Starting phenix.real_space_refine on Wed Nov 19 19:03:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ri9_4886/11_2025/6ri9_4886.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ri9_4886/11_2025/6ri9_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_4886/11_2025/6ri9_4886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ri9_4886/11_2025/6ri9_4886.map" model { file = "/net/cci-nas-00/data/ceres_data/6ri9_4886/11_2025/6ri9_4886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ri9_4886/11_2025/6ri9_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: {'RNA': 13} Modifications used: {'5*END': 1, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna3p': 12} 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: 6.14, per 1000 atoms: 0.23 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: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.28 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: 7.12 Time building geometry restraints manager: 3.38 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=" CA ALA A 230 " pdb=" C ALA A 230 " ideal model delta sigma weight residual 1.522 1.460 0.062 1.72e-02 3.38e+03 1.30e+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: 15831 26.68 - 53.36: 437 53.36 - 80.04: 86 80.04 - 106.72: 5 106.72 - 133.40: 1 Dihedral angle restraints: 16360 sinusoidal: 7218 harmonic: 9142 Sorted by residual: dihedral pdb=" CA ARG D 47 " pdb=" C ARG D 47 " pdb=" N THR D 48 " pdb=" CA THR D 48 " ideal model delta harmonic sigma weight residual 180.00 148.33 31.67 0 5.00e+00 4.00e-02 4.01e+01 dihedral pdb=" CA VAL B 19 " pdb=" C VAL B 19 " pdb=" N SER B 20 " pdb=" CA SER B 20 " ideal model delta harmonic sigma weight residual -180.00 -148.35 -31.65 0 5.00e+00 4.00e-02 4.01e+01 dihedral pdb=" CA ILE D 416 " pdb=" C ILE D 416 " pdb=" N ARG D 417 " pdb=" CA ARG D 417 " ideal model delta harmonic sigma weight residual -180.00 -150.26 -29.74 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 16357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.384: 4168 0.384 - 0.768: 0 0.768 - 1.152: 0 1.152 - 1.536: 0 1.536 - 1.920: 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 2.35 0.43 1.92 2.00e-01 2.50e+01 9.21e+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=" CB VAL D 357 " pdb=" CA VAL D 357 " pdb=" CG1 VAL D 357 " pdb=" CG2 VAL D 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 32.350 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.199 26795 Z= 0.576 Angle : 1.169 44.681 36465 Z= 0.603 Chirality : 0.062 1.920 4169 Planarity : 0.006 0.064 4551 Dihedral : 12.500 133.404 10480 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 covalent geometry : bond 0.01216 (26788) covalent geometry : angle 1.13615 (36459) hydrogen bonds : bond 0.11991 ( 1145) hydrogen bonds : angle 7.25147 ( 3096) metal coordination : bond 0.14007 ( 7) metal coordination : angle 21.59466 ( 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 : 0.991 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: 0.2216 time to fit residues: 94.2279 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 : 0.942 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 128 HIS C 65 ASN C 69 GLN C 150 HIS C 330 HIS C 513 GLN C 832 HIS C1080 ASN C1116 HIS C1146 GLN C1256 GLN C1268 GLN D 157 GLN D 232 ASN D 488 ASN D 865 HIS D1049 GLN D1195 GLN E 31 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.067470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.049178 restraints weight = 109486.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.050760 restraints weight = 54678.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.051772 restraints weight = 35447.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.052420 restraints weight = 27140.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.052751 restraints weight = 23097.292| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 26795 Z= 0.154 Angle : 0.694 28.258 36465 Z= 0.355 Chirality : 0.052 1.886 4169 Planarity : 0.005 0.057 4551 Dihedral : 13.990 140.654 4246 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.03 % Allowed : 6.74 % Favored : 92.23 % 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: -2.80 (0.14), residues: 3169 helix: -0.46 (0.14), residues: 1141 sheet: -2.16 (0.24), residues: 369 loop : -2.91 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 974 TYR 0.020 0.002 TYR D 382 PHE 0.015 0.001 PHE C 514 TRP 0.014 0.001 TRP D 686 HIS 0.008 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00338 (26788) covalent geometry : angle 0.69143 (36459) hydrogen