Starting phenix.real_space_refine on Tue Feb 20 00:29:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri9_4886/02_2024/6ri9_4886.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri9_4886/02_2024/6ri9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri9_4886/02_2024/6ri9_4886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri9_4886/02_2024/6ri9_4886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri9_4886/02_2024/6ri9_4886.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri9_4886/02_2024/6ri9_4886.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 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 Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 14.69, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 11.42 Conformation dependent library (CDL) restraints added in 4.8 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: 9.14 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: 11.82 Time building geometry restraints manager: 12.09 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: 80.95 - 91.58: 2 91.58 - 102.21: 176 102.21 - 112.84: 15810 112.84 - 123.47: 19416 123.47 - 134.10: 1055 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 2.440 nonbonded pdb=" OG1 THR C 164 " pdb=" O LYS C 169 " model vdw 2.081 2.440 ... (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 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.600 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 82.730 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.140 ------------------------------------------------------------------------------- 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 0.135 26788 Z= 0.795 Angle : 1.136 27.054 36459 Z= 0.601 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.022 0.003 TRP D 409 HIS 0.009 0.002 HIS D 897 PHE 0.028 0.003 PHE D 227 TYR 0.036 0.004 TYR D 382 ARG 0.013 0.001 ARG C 10 *********************** 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 fitting. rotamer outliers: 2 poor density : 284 time to evaluate : 3.470 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: 0.4695 time to fit residues: 198.5143 Evaluate side-chains 142 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 0.9980 chunk 243 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 83 optimal weight: 30.0000 chunk 164 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 251 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 187 optimal weight: 8.9990 chunk 291 optimal weight: 6.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN C 65 ASN C 69 GLN C 150 HIS C 513 GLN C 580 GLN C 832 HIS C1080 ASN C1116 HIS C1146 GLN C1256 GLN C1268 GLN D 45 ASN D 232 ASN D 865 HIS D1049 GLN D1195 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26788 Z= 0.270 Angle : 0.694 26.706 36459 Z= 0.357 Chirality : 0.053 1.935 4169 Planarity : 0.005 0.058 4551 Dihedral : 14.018 141.219 4246 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.22 % Allowed : 6.92 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.14), residues: 3169 helix: -0.51 (0.14), residues: 1148 sheet: -2.13 (0.25), residues: 365 loop : -3.00 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 686 HIS 0.013 0.001 HIS C 343 PHE 0.018 0.002 PHE D1034 TYR 0.021 0.002 TYR D 382 ARG 0.007 0.001 ARG A 12 *********************** 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 207 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.7735 (ttm) cc_final: 0.7305 (tmm) REVERT: C 569 ILE cc_start: 0.9218 (mt) cc_final: 0.8993 (tp) REVERT: C 681 MET cc_start: 0.8004 (mtp) cc_final: 0.6937 (mtt) REVERT: C 739 ASP cc_start: 0.8851 (p0) cc_final: 0.8389 (t0) REVERT: D 625 MET cc_start: 0.8632 (ttp) cc_final: 0.8367 (ttp) REVERT: D 870 ASP cc_start: 0.8878 (m-30) cc_final: 0.8666 (t0) REVERT: D 1040 MET cc_start: 0.5620 (mtp) cc_final: 0.5333 (mtp) outliers start: 33 outliers final: 18 residues processed: 198 average time/residue: 0.4109 time to fit residues: 129.0498 Evaluate side-chains 144 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 357 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 153 ASN Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 61 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 162 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 242 optimal weight: 8.9990 chunk 198 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 292 optimal weight: 20.0000 chunk 315 optimal weight: 2.9990 chunk 260 optimal weight: 5.9990 chunk 289 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS C 330 HIS ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN D 157 GLN D 341 ASN D 910 ASN D1195 GLN E 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 26788 Z= 0.515 Angle : 0.800 26.419 36459 Z= 0.405 Chirality : 0.055 1.927 4169 Planarity : 0.005 0.054 4551 Dihedral : 14.097 145.743 4246 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 2.62 % Allowed : 9.87 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.14), residues: 3169 helix: 0.05 (0.15), residues: 1146 sheet: -1.83 (0.26), residues: 347 loop : -2.79 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 409 HIS 0.008 0.002 HIS C 526 PHE 0.019 0.002 PHE C 188 TYR 0.021 0.002 TYR D 631 ARG 0.005 0.001 ARG D 220 *********************** 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 201 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 130 time to evaluate : 3.