Starting phenix.real_space_refine on Sun May 25 09:32:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ri9_4886/05_2025/6ri9_4886.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ri9_4886/05_2025/6ri9_4886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ri9_4886/05_2025/6ri9_4886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ri9_4886/05_2025/6ri9_4886.map" model { file = "/net/cci-nas-00/data/ceres_data/6ri9_4886/05_2025/6ri9_4886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ri9_4886/05_2025/6ri9_4886.cif" } 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. Time to flip 4 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 18.00, per 1000 atoms: 0.69 Number of scatterers: 26264 At special positions: 0 Unit cell: (129.107, 158.983, 167.519, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 63 15.00 Mg 1 11.99 O 5193 8.00 N 4648 7.00 C 16251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.60 Conformation dependent library (CDL) restraints added in 3.4 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: 9.99 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: 13.27 Time building geometry restraints manager: 8.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6173 1.32 - 1.44: 5210 1.44 - 1.56: 15097 1.56 - 1.68: 124 1.68 - 1.81: 184 Bond restraints: 26788 Sorted by residual: bond pdb=" C SER B 178 " pdb=" N PRO B 179 " ideal model delta sigma weight residual 1.337 1.261 0.076 1.11e-02 8.12e+03 4.66e+01 bond pdb=" CA GLN C 659 " pdb=" C GLN C 659 " ideal model delta sigma weight residual 1.524 1.393 0.131 2.25e-02 1.98e+03 3.38e+01 bond pdb=" C VAL C 690 " pdb=" N PRO C 691 " ideal model delta sigma weight residual 1.332 1.280 0.052 1.12e-02 7.97e+03 2.18e+01 bond pdb=" C VAL D 501 " pdb=" N PRO D 502 " ideal model delta sigma weight residual 1.331 1.282 0.050 1.21e-02 6.83e+03 1.69e+01 bond pdb=" CA ALA A 230 " pdb=" C ALA A 230 " ideal model delta sigma weight residual 1.522 1.460 0.062 1.72e-02 3.38e+03 1.30e+01 ... (remaining 26783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.41: 36292 5.41 - 10.82: 150 10.82 - 16.23: 14 16.23 - 21.64: 0 21.64 - 27.05: 3 Bond angle restraints: 36459 Sorted by residual: angle pdb=" O3' DG T 24 " pdb=" P DG T 25 " pdb=" OP1 DG T 25 " ideal model delta sigma weight residual 108.00 80.95 27.05 3.00e+00 1.11e-01 8.13e+01 angle pdb=" O3' DG T 24 " pdb=" P DG T 25 " pdb=" OP2 DG T 25 " ideal model delta sigma weight residual 108.00 83.99 24.01 3.00e+00 1.11e-01 6.40e+01 angle pdb=" C LYS D 321 " pdb=" N ARG D 322 " pdb=" CA ARG D 322 " ideal model delta sigma weight residual 122.38 100.26 22.12 2.90e+00 1.19e-01 5.82e+01 angle pdb=" C HIS D 897 " pdb=" N CYS D 898 " pdb=" CA CYS D 898 " ideal model delta sigma weight residual 122.56 110.63 11.93 1.72e+00 3.38e-01 4.81e+01 angle pdb=" CA CYS D 898 " pdb=" C CYS D 898 " pdb=" N TYR D 899 " ideal model delta sigma weight residual 118.13 125.86 -7.73 1.28e+00 6.10e-01 3.65e+01 ... (remaining 36454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.68: 15831 26.68 - 53.36: 437 53.36 - 80.04: 86 80.04 - 106.72: 5 106.72 - 133.40: 1 Dihedral angle restraints: 16360 sinusoidal: 7218 harmonic: 9142 Sorted by residual: dihedral pdb=" CA ARG D 47 " pdb=" C ARG D 47 " pdb=" N THR D 48 " pdb=" CA THR D 48 " ideal model delta harmonic sigma weight residual 180.00 148.33 31.67 0 5.00e+00 4.00e-02 4.01e+01 dihedral pdb=" CA VAL B 19 " pdb=" C VAL B 19 " pdb=" N SER B 20 " pdb=" CA SER B 20 " ideal model delta harmonic sigma weight residual -180.00 -148.35 -31.65 0 5.00e+00 4.00e-02 4.01e+01 dihedral pdb=" CA ILE D 416 " pdb=" C ILE D 416 " pdb=" N ARG D 417 " pdb=" CA ARG D 417 " ideal model delta harmonic sigma weight residual -180.00 -150.26 -29.74 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 16357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.384: 4168 0.384 - 0.768: 0 0.768 - 1.152: 0 1.152 - 1.536: 0 1.536 - 1.920: 1 Chirality restraints: 4169 Sorted by residual: chirality pdb=" P DG T 25 " pdb=" OP1 DG T 25 " pdb=" OP2 