bonds : bond 0.05680 ( 1145) hydrogen bonds : angle 5.17706 ( 3096) metal coordination : bond 0.00725 ( 7) metal coordination : angle 4.79383 ( 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 215 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ASP cc_start: 0.8161 (m-30) cc_final: 0.7731 (p0) REVERT: A 200 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8436 (ptmt) REVERT: B 41 ASN cc_start: 0.8942 (t0) cc_final: 0.8710 (t0) REVERT: C 239 MET cc_start: 0.7658 (ttm) cc_final: 0.7225 (tmm) REVERT: C 569 ILE cc_start: 0.9132 (mt) cc_final: 0.8867 (tt) REVERT: C 681 MET cc_start: 0.7994 (mtp) cc_final: 0.6983 (mtt) REVERT: C 685 MET cc_start: 0.8401 (mtm) cc_final: 0.8002 (mtm) REVERT: C 739 ASP cc_start: 0.8703 (p0) cc_final: 0.8340 (t0) REVERT: D 117 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9302 (tm) REVERT: D 870 ASP cc_start: 0.8879 (m-30) cc_final: 0.8643 (t0) REVERT: E 15 ASN cc_start: 0.8069 (t0) cc_final: 0.7820 (t0) REVERT: E 48 VAL cc_start: 0.9341 (t) cc_final: 0.9129 (p) REVERT: E 72 GLN cc_start: 0.9033 (tt0) cc_final: 0.8831 (pt0) outliers start: 28 outliers final: 13 residues processed: 207 average time/residue: 0.1883 time to fit residues: 61.6372 Evaluate side-chains 144 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain C residue 29 SER 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 550 VAL Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 357 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: 8.9990 chunk 101 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 271 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 284 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 137 ASN B 160 HIS C 673 HIS ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS 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 = 0.3417 r_free = 0.3417 target = 0.066418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.047850 restraints weight = 109339.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.049423 restraints weight = 54703.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.050431 restraints weight = 35465.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.051047 restraints weight = 27198.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.051451 restraints weight = 23260.716| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26795 Z= 0.179 Angle : 0.657 26.956 36465 Z= 0.333 Chirality : 0.052 1.909 4169 Planarity : 0.005 0.053 4551 Dihedral : 13.866 145.356 4246 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.77 % Allowed : 8.47 % Favored : 89.76 % 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: -1.92 (0.14), residues: 3169 helix: 0.48 (0.15), residues: 1148 sheet: -1.72 (0.25), residues: 372 loop : -2.57 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 322 TYR 0.017 0.001 TYR D 382 PHE 0.015 0.001 PHE C 405 TRP 0.012 0.001 TRP D 686 HIS 0.004 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00407 (26788) covalent geometry : angle 0.65592 (36459) hydrogen bonds : bond 0.05254 ( 1145) hydrogen bonds : angle 4.78666 ( 3096) metal coordination : bond 0.00952 ( 7) metal coordination : angle 2.72502 ( 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: 48 poor density : 138 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8991 (t0) cc_final: 0.8758 (t0) REVERT: B 145 LYS cc_start: 0.9157 (ttmt) cc_final: 0.8952 (tptt) REVERT: B 194 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8339 (mp10) REVERT: B 200 LYS cc_start: 0.9039 (tmtp) cc_final: 0.8731 (tttm) REVERT: C 239 MET cc_start: 0.7869 (ttm) cc_final: 0.7322 (tmm) REVERT: C 510 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8515 (pt0) REVERT: C 569 ILE cc_start: 0.9196 (mt) cc_final: 0.8938 (tp) REVERT: C 681 MET cc_start: 0.8101 (mtp) cc_final: 0.7082 (mtt) REVERT: C 685 MET cc_start: 0.8393 (mtm) cc_final: 0.8137 (mtm) REVERT: C 739 ASP cc_start: 0.8746 (p0) cc_final: 0.8420 (t0) REVERT: C 1085 MET cc_start: 0.9218 (mmp) cc_final: 0.8965 (mmp) REVERT: C 1131 MET cc_start: 0.8720 (ttm) cc_final: 0.8427 (ttm) REVERT: D 29 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8389 (ttp) REVERT: D 802 ASP cc_start: 0.7904 (m-30) cc_final: 0.7690 (t0) REVERT: D 870 ASP cc_start: 0.8889 (m-30) cc_final: 0.8680 (t0) REVERT: E 15 ASN cc_start: 0.8164 (t0) cc_final: 0.7961 (t0) REVERT: E 56 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8564 (mm-30) outliers start: 48 outliers final: 21 residues processed: 172 average time/residue: 0.1729 time to fit residues: 48.9500 Evaluate side-chains 150 