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASN cc_start: 0.8578 (m-40) cc_final: 0.8373 (t0) REVERT: C 239 MET cc_start: 0.7759 (ttm) cc_final: 0.7371 (tmm) REVERT: C 459 MET cc_start: 0.9127 (mpp) cc_final: 0.8902 (mtm) REVERT: C 742 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7715 (m-80) REVERT: C 1028 LYS cc_start: 0.8178 (ptpp) cc_final: 0.7554 (ptpp) REVERT: C 1131 MET cc_start: 0.8652 (ttm) cc_final: 0.8445 (ttm) REVERT: D 479 GLU cc_start: 0.8433 (tt0) cc_final: 0.8122 (tt0) REVERT: D 625 MET cc_start: 0.8851 (ttp) cc_final: 0.8463 (ttp) REVERT: D 1040 MET cc_start: 0.5730 (mtp) cc_final: 0.5385 (mtp) REVERT: E 56 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8393 (mm-30) REVERT: E 69 ARG cc_start: 0.8963 (ttp80) cc_final: 0.8621 (ttp80) outliers start: 71 outliers final: 38 residues processed: 188 average time/residue: 0.3618 time to fit residues: 111.3408 Evaluate side-chains 154 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 115 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 85 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 185 ASP Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 1082 ILE 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 153 ASN 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 566 LYS Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 15 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 61 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 288 optimal weight: 10.0000 chunk 219 optimal weight: 0.5980 chunk 151 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 196 optimal weight: 8.9990 chunk 293 optimal weight: 20.0000 chunk 310 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 277 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 489 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26788 Z= 0.201 Angle : 0.624 26.037 36459 Z= 0.317 Chirality : 0.051 1.939 4169 Planarity : 0.004 0.052 4551 Dihedral : 13.911 142.606 4246 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.03 % Allowed : 10.90 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.15), residues: 3169 helix: 0.80 (0.16), residues: 1145 sheet: -1.63 (0.26), residues: 374 loop : -2.37 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 580 HIS 0.004 0.001 HIS B 66 PHE 0.013 0.001 PHE C 514 TYR 0.015 0.001 TYR D 631 ARG 0.004 0.000 ARG D 322 *********************** 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 195 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 140 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8926 (t0) REVERT: C 239 MET cc_start: 0.7968 (ttm) cc_final: 0.7507 (tmm) REVERT: C 459 MET cc_start: 0.9074 (mpp) cc_final: 0.8767 (mtm) REVERT: C 488 MET cc_start: 0.8759 (tpp) cc_final: 0.8443 (tpp) REVERT: C 569 ILE cc_start: 0.9225 (mt) cc_final: 0.8943 (tp) REVERT: C 739 ASP cc_start: 0.8747 (p0) cc_final: 0.8366 (t0) REVERT: C 742 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: C 800 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7778 (mtp) REVERT: D 479 GLU cc_start: 0.8337 (tt0) cc_final: 0.8059 (tt0) REVERT: D 870 ASP cc_start: 0.8882 (m-30) cc_final: 0.8659 (t0) REVERT: E 72 GLN cc_start: 0.8887 (tt0) cc_final: 0.8631 (pt0) outliers start: 55 outliers final: 31 residues processed: 185 average time/residue: 0.3519 time to fit residues: 107.6755 Evaluate side-chains 160 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 3.132 ------------------------------------------------------------------------------- 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 199 ASP Chi-restraints excluded: chain A residue 205 MET 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 185 ASP Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 486 THR 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 966 ILE Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain E residue 15 ASN Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 61 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 258 optimal weight: 0.7980 chunk 176 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 264 optimal weight: 3.9990 chunk 214 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 158 optimal weight: 0.8980 chunk 278 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 66 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 26788 Z= 0.150 Angle : 0.580 26.014 36459 Z= 0.293 Chirality : 0.050 1.929 4169 Planarity : 0.004 0.050 4551 Dihedral : 13.770 142.630 4246 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.95 % Allowed : 11.