= 0.325 Chirality : 0.052 1.861 4169 Planarity : 0.004 0.048 4551 Dihedral : 13.348 144.975 4196 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.77 % Allowed : 11.45 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.15), residues: 3169 helix: 1.18 (0.16), residues: 1139 sheet: -1.20 (0.26), residues: 384 loop : -1.87 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1036 TYR 0.014 0.001 TYR D 631 PHE 0.059 0.001 PHE D1034 TRP 0.008 0.001 TRP D 115 HIS 0.004 0.001 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (26788) covalent geometry : angle 0.64820 / 0.33 (36459) hydrogen bonds : bond 0.05071 / 5.60 ( 1145) hydrogen bonds : angle 4.51125 / 4.98 ( 3096) metal coordination : bond 0.00842 / 0.86 ( 7) metal coordination : angle 2.71350 / 2.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 120 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.9008 (t0) cc_final: 0.8760 (t0) REVERT: B 186 ASN cc_start: 0.8587 (t0) cc_final: 0.8165 (t0) REVERT: C 239 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7525 (tmm) REVERT: C 265 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7542 (mmpt) REVERT: C 488 MET cc_start: 0.8625 (tpp) cc_final: 0.8396 (tpp) REVERT: C 510 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8570 (pt0) REVERT: C 569 ILE cc_start: 0.9105 (mt) cc_final: 0.8844 (tp) REVERT: C 800 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8046 (mtp) REVERT: C 979 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.5852 (tp) REVERT: C 1131 MET cc_start: 0.8948 (ttm) cc_final: 0.8739 (ttm) REVERT: D 130 MET cc_start: 0.8722 (ttm) cc_final: 0.8451 (ptm) REVERT: D 479 GLU cc_start: 0.8707 (tt0) cc_final: 0.8251 (tt0) REVERT: D 644 MET cc_start: 0.8713 (tpp) cc_final: 0.7948 (mmt) REVERT: D 802 ASP cc_start: 0.8126 (m-30) cc_final: 0.7888 (t0) REVERT: D 870 ASP cc_start: 0.9032 (m-30) cc_final: 0.8751 (t0) REVERT: E 72 GLN cc_start: 0.8760 (pt0) cc_final: 0.8523 (tm-30) outliers start: 48 outliers final: 39 residues processed: 154 average time/residue: 0.1720 time to fit residues: 44.5393 Evaluate side-chains 161 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 98 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 231 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 312 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 chunk 282 optimal weight: 0.0570 chunk 217 optimal weight: 0.0470 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.066113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.047466 restraints weight = 108819.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.049136 restraints weight = 53103.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.050215 restraints weight = 33763.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.050883 restraints weight = 25447.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.051334 restraints weight = 21444.080| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26795 Z= 0.110 Angle : 0.613 25.827 36465 Z= 0.308 Chirality : 0.051 1.862 4169 Planarity : 0.004 0.047 4551 Dihedral : 13.249 141.624 4196 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.29 % Allowed : 12.01 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.15), residues: 3169 helix: 1.23 (0.16), residues: 1146 sheet: -0.97 (0.27), residues: 372 loop : -1.75 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 3 TYR 0.013 0.001 TYR D 631 PHE 0.027 0.001 PHE D1034 TRP 0.012 0.001 TRP D 580 HIS 0.004 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (26788) covalent geometry : angle 0.61267 / 0.31 (36459) hydrogen bonds : bond 0.04922 / 5.44 ( 1145) hydrogen bonds : angle 4.37741 / 4.82 ( 3096) metal coordination : bond 0.00334 / 0.34 ( 7) metal coordination : angle 2.45575 / 2.41 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8927 (t0) cc_final: 0.8666 (t0) REVERT: B 186 ASN cc_start: 0.8570 (t0) cc_final: 0.8156 (t0) REVERT: B 200 LYS cc_start: 0.8936 (tttp) cc_final: 0.8721 (ttpp) REVERT: C 239 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7530 (tmm) REVERT: C 265 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7596 (mmpt) REVERT: C 464 PHE cc_start: 0.9221 (t80) cc_final: 0.8973 (t80) REVERT: C 488 MET cc_start: 0.8649 (tpp) cc_final: 0.8422 (tpp) REVERT: C 800 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7973 (mtp) REVERT: C 979 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.5758 (tp) REVERT: C 1131 MET cc_start: 0.8932 (ttm) cc_final: 0.8699 (ttm) REVERT: D 130 MET cc_start: 0.8703 (ttm) cc_final: 0.8457 (ttt) REVERT: D 479 GLU cc_start: 0.8681 (tt0) cc_final: 0.8210 (tt0) REVERT: D 724 MET cc_start: 0.9030 (ttp) cc_final: 0.8691 (ttm) REVERT: D 802 ASP cc_start: 0.8079 (m-30) cc_final: 0.7838 (t0) REVERT: D 870 ASP cc_start: 0.9010 (m-30) cc_final: 0.8725 (t0) REVERT: D 1040 MET cc_start: 0.4992 (mtp) cc_final: 0.4698 (mtp) outliers start: 35 outliers final: 27 residues processed: 153 average time/residue: 0.1667 time to fit residues: 43.2975 Evaluate side-chains 151 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain E residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 305 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 204 optimal weight: 0.0970 chunk 72 optimal weight: 0.0000 chunk 309 optimal weight: 7.9990 chunk 267 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** 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 = 0.3370 r_free = 0.3370 target = 0.065573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.046966 restraints weight = 108922.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.048622 restraints weight = 53350.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.049677 restraints weight = 33898.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.050352 restraints weight = 25573.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.050785 restraints weight = 21513.845| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26795 Z= 0.138 Angle : 0.621 25.866 36465 Z= 0.310 Chirality : 0.051 1.858 4169 Planarity : 0.004 0.049 4551 Dihedral : 13.231 143.208 4196 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.29 % Allowed : 12.08 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.15), residues: 3169 helix: 1.28 (0.16), residues: 1146 sheet: -0.99 (0.27), residues: 378 loop : -1.75 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 3 TYR 0.013 0.001 TYR D 631 PHE 0.017 0.001 PHE D1034 TRP 0.008 0.001 TRP D 115 HIS 0.004 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (26788) covalent geometry : angle 0.62021 / 0.31 (36459) hydrogen bonds : bond 0.04909 / 5.43 ( 1145) hydrogen bonds : angle 4.38983 / 4.85 ( 3096) metal coordination : bond 0.00576 / 0.58 ( 7) metal coordination : angle 2.57342 / 2.70 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4225.65 seconds wall clock time: 74 minutes 0.80 seconds (4440.80 seconds total)