DG T 25 " pdb=" O5' DG T 25 " both_signs ideal model delta sigma weight residual True 2.35 0.43 1.92 2.00e-01 2.50e+01 9.21e+01 chirality pdb=" CA GLN C 659 " pdb=" N GLN C 659 " pdb=" C GLN C 659 " pdb=" CB GLN C 659 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB VAL D 357 " pdb=" CA VAL D 357 " pdb=" CG1 VAL D 357 " pdb=" CG2 VAL D 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 4166 not shown) Planarity restraints: 4551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 204 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.47e+00 pdb=" N PRO C 205 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 205 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 205 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 250 " -0.041 5.00e-02 4.00e+02 6.26e-02 6.28e+00 pdb=" N PRO D 251 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 251 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 251 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C1080 " -0.039 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO C1081 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO C1081 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C1081 " -0.032 5.00e-02 4.00e+02 ... (remaining 4548 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 237 2.48 - 3.08: 21518 3.08 - 3.69: 38581 3.69 - 4.29: 54267 4.29 - 4.90: 85981 Nonbonded interactions: 200584 Sorted by model distance: nonbonded pdb=" OP1 U R 11 " pdb="MG MG D1503 " model vdw 1.871 2.170 nonbonded pdb=" O3' G R 10 " pdb="MG MG D1503 " model vdw 1.895 2.170 nonbonded pdb=" O2 DC N 39 " pdb=" N2 DG T 1 " model vdw 2.021 2.496 nonbonded pdb=" O MET D 29 " pdb=" OG SER D 32 " model vdw 2.072 3.040 nonbonded pdb=" OG1 THR C 164 " pdb=" O LYS C 169 " model vdw 2.081 3.040 ... (remaining 200579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 232) selection = (chain 'B' and resid 7 through 232) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 0.030 Extract box with map and model: 0.920 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 77.230 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.199 26795 Z= 0.576 Angle : 1.169 44.681 36465 Z= 0.603 Chirality : 0.062 1.920 4169 Planarity : 0.006 0.064 4551 Dihedral : 12.500 133.404 10480 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.75 % Favored : 84.13 % Rotamer: Outliers : 0.07 % Allowed : 1.44 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.11991 ( 1145) hydrogen bonds : angle 7.25147 ( 3096) metal coordination : bond 0.14007 ( 7) metal coordination : angle 21.59466 ( 6) covalent geometry : bond 0.01216 (26788) covalent geometry : angle 1.13615 (36459) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 2.822 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: 0.4574 time to fit residues: 194.3626 Evaluate side-chains 142 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 2.879 ------------------------------------------------------------------------------- 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: 4.9990 chunk 243 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 83 optimal weight: 30.0000 chunk 164 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 251 optimal weight: 0.0770 chunk 97 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 291 optimal weight: 9.9990 overall best weight: 2.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 128 HIS C 65 ASN C 69 GLN C 150 HIS C 330 HIS C 513 GLN C 832 HIS C1080 ASN C1116 HIS C1146 GLN C1256 GLN C1268 GLN D 157 GLN D 488 ASN D 865 HIS D1049 GLN D1195 GLN E 31 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.066976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.048538 restraints weight = 108245.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.050094 restraints weight = 54751.