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 3169 helix: 1.16 (0.16), residues: 1149 sheet: -1.22 (0.27), residues: 362 loop : -2.08 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 115 HIS 0.004 0.001 HIS D 865 PHE 0.011 0.001 PHE C 405 TYR 0.012 0.001 TYR D 631 ARG 0.005 0.000 ARG D 322 *********************** 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 192 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 139 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.7911 (ttm) cc_final: 0.7521 (tmm) REVERT: C 459 MET cc_start: 0.9080 (mpp) cc_final: 0.8720 (mtm) REVERT: C 464 PHE cc_start: 0.9196 (t80) cc_final: 0.8935 (t80) REVERT: C 739 ASP cc_start: 0.8667 (p0) cc_final: 0.8341 (t0) REVERT: C 800 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7768 (mtp) REVERT: D 321 LYS cc_start: 0.8329 (mmtm) cc_final: 0.8125 (mmtt) REVERT: D 479 GLU cc_start: 0.8348 (tt0) cc_final: 0.8079 (tt0) REVERT: D 802 ASP cc_start: 0.7562 (m-30) cc_final: 0.7354 (t0) REVERT: E 56 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8236 (mm-30) REVERT: E 72 GLN cc_start: 0.8801 (tt0) cc_final: 0.8561 (pt0) outliers start: 53 outliers final: 29 residues processed: 181 average time/residue: 0.3564 time to fit residues: 107.6785 Evaluate side-chains 155 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 2.956 ------------------------------------------------------------------------------- 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 B residue 21 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 357 VAL 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 823 THR Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 0.6980 chunk 279 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 182 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 310 optimal weight: 10.0000 chunk 257 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 163 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 147 GLN B 41 ASN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26788 Z= 0.134 Angle : 0.565 25.949 36459 Z= 0.282 Chirality : 0.050 1.921 4169 Planarity : 0.004 0.054 4551 Dihedral : 13.660 145.073 4246 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.77 % Allowed : 11.53 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 3169 helix: 1.40 (0.16), residues: 1149 sheet: -0.86 (0.28), residues: 361 loop : -1.86 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 115 HIS 0.004 0.001 HIS B 66 PHE 0.011 0.001 PHE C 514 TYR 0.013 0.001 TYR D 631 ARG 0.004 0.000 ARG C1106 *********************** 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 189 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 141 time to evaluate : 3.036 Fit side-chains revert: symmetry clash REVERT: C 265 LYS cc_start: 0.7643 (mmtt) cc_final: 0.7292 (mmpt) REVERT: C 459 MET cc_start: 0.9068 (mpp) cc_final: 0.8704 (mtm) REVERT: C 464 PHE cc_start: 0.9135 (t80) cc_final: 0.8920 (t80) REVERT: C 488 MET cc_start: 0.8733 (tpp) cc_final: 0.8433 (tpp) REVERT: C 515 MET cc_start: 0.8365 (ttm) cc_final: 0.7810 (ttp) REVERT: C 704 MET cc_start: 0.8498 (mmm) cc_final: 0.8084 (mmm) REVERT: C 739 ASP cc_start: 0.8648 (p0) cc_final: 0.8369 (t0) REVERT: D 479 GLU cc_start: 0.8337 (tt0) cc_final: 0.8102 (tt0) REVERT: E 56 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8496 (mm-30) outliers start: 48 outliers final: 24 residues processed: 179 average time/residue: 0.3751 time to fit residues: 111.9555 Evaluate side-chains 149 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 3.027 ------------------------------------------------------------------------------- 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 199 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 173 VAL 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 351 LEU Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain E residue 61 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 299 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 chunk 309 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26788 Z= 0.258 Angle : 0.612 26.207 36459 Z= 0.305 Chirality : 0.050 1.909 4169 Planarity : 0.004 