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 173 VAL Chi-restraints excluded: chain C residue 29 SER 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 510 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL 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 D residue 29 MET 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 466 MET 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: 6.9990 chunk 299 optimal weight: 0.7980 chunk 277 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 235 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 chunk 266 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 808 ASN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.065666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.046932 restraints weight = 108705.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.048472 restraints weight = 55299.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.049468 restraints weight = 36304.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.050090 restraints weight = 28011.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.050422 restraints weight = 23992.594| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26795 Z= 0.214 Angle : 0.661 27.172 36465 Z= 0.335 Chirality : 0.052 1.891 4169 Planarity : 0.004 0.055 4551 Dihedral : 13.892 142.658 4246 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.58 % Allowed : 9.24 % Favored : 88.18 % 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: -1.51 (0.15), residues: 3169 helix: 0.82 (0.15), residues: 1146 sheet: -1.53 (0.25), residues: 386 loop : -2.30 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 974 TYR 0.016 0.001 TYR D 631 PHE 0.013 0.002 PHE C 514 TRP 0.012 0.001 TRP D 686 HIS 0.006 0.001 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00483 (26788) covalent geometry : angle 0.66053 (36459) hydrogen bonds : bond 0.05237 ( 1145) hydrogen bonds : angle 4.69269 ( 3096) metal coordination : bond 0.01083 ( 7) metal coordination : angle 2.67816 ( 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 203 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 133 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.9059 (t0) cc_final: 0.8798 (t0) REVERT: B 186 ASN cc_start: 0.8594 (m-40) cc_final: 0.8169 (t0) REVERT: C 239 MET cc_start: 0.7782 (ttm) cc_final: 0.7300 (tmm) REVERT: C 569 ILE cc_start: 0.9208 (mt) cc_final: 0.8894 (tp) REVERT: C 573 ASN cc_start: 0.8502 (m110) cc_final: 0.8281 (p0) REVERT: C 681 MET cc_start: 0.8092 (mtp) cc_final: 0.7061 (mtt) REVERT: C 685 MET cc_start: 0.8436 (mtm) cc_final: 0.8194 (mtm) REVERT: C 742 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: C 800 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7929 (mtp) REVERT: C 1024 GLU cc_start: 0.8726 (tt0) cc_final: 0.8520 (tp30) REVERT: C 1131 MET cc_start: 0.8804 (ttm) cc_final: 0.8594 (ttm) REVERT: D 479 GLU cc_start: 0.8533 (tt0) cc_final: 0.8261 (tt0) REVERT: D 802 ASP cc_start: 0.7934 (m-30) cc_final: 0.7695 (t0) REVERT: D 822 MET cc_start: 0.9029 (mmm) cc_final: 0.8222 (mmm) REVERT: D 870 ASP cc_start: 0.8964 (m-30) cc_final: 0.8726 (t0) REVERT: E 4 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8620 (p) REVERT: E 15 ASN cc_start: 0.8149 (t0) cc_final: 0.7914 (t0) outliers start: 70 outliers final: 31 residues processed: 188 average time/residue: 0.1714 time to fit residues: 53.3996 Evaluate side-chains 159 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 173 VAL 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 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 510 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 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 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 466 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 810 THR Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain E residue 4 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 186 optimal weight: 5.9990 chunk 290 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 299 optimal weight: 0.9990 chunk 196 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.065555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.046736 restraints weight = 109764.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.048277 restraints weight = 55700.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.049240 restraints weight = 36570.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.049901 restraints weight = 28299.