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.051090 restraints weight = 35749.263| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26795 Z= 0.166 Angle : 0.704 28.323 36465 Z= 0.360 Chirality : 0.053 1.892 4169 Planarity : 0.005 0.059 4551 Dihedral : 14.000 140.919 4246 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.07 % Allowed : 6.74 % Favored : 92.19 % 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: -2.76 (0.14), residues: 3169 helix: -0.41 (0.14), residues: 1141 sheet: -2.15 (0.24), residues: 369 loop : -2.90 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 686 HIS 0.009 0.001 HIS C 343 PHE 0.017 0.001 PHE C 514 TYR 0.021 0.002 TYR D 382 ARG 0.007 0.001 ARG C 974 Details of bonding type rmsd hydrogen bonds : bond 0.05683 ( 1145) hydrogen bonds : angle 5.16997 ( 3096) metal coordination : bond 0.00835 ( 7) metal coordination : angle 4.85854 ( 6) covalent geometry : bond 0.00367 (26788) covalent geometry : angle 0.70114 (36459) *********************** 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 208 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8480 (ptmt) REVERT: B 41 ASN cc_start: 0.8953 (t0) cc_final: 0.8724 (t0) REVERT: C 239 MET cc_start: 0.7690 (ttm) cc_final: 0.7247 (tmm) REVERT: C 569 ILE cc_start: 0.9159 (mt) cc_final: 0.8937 (tp) REVERT: C 681 MET cc_start: 0.8034 (mtp) cc_final: 0.6942 (mtt) REVERT: C 685 MET cc_start: 0.8445 (mtm) cc_final: 0.8070 (mtm) REVERT: C 739 ASP cc_start: 0.8687 (p0) cc_final: 0.8380 (t0) REVERT: D 117 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9294 (tm) REVERT: D 625 MET cc_start: 0.8687 (ttp) cc_final: 0.8421 (ttp) REVERT: D 822 MET cc_start: 0.8673 (mmm) cc_final: 0.8062 (mmm) REVERT: D 870 ASP cc_start: 0.8943 (m-30) cc_final: 0.8676 (t0) REVERT: D 1040 MET cc_start: 0.5526 (mtp) cc_final: 0.5247 (mtp) REVERT: E 15 ASN cc_start: 0.8158 (t0) cc_final: 0.7843 (t0) REVERT: E 48 VAL cc_start: 0.9361 (t) cc_final: 0.9149 (p) REVERT: E 72 GLN cc_start: 0.9075 (tt0) cc_final: 0.8864 (pt0) outliers start: 29 outliers final: 14 residues processed: 198 average time/residue: 0.3914 time to fit residues: 124.0076 Evaluate side-chains 146 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 64 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 239 optimal weight: 5.9990 chunk 125 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 214 optimal weight: 0.0060 chunk 135 optimal weight: 0.0570 chunk 308 optimal weight: 6.9990 overall best weight: 0.4914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS C 673 HIS C 760 ASN C1220 GLN C1313 HIS D1195 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.068708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.050280 restraints weight = 108624.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.051892 restraints weight = 54032.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.052934 restraints weight = 34959.114| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26795 Z= 0.114 Angle : 0.616 26.676 36465 Z= 0.312 Chirality : 0.051 1.914 4169 Planarity : 0.004 0.052 4551 Dihedral : 13.790 147.132 4246 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.36 % Allowed : 8.47 % Favored : 90.17 % 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: -1.68 (0.15), residues: 3169 helix: 0.70 (0.15), residues: 1147 sheet: -1.62 (0.25), residues: 377 loop : -2.43 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 686 HIS 0.005 0.001 HIS C 343 PHE 0.015 0.001 PHE C 405 TYR 0.016 0.001 TYR D 382 ARG 0.010 0.000 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.04956 ( 1145) hydrogen bonds : angle 4.58378 ( 3096) metal coordination : bond 0.00402 ( 7) metal coordination : angle 2.83477 ( 6) covalent geometry : bond 0.00239 (26788) covalent geometry : angle 0.61496 (36459) *********************** 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 200 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8883 (t0) cc_final: 0.8626 (t0) REVERT: B 200 LYS cc_start: 0.8880 (tmtp) cc_final: 0.8407 (tttp) REVERT: C 239 MET cc_start: 0.7912 (ttm) cc_final: 0.7278 (tmm) REVERT: C 464 PHE cc_start: 0.9180 (t80) cc_final: 0.8946 (t80) REVERT: C 510 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8612 (pt0) REVERT: C 569 ILE cc_start: 0.9146 (mt) cc_final: 0.8945 (tp) REVERT: C 681 MET cc_start: 0.7980 (mtp) cc_final: 0.6823 (mtt) REVERT: C 685 MET cc_start: 0.8349 (mtm) cc_final: 0.8057 (mtm) REVERT: C 739 ASP cc_start: 0.8682 (p0) cc_final: 0.8418 (t0) REVERT: C 1131 MET cc_start: 0.8700 (ttm) cc_final: 0.8400 (ttm) REVERT: D 330 MET cc_start: 0.8590 (ttm) cc_final: 0.8135 (ttm) REVERT: D 822 MET cc_start: 0.8673 (mmm) cc_final: 0.7998 (mmm) REVERT: D 1040 MET cc_start: 0.5560 (mtp) cc_final: 0.5258 (mtp) REVERT: E 56 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8575 (mm-30) REVERT: E 72 GLN cc_start: 0.9021 (tt0) cc_final: 0.8809 (pt0) outliers start: 37 outliers final: 13 residues processed: 190 average time/residue: 0.3413 time to fit residues: 106.5646 Evaluate side-chains 135 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 1080 ILE 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: 4.9990 chunk 4 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 173 optimal weight: 9.9990 chunk 283 optimal weight: 40.0000 chunk 66 optimal weight: 0.7980 chunk 165 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 222 optimal weight: 4.9990 chunk 234 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS C 760 ASN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN D 910 ASN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.065550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.046799 restraints weight = 110659.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.048324 restraints weight = 55855.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.049312 restraints weight = 36506.704| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 26795 Z= 0.268 Angle : 0.701 26.863 36465 Z= 0.353 Chirality : 0.052 1.901 4169 Planarity : 0.005 0.055 4551 Dihedral : 13.880 141.958 4246 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.45 % Favored : 92.52 % Rotamer: Outliers : 2.32 % Allowed : 9.28 % Favored : 88.40 % 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: -1.48 (0.15), residues: 3169 helix: 0.85 (0.15), residues: 1146 sheet: -1.53 (0.25), residues: 387 loop : -2.29 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 686 HIS 0.007 0.001 HIS C 526 PHE 0.014 0.002 PHE C 405 TYR 0.015 0.002 TYR D 631 ARG 0.006 0.000 ARG C 974 Details of bonding type rmsd hydrogen bonds : bond 0.05361 ( 1145) hydrogen bonds : angle 4.74239 ( 3096) metal coordination : bond 0.01344 ( 7) metal coordination : angle 2.16997 ( 6) covalent geometry : bond 0.00609 (26788) covalent geometry : angle 0.70004 (36459) *********************** 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 193 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 130 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.9063 (t0) cc_final: 0.8811 (t0) REVERT: B 192 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8502 (m) REVERT: C 239 MET cc_start: 0.7853 (ttm) cc_final: 0.7395 (tmm) REVERT: C 265 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7723 (mmpt) REVERT: C 510 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8471 (pt0) REVERT: C 569 ILE cc_start: 0.9231 (mt) cc_final: 0.8939 (tp) REVERT: C 742 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: C 800 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7945 (mtp) REVERT: C 1028 LYS cc_start: 0.8219 (ptpp) cc_final: 0.7594 (ptpp) REVERT: C 1131 MET cc_start: 0.8769 (ttm) cc_final: 0.8551 (ttm) REVERT: D 330 MET cc_start: 0.8636 (ttm) cc_final: 0.8376 (ttm) REVERT: D 1040 MET cc_start: 0.5431 (mtp) cc_final: 0.5103 (mtp) REVERT: E 4 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8841 (p) REVERT: E 72 GLN cc_start: 0.9057 (tt0) cc_final: 0.8855 (pt0) outliers start: 63 outliers final: 26 residues processed: 179 average time/residue: 0.3593 time to fit residues: 106.0229 Evaluate side-chains 151 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 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 510 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 742 TYR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 62 GLN 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 274 optimal weight: 0.0030 chunk 238 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 270 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 262 optimal weight: 0.5980 chunk 248 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.067717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.049073 restraints weight = 108861.