0.049 4551 Dihedral : 13.712 144.509 4246 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.66 % Allowed : 11.86 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 3169 helix: 1.47 (0.16), residues: 1142 sheet: -1.07 (0.27), residues: 386 loop : -1.78 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 686 HIS 0.007 0.001 HIS B 23 PHE 0.012 0.001 PHE C 514 TYR 0.013 0.001 TYR D 631 ARG 0.006 0.000 ARG D 312 *********************** 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 173 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 128 time to evaluate : 3.100 Fit side-chains REVERT: C 265 LYS cc_start: 0.7807 (mmtt) cc_final: 0.7385 (mmpt) REVERT: C 459 MET cc_start: 0.9135 (mpp) cc_final: 0.8774 (mtm) REVERT: C 464 PHE cc_start: 0.9208 (t80) cc_final: 0.8993 (t80) REVERT: C 488 MET cc_start: 0.8852 (tpp) cc_final: 0.8516 (tpp) REVERT: C 515 MET cc_start: 0.8446 (ttm) cc_final: 0.7916 (ttp) REVERT: C 739 ASP cc_start: 0.8620 (p0) cc_final: 0.8329 (t0) REVERT: E 56 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8543 (mm-30) outliers start: 45 outliers final: 32 residues processed: 162 average time/residue: 0.3440 time to fit residues: 94.3721 Evaluate side-chains 150 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 118 time to evaluate : 3.306 ------------------------------------------------------------------------------- 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 199 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain C residue 1128 ILE 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 93 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 61 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 191 optimal weight: 9.9990 chunk 123 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 196 optimal weight: 10.0000 chunk 210 optimal weight: 0.0060 chunk 152 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 243 optimal weight: 2.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26788 Z= 0.172 Angle : 0.571 26.004 36459 Z= 0.285 Chirality : 0.050 1.916 4169 Planarity : 0.004 0.048 4551 Dihedral : 13.668 144.429 4246 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.55 % Allowed : 12.38 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 3169 helix: 1.53 (0.16), residues: 1148 sheet: -0.86 (0.28), residues: 379 loop : -1.71 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 580 HIS 0.008 0.001 HIS B 23 PHE 0.014 0.001 PHE D 461 TYR 0.012 0.001 TYR D 631 ARG 0.005 0.000 ARG D 312 *********************** 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 166 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 124 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 265 LYS cc_start: 0.7782 (mmtt) cc_final: 0.7389 (mmpt) REVERT: C 459 MET cc_start: 0.9098 (mpp) cc_final: 0.8769 (mtm) REVERT: C 464 PHE cc_start: 0.9193 (t80) cc_final: 0.8948 (t80) REVERT: C 515 MET cc_start: 0.8453 (ttm) cc_final: 0.7881 (ttp) REVERT: C 739 ASP cc_start: 0.8553 (p0) cc_final: 0.8328 (t0) outliers start: 42 outliers final: 30 residues processed: 156 average time/residue: 0.3520 time to fit residues: 93.0302 Evaluate side-chains 150 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 3.083 ------------------------------------------------------------------------------- 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 A residue 199 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain C residue 1128 ILE 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 188 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 674 THR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 62 GLN 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 281 optimal weight: 7.9990 chunk 296 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 288 optimal weight: 8.9990 chunk 173 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 260 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 chunk 287 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 137 ASN C 618 GLN C 760 ASN C 808 ASN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 26788 Z= 0.425 Angle : 0.720 26.425 36459 Z= 0.361 Chirality : 0.053 1.905 4169 Planarity : 0.005 0.056 4551 Dihedral : 13.888 143.300 4246 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.92 % Allowed : 11.