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.050302 restraints weight = 24138.806| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 26795 Z= 0.216 Angle : 0.656 26.960 36465 Z= 0.331 Chirality : 0.051 1.896 4169 Planarity : 0.004 0.052 4551 Dihedral : 13.922 142.861 4246 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.43 % Allowed : 9.76 % Favored : 87.81 % 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: -1.25 (0.15), residues: 3169 helix: 1.03 (0.16), residues: 1139 sheet: -1.39 (0.26), residues: 391 loop : -2.13 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 69 TYR 0.016 0.001 TYR D 631 PHE 0.012 0.001 PHE C 405 TRP 0.009 0.001 TRP D 686 HIS 0.005 0.001 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00489 (26788) covalent geometry : angle 0.65433 (36459) hydrogen bonds : bond 0.05160 ( 1145) hydrogen bonds : angle 4.66093 ( 3096) metal coordination : bond 0.01428 ( 7) metal coordination : angle 3.33578 ( 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 200 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 134 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASN cc_start: 0.8591 (m-40) cc_final: 0.8235 (t0) REVERT: B 194 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8329 (mp10) REVERT: C 239 MET cc_start: 0.7927 (ttm) cc_final: 0.7595 (tmm) REVERT: C 459 MET cc_start: 0.9147 (mtm) cc_final: 0.8783 (mtm) REVERT: C 510 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8550 (pt0) REVERT: C 569 ILE cc_start: 0.9200 (mt) cc_final: 0.8910 (tp) REVERT: C 681 MET cc_start: 0.8118 (mtp) cc_final: 0.7090 (mtt) REVERT: C 742 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7748 (m-80) REVERT: C 800 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7896 (mtp) REVERT: C 1024 GLU cc_start: 0.8732 (tt0) cc_final: 0.8511 (tp30) REVERT: C 1131 MET cc_start: 0.8794 (ttm) cc_final: 0.8538 (ttm) REVERT: C 1319 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7566 (tmm) REVERT: D 479 GLU cc_start: 0.8577 (tt0) cc_final: 0.8364 (tt0) REVERT: D 604 MET cc_start: 0.9018 (tmm) cc_final: 0.8801 (tmm) REVERT: D 870 ASP cc_start: 0.8954 (m-30) cc_final: 0.8728 (t0) REVERT: E 15 ASN cc_start: 0.8126 (t0) cc_final: 0.7886 (t0) REVERT: E 56 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8532 (mm-30) outliers start: 66 outliers final: 38 residues processed: 183 average time/residue: 0.1678 time to fit residues: 50.7043 Evaluate side-chains 168 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 5 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 173 VAL 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 132 ASP Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL 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 963 GLU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1319 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 355 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 1034 PHE 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 62 GLN 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: 10.0000 chunk 150 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 230 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 272 optimal weight: 30.0000 chunk 320 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** 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 = 0.3390 r_free = 0.3390 target = 0.065362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.046519 restraints weight = 110173.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.048051 restraints weight = 55900.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.049023 restraints weight = 36748.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.049660 restraints weight = 28430.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.050049 restraints weight = 24379.420| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 26795 Z= 0.225 Angle : 0.665 26.890 36465 Z= 0.335 Chirality : 0.052 1.893 4169 Planarity : 0.004 0.050 4551 Dihedral : 13.947 142.073 4246 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.47 % Allowed : 10.50 % Favored : 87.03 % 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: -1.15 (0.15), residues: 3169 helix: 1.08 (0.16), residues: 1139 sheet: -1.27 (0.26), residues: 393 loop : -2.06 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 678 TYR 0.017 0.001 TYR D 631 PHE 0.014 0.001 PHE C 514 TRP 0.008 0.001 TRP D 686 HIS 0.005 0.001 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00510 (26788) covalent geometry : angle 0.66226 (36459) hydrogen bonds : bond 0.05166 ( 1145) hydrogen bonds : angle 4.66417 ( 3096) metal coordination : bond 0.01278 ( 7) metal coordination : angle 4.76462 ( 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 198 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 131 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASN cc_start: 0.8570 (m-40) cc_final: 0.8221 (t0) REVERT: C 239 MET cc_start: 0.7814 (ttm) cc_final: 0.7441 (tmm) REVERT: C 265 LYS cc_start: 0.8026 (mmtt) cc_final: 0.7626 (mmpt) REVERT: C 459 MET cc_start: 0.9185 (mtm) cc_final: 0.8852 (mtm) REVERT: C 510 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8555 (pt0) REVERT: C 515 MET cc_start: 0.8529 (ttm) cc_final: 0.8304 (ttp) REVERT: C 569 ILE cc_start: 0.9186 (mt) cc_final: 0.8906 (tp) REVERT: C 742 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7745 (m-80) REVERT: C 800 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7917 (mtp) REVERT: C 1024 GLU cc_start: 0.8828 (tt0) cc_final: 0.8575 (tp30) REVERT: C 1131 MET cc_start: 0.8833 (ttm) cc_final: 0.8552 (ttm) REVERT: C 1319 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7770 (tmm) REVERT: D 479 GLU cc_start: 0.8584 (tt0) cc_final: 0.8351 (tt0) REVERT: D 604 MET cc_start: 0.9036 (tmm) cc_final: 0.8757 (tmm) REVERT: D 870 ASP cc_start: 0.8978 (m-30) cc_final: 0.8762 (t0) REVERT: E 15 ASN cc_start: 0.8188 (t0) cc_final: 0.7917 (t0) REVERT: E 56 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8560 (mm-30) outliers start: 67 outliers final: 44 residues processed: 182 average time/residue: 0.1691 time to fit residues: 51.2068 Evaluate side-chains 173 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 5 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 173 VAL 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 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 351 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 589 THR 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 1082 ILE Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 624 ILE 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 1034 PHE Chi-restraints excluded: chain D residue 1056 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 35 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 297 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 296 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 252 optimal weight: 4.9990 chunk 237 optimal weight: 0.1980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 HIS ** 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 = 0.3408 r_free = 0.3408 target = 0.066116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.047275 restraints weight = 108705.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.048852 restraints weight = 54722.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.049846 restraints weight = 35669.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.050474 restraints weight = 27542.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.050847 restraints weight = 23600.246| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26795 Z= 0.160 Angle : 0.622 26.772 36465 Z= 0.312 Chirality : 0.051 1.894 4169 Planarity : 0.004 0.049 4551 Dihedral : 13.894 142.184 4246 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.21 % Allowed : 11.05 % Favored : 86.74 % 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: -0.96 (0.15), residues: 3169 helix: 1.23 (0.16), residues: 1145 sheet: -1.20 (0.26), residues: 385 loop : -1.94 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 3 TYR 0.015 0.001 TYR D 631 PHE 0.012 0.001 PHE C 514 TRP 0.010 0.001 TRP D 580 HIS 0.004 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00363 (26788) covalent geometry : angle 0.62017 (36459) hydrogen bonds : bond 0.04906 ( 1145) hydrogen bonds : angle 4.48590 ( 3096) metal coordination : bond 0.00825 ( 7) metal coordination : angle 3.81621 ( 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 190 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 130 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASN cc_start: 0.8603 (m-40) cc_final: 0.8255 (t0) REVERT: C 207 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8721 (p) REVERT: C 239 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7439 (tmm) REVERT: C 265 LYS cc_start: 0.8022 (mmtt) cc_final: 0.7576 (mmpt) REVERT: C 459 MET cc_start: 0.9166 (mtm) cc_final: 0.8807 (mtm) REVERT: C 510 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8541 (pt0) REVERT: C 515 MET cc_start: 0.8453 (ttm) cc_final: 0.8153 (ttp) REVERT: C 569 ILE cc_start: 0.9159 (mt) cc_final: 0.8911 (tp) REVERT: C 800 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7885 (mtp) REVERT: C 1024 GLU