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 3169 helix: 1.30 (0.16), residues: 1136 sheet: -1.01 (0.27), residues: 384 loop : -1.79 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 115 HIS 0.013 0.001 HIS B 23 PHE 0.017 0.002 PHE C 514 TYR 0.019 0.002 TYR C1087 ARG 0.005 0.001 ARG D 312 *********************** 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 170 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 118 time to evaluate : 2.757 Fit side-chains revert: symmetry clash REVERT: B 142 MET cc_start: 0.8428 (pmm) cc_final: 0.8168 (pmm) REVERT: C 239 MET cc_start: 0.7495 (ttm) cc_final: 0.7136 (tmm) REVERT: C 265 LYS cc_start: 0.7813 (mmtt) cc_final: 0.7382 (mmpt) REVERT: C 459 MET cc_start: 0.9172 (mpp) cc_final: 0.8813 (mtm) REVERT: C 488 MET cc_start: 0.8809 (tpp) cc_final: 0.8562 (tpp) REVERT: C 515 MET cc_start: 0.8535 (ttm) cc_final: 0.7968 (ttp) REVERT: C 739 ASP cc_start: 0.8657 (p0) cc_final: 0.8425 (t0) REVERT: E 56 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8574 (mm-30) outliers start: 52 outliers final: 38 residues processed: 161 average time/residue: 0.3438 time to fit residues: 94.7357 Evaluate side-chains 154 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 116 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 31 LEU 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 A residue 199 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 5 VAL 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 185 ASP Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 486 THR 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 805 MET Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 355 ILE 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 823 THR Chi-restraints excluded: chain D residue 1063 ASP Chi-restraints excluded: chain D residue 1248 ILE Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 4.9990 chunk 304 optimal weight: 0.2980 chunk 186 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 319 optimal weight: 5.9990 chunk 294 optimal weight: 0.0870 chunk 254 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26788 Z= 0.154 Angle : 0.603 25.935 36459 Z= 0.297 Chirality : 0.050 1.916 4169 Planarity : 0.004 0.048 4551 Dihedral : 13.724 143.317 4246 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.25 % Allowed : 12.78 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 3169 helix: 1.47 (0.16), residues: 1143 sheet: -0.81 (0.28), residues: 379 loop : -1.65 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 580 HIS 0.006 0.001 HIS B 23 PHE 0.012 0.001 PHE C 514 TYR 0.011 0.001 TYR D 631 ARG 0.005 0.000 ARG D 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 2.826 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.8823 (mmm) cc_final: 0.8613 (mmm) REVERT: C 265 LYS cc_start: 0.7815 (mmtt) cc_final: 0.7381 (mmpt) REVERT: C 459 MET cc_start: 0.9078 (mpp) cc_final: 0.8819 (mtm) REVERT: C 464 PHE cc_start: 0.9215 (t80) cc_final: 0.8922 (t80) REVERT: C 488 MET cc_start: 0.8702 (tpp) cc_final: 0.8443 (tpp) REVERT: C 515 MET cc_start: 0.8417 (ttm) cc_final: 0.7878 (ttp) REVERT: C 1119 MET cc_start: 0.8753 (tpp) cc_final: 0.8374 (tpp) REVERT: D 130 MET cc_start: 0.8518 (ptm) cc_final: 0.8175 (ppp) REVERT: D 566 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7611 (ptmm) outliers start: 34 outliers final: 28 residues processed: 154 average time/residue: 0.3391 time to fit residues: 88.7387 Evaluate side-chains 147 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 31 LEU 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 A residue 199 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 486 THR 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 984 VAL Chi-restraints excluded: chain C residue 1128 ILE 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 299 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain E residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 7.9990 chunk 271 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 234 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS E 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.064222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.045471 restraints weight = 110913.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.047051 restraints weight = 55094.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.048089 restraints weight = 35603.592| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 26788 Z= 0.364 Angle : 0.692 26.346 36459 Z= 0.344 Chirality : 0.052 1.904 4169 Planarity : 0.004 0.051 4551 Dihedral : 13.810 143.038 4246 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 1.51 % Allowed : 12.67 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3169 helix: 1.40 (0.16), residues: 1143 sheet: -0.99 (0.27), residues: 391 loop : -1.70 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 115 HIS 0.011 0.001 HIS B 23 PHE 0.014 0.002 PHE C 35 TYR 0.016 0.001 TYR D 631 ARG 0.005 0.000 ARG D 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4214.61 seconds wall clock time: 83 minutes 5.32 seconds (4985.32 seconds total)