cc_start: 0.8851 (tt0) cc_final: 0.8620 (tp30) REVERT: C 1131 MET cc_start: 0.8799 (ttm) cc_final: 0.8529 (ttm) REVERT: C 1319 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7509 (tmm) REVERT: D 330 MET cc_start: 0.8645 (ttm) cc_final: 0.8417 (ttm) REVERT: D 479 GLU cc_start: 0.8557 (tt0) cc_final: 0.8327 (tt0) REVERT: D 870 ASP cc_start: 0.8957 (m-30) cc_final: 0.8737 (t0) REVERT: E 8 ASP cc_start: 0.8747 (m-30) cc_final: 0.8366 (p0) REVERT: E 56 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8589 (mm-30) REVERT: E 72 GLN cc_start: 0.8951 (tt0) cc_final: 0.8690 (pt0) outliers start: 60 outliers final: 43 residues processed: 176 average time/residue: 0.1606 time to fit residues: 47.6884 Evaluate side-chains 170 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 5 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 173 VAL 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 132 ASP Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 207 THR 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 351 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 589 THR 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 1082 ILE Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 188 LEU 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 674 THR 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 1034 PHE Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 62 GLN 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: 9.9990 chunk 67 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 297 optimal weight: 0.0670 chunk 231 optimal weight: 0.5980 chunk 118 optimal weight: 7.9990 chunk 169 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 overall best weight: 1.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 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 = 0.3430 r_free = 0.3430 target = 0.067073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.048327 restraints weight = 108559.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.049917 restraints weight = 54195.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.050950 restraints weight = 35192.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.051598 restraints weight = 26940.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.051936 restraints weight = 22990.319| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3872 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= 0.121 Angle : 0.595 26.665 36465 Z= 0.298 Chirality : 0.050 1.893 4169 Planarity : 0.004 0.048 4551 Dihedral : 13.789 142.128 4246 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.88 % Allowed : 11.57 % Favored : 86.56 % 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: -0.71 (0.15), residues: 3169 helix: 1.41 (0.16), residues: 1145 sheet: -0.98 (0.27), residues: 380 loop : -1.79 (0.15), residues: 1644 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 0.010 0.001 PHE C 514 TRP 0.010 0.001 TRP D 580 HIS 0.003 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00273 (26788) covalent geometry : angle 0.59324 (36459) hydrogen bonds : bond 0.04672 ( 1145) hydrogen bonds : angle 4.32639 ( 3096) metal coordination : bond 0.00551 ( 7) metal coordination : angle 3.64699 ( 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 187 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 136 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.9208 (OUTLIER) cc_final: 0.8798 (t0) REVERT: B 186 ASN cc_start: 0.8600 (m-40) cc_final: 0.8295 (t0) REVERT: C 207 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8687 (p) REVERT: C 265 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7551 (mmpt) REVERT: C 459 MET cc_start: 0.9112 (mtm) cc_final: 0.8698 (mtm) REVERT: C 464 PHE cc_start: 0.9236 (t80) cc_final: 0.8909 (t80) REVERT: C 515 MET cc_start: 0.8391 (ttm) cc_final: 0.8048 (ttp) REVERT: C 800 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7904 (mtp) REVERT: C 1024 GLU cc_start: 0.8825 (tt0) cc_final: 0.8595 (tp30) REVERT: C 1131 MET cc_start: 0.8819 (ttm) cc_final: 0.8523 (ttm) REVERT: D 479 GLU cc_start: 0.8532 (tt0) cc_final: 0.8218 (tt0) REVERT: D 870 ASP cc_start: 0.8948 (m-30) cc_final: 0.8711 (t0) REVERT: E 8 ASP cc_start: 0.8759 (m-30) cc_final: 0.8382 (p0) REVERT: E 72 GLN cc_start: 0.8920 (tt0) cc_final: 0.8674 (pt0) outliers start: 51 outliers final: 35 residues processed: 177 average time/residue: 0.1586 time to fit residues: 47.4602 Evaluate side-chains 161 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 5 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 173 VAL 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 207 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 471 VAL 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 1056 VAL 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 304 ASP Chi-restraints excluded: chain D residue 324 LEU 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 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 1056 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 243 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 181 optimal weight: 0.2980 chunk 208 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 265 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 194 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 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 = 0.3416 r_free = 0.3416 target = 0.066478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.047740 restraints weight = 108768.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.049322 restraints weight = 54498.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.050345 restraints weight = 35448.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.050994 restraints weight = 27116.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.051331 restraints weight = 23123.298| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26795 Z= 0.156 Angle : 0.621 26.629 36465 Z= 0.308 Chirality : 0.050 1.891 4169 Planarity : 0.004 0.047 4551 Dihedral : 13.792 143.617 4246 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.80 % Allowed : 11.86 % Favored : 86.34 % 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: -0.68 (0.15), residues: 3169 helix: 1.40 (0.16), residues: 1147 sheet: -0.98 (0.27), residues: 385 loop : -1.75 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1036 TYR 0.014 0.001 TYR D 631 PHE 0.039 0.001 PHE D1034 TRP 0.009 0.001 TRP D 115 HIS 0.004 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00355 (26788) covalent geometry : angle 0.61944 (36459) hydrogen bonds : bond 0.04758 ( 1145) hydrogen bonds : angle 4.35732 ( 3096) metal coordination : bond 0.00783 ( 7) metal coordination : angle 3.43575 ( 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 175 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASN cc_start: 0.8584 (m-40) cc_final: 0.8306 (t0) REVERT: C 207 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8704 (p) REVERT: C 265 LYS cc_start: 0.7959 (mmtt) cc_final: 0.7514 (mmpt) REVERT: C 459 MET cc_start: 0.9121 (mtm) cc_final: 0.8718 (mtm) REVERT: C 464 PHE cc_start: 0.9254 (t80) cc_final: 0.8954 (t80) REVERT: C 800 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7899 (mtp) REVERT: C 1024 GLU cc_start: 0.8805 (tt0) cc_final: 0.8579 (tp30) REVERT: C 1131 MET cc_start: 0.8787 (ttm) cc_final: 0.8505 (ttm) REVERT: D 479 GLU cc_start: 0.8495 (tt0) cc_final: 0.8195 (tt0) REVERT: D 870 ASP cc_start: 0.8952 (m-30) cc_final: 0.8728 (t0) REVERT: D 1036 ARG cc_start: 0.7808 (mtm110) cc_final: 0.7591 (mtm180) REVERT: E 8 ASP cc_start: 0.8742 (m-30) cc_final: 0.8398 (p0) REVERT: E 56 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8680 (mt-10) REVERT: E 72 GLN cc_start: 0.8885 (tt0) cc_final: 0.8642 (pt0) outliers start: 49 outliers final: 39 residues processed: 166 average time/residue: 0.1704 time to fit residues: 46.6419 Evaluate side-chains 163 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 5 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 173 VAL 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 207 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 589 THR 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 1082 ILE Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 299 LEU 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 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 1056 LEU Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 62 GLN 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: 5.9990 chunk 91 optimal weight: 0.2980 chunk 231 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 312 optimal weight: 0.6980 chunk 73 optimal weight: 0.2980 chunk 171 optimal weight: 1.9990 chunk 290 optimal weight: 0.9990 chunk 282 optimal weight: 0.3980 chunk 217 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.067019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.048489 restraints weight = 107876.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.050186 restraints weight = 52162.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.051280 restraints weight = 32962.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.051988 restraints weight = 24707.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.052438 restraints weight = 20755.920| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26795 Z= 0.104 Angle : 0.596 26.482 36465 Z= 0.294 Chirality : 0.050 1.895 4169 Planarity : 0.004 0.047 4551 Dihedral : 13.691 143.822 4246 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.25 % Allowed : 12.23 % Favored : 86.52 % 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: -0.51 (0.15), residues: 3169 helix: 1.48 (0.16), residues: 1149 sheet: -0.71 (0.27), residues: 380 loop : -1.64 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 191 TYR 0.012 0.001 TYR D 631 PHE 0.010 0.001 PHE C 514 TRP 0.011 0.001 TRP D 580 HIS 0.004 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00227 (26788) covalent geometry : angle 0.59404 (36459) hydrogen bonds : bond 0.04543 ( 1145) hydrogen bonds : angle 4.21281 ( 3096) metal coordination : bond 0.00382 ( 7) metal coordination : angle 3.47313 ( 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 179 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9262 (mmm) cc_final: 0.9032 (mmm) REVERT: B 186 ASN cc_start: 0.8565 (m-40) cc_final: 0.8240 (t0) REVERT: C 265 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7511 (mmpt) REVERT: C 459 MET cc_start: 0.9070 (mtm) cc_final: 0.8519 (mtm) REVERT: C 464 PHE cc_start: 0.9186 (t80) cc_final: 0.8863 (t80) REVERT: C 488 MET cc_start: 0.8722 (tpp) cc_final: 0.8441 (tpp) REVERT: C 800 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8167 (mtp) REVERT: C 1024 GLU cc_start: 0.8844 (tt0) cc_final: 0.8609 (tp30) REVERT: C 1131 MET cc_start: 0.8897 (ttm) cc_final: 0.8641 (ttm) REVERT: D 130 MET cc_start: 0.8834 (ptm) cc_final: 0.8101 (ppp) REVERT: D 479 GLU cc_start: 0.8745 (tt0) cc_final: 0.8321 (tt0) REVERT: D 581 MET cc_start: 0.8450 (mmm) cc_final: 0.8193 (mtp) REVERT: D 870 ASP cc_start: 0.8982 (m-30) cc_final: 0.8723 (t0) REVERT: E 8 ASP cc_start: 0.8877 (m-30) cc_final: 0.8443 (p0) REVERT: E 56 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8734 (mt-10) REVERT: E 72 GLN cc_start: 0.8914 (tt0) cc_final: 0.8644 (pt0) outliers start: 34 outliers final: 26 residues processed: 174 average time/residue: 0.1692 time to fit residues: 48.4362 Evaluate side-chains 153 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 173 VAL 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 210 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 589 THR 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 D residue 128 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 299 LEU 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 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: 10.0000 chunk 207 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 283 optimal weight: 20.0000 chunk 204 optimal weight: 0.4980 chunk 72 optimal weight: 0.5980 chunk 309 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 270 optimal weight: 1.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 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 = 0.3425 r_free = 0.3425 target = 0.066830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.048053 restraints weight = 108845.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.049640 restraints weight = 54875.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.050653 restraints weight = 35701.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.051288 restraints weight = 27465.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.051600 restraints weight = 23475.029| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26795 Z= 0.162 Angle : 0.622 26.564 36465 Z= 0.308 Chirality : 0.050 1.890 4169 Planarity : 0.004 0.050 4551 Dihedral : 13.692 143.806 4246 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.51 % Allowed : 12.30 % Favored : 86.19 % 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: -0.44 (0.15), residues: 3169 helix: 1.56 (0.16), residues: 1141 sheet: -0.68 (0.28), residues: 376 loop : -1.61 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 3 TYR 0.014 0.001 TYR D 631 PHE 0.012 0.001 PHE C 514 TRP 0.008 0.001 TRP D 115 HIS 0.011 0.001 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00369 (26788) covalent geometry : angle 0.62027 (36459) hydrogen bonds : bond 0.04699 ( 1145) hydrogen bonds : angle 4.29016 ( 3096) metal coordination : bond 0.00827 ( 7) metal coordination : angle 3.23390 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4360.18 seconds wall clock time: 76 minutes 7.25 seconds (4567.25 seconds total)