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.050671 restraints weight = 54036.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.051703 restraints weight = 34956.784| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26795 Z= 0.111 Angle : 0.595 26.869 36465 Z= 0.299 Chirality : 0.050 1.896 4169 Planarity : 0.004 0.053 4551 Dihedral : 13.772 141.883 4246 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.51 % Allowed : 10.24 % Favored : 88.25 % 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: -1.07 (0.15), residues: 3169 helix: 1.16 (0.16), residues: 1146 sheet: -1.28 (0.26), residues: 384 loop : -2.03 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 580 HIS 0.004 0.001 HIS A 23 PHE 0.010 0.001 PHE C 405 TYR 0.012 0.001 TYR D 631 ARG 0.004 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.04813 ( 1145) hydrogen bonds : angle 4.38801 ( 3096) metal coordination : bond 0.00350 ( 7) metal coordination : angle 2.27934 ( 6) covalent geometry : bond 0.00241 (26788) covalent geometry : angle 0.59480 (36459) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8984 (t0) cc_final: 0.8703 (t0) REVERT: B 186 ASN cc_start: 0.8556 (t0) cc_final: 0.8172 (t0) REVERT: B 192 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8481 (m) REVERT: C 239 MET cc_start: 0.8006 (ttm) cc_final: 0.7540 (tmm) REVERT: C 464 PHE cc_start: 0.9174 (t80) cc_final: 0.8944 (t80) REVERT: C 510 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8642 (pt0) REVERT: C 800 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8161 (mtp) REVERT: C 1131 MET cc_start: 0.8795 (ttm) cc_final: 0.8528 (ttm) REVERT: D 479 GLU cc_start: 0.8605 (tt0) cc_final: 0.8291 (tt0) REVERT: D 604 MET cc_start: 0.9015 (tmm) cc_final: 0.8788 (tmm) REVERT: D 1040 MET cc_start: 0.5573 (mtp) cc_final: 0.5305 (mtp) REVERT: D 1260 MET cc_start: 0.9423 (ttp) cc_final: 0.9215 (ttm) REVERT: E 56 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8526 (mm-30) REVERT: E 72 GLN cc_start: 0.8985 (tt0) cc_final: 0.8778 (pt0) outliers start: 41 outliers final: 22 residues processed: 163 average time/residue: 0.3552 time to fit residues: 96.0130 Evaluate side-chains 147 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain D residue 93 THR 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 810 THR Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain E residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 320 optimal weight: 10.0000 chunk 301 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 181 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 210 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 255 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.066959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.048259 restraints weight = 108626.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.049834 restraints weight = 54692.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.050839 restraints weight = 35571.034| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26795 Z= 0.144 Angle : 0.596 26.939 36465 Z= 0.299 Chirality : 0.050 1.888 4169 Planarity : 0.004 0.050 4551 Dihedral : 13.753 141.280 4246 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.95 % Allowed : 10.06 % Favored : 87.99 % 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: -0.84 (0.15), residues: 3169 helix: 1.32 (0.16), residues: 1145 sheet: -1.13 (0.26), residues: 394 loop : -1.87 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 686 HIS 0.004 0.001 HIS D 430 PHE 0.012 0.001 PHE C 514 TYR 0.013 0.001 TYR D 631 ARG 0.007 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.04770 ( 1145) hydrogen bonds : angle 4.33552 ( 3096) metal coordination : bond 0.00820 ( 7) metal coordination : angle 3.15207 ( 6) covalent geometry : bond 0.00326 (26788) covalent geometry : angle 0.59484 (36459) *********************** 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 177 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.9035 (t0) cc_final: 0.8742 (t0) REVERT: B 186 ASN cc_start: 0.8525 (t0) cc_final: 0.8152 (t0) REVERT: C 239 MET cc_start: 0.7985 (ttm) cc_final: 0.7592 (tmm) REVERT: C 265 LYS cc_start: 0.8072 (mmtt) cc_final: 0.7628 (mmpt) REVERT: C 464 PHE cc_start: 0.9208 (t80) cc_final: 0.8989 (t80) REVERT: C 510 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8598 (pt0) REVERT: C 800 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8065 (mtp) REVERT: C 1131 MET cc_start: 0.8796 (ttm) cc_final: 0.8580 (ttm) REVERT: D 479 GLU cc_start: 0.8608 (tt0) cc_final: 0.8394 (tt0) REVERT: D 822 MET cc_start: 0.8990 (mmm) cc_final: 0.8298 (mmm) REVERT: D 1040 MET cc_start: 0.5600 (mtp) cc_final: 0.5315 (mtp) REVERT: E 56 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8583 (mm-30) REVERT: E 72 GLN cc_start: 0.9005 (tt0) cc_final: 0.8789 (pt0) outliers start: 53 outliers final: 26 residues processed: 166 average time/residue: 0.3362 time to fit residues: 93.6338 Evaluate side-chains 149 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 20 SER 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 39 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 34 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 195 optimal weight: 0.2980 chunk 217 optimal weight: 5.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.065535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.047084 restraints weight = 108778.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.048704 restraints weight = 53104.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.049766 restraints weight = 33796.314| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26795 Z= 0.154 Angle : 0.606 26.754 36465 Z= 0.302 Chirality : 0.050 1.890 4169 Planarity : 0.004 0.047 4551 Dihedral : 13.771 143.255 4246 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.55 % Allowed : 10.57 % Favored : 87.88 % 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: 1.37 (0.16), residues: 1145 sheet: -1.02 (0.26), residues: 393 loop : -1.80 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 580 HIS 0.004 0.001 HIS C 526 PHE 0.015 0.001 PHE D 461 TYR 0.014 0.001 TYR D 631 ARG 0.004 0.000 ARG C 245 Details of bonding type rmsd hydrogen bonds : bond 0.04778 ( 1145) hydrogen bonds : angle 4.33335 ( 3096) metal coordination : bond 0.00974 ( 7) metal coordination : angle 4.19177 ( 6) covalent geometry : bond 0.00349 (26788) covalent geometry : angle 0.60359 (36459) *********************** 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 164 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.9034 (t0) cc_final: 0.8763 (t0) REVERT: B 186 ASN cc_start: 0.8615 (t0) cc_final: 0.8237 (t0) REVERT: C 239 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7523 (tmm) REVERT: C 265 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7571 (mmpt) REVERT: C 464 PHE cc_start: 0.9222 (t80) cc_final: 0.8995 (t80) REVERT: C 488 MET cc_start: 0.8681 (tpp) cc_final: 0.8403 (tpp) REVERT: C 510 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8562 (pt0) REVERT: C 800 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8184 (mtp) REVERT: C 1131 MET cc_start: 0.8902 (ttm) cc_final: 0.8649 (ttm) REVERT: D 479 GLU cc_start: 0.8791 (tt0) cc_final: 0.8410 (tt0) REVERT: D 604 MET cc_start: 0.9134 (tmm) cc_final: 0.8917 (tmm) REVERT: D 822 MET cc_start: 0.9117 (mmm) cc_final: 0.8269 (mmm) REVERT: D 1040 MET cc_start: 0.5788 (mtp) cc_final: 0.5513 (mtp) REVERT: E 8 ASP cc_start: 0.8957 (m-30) cc_final: 0.8579 (p0) REVERT: E 56 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8746 (mm-30) REVERT: E 72 GLN cc_start: 0.9040 (tt0) cc_final: 0.8788 (pt0) outliers start: 42 outliers final: 30 residues processed: 151 average time/residue: 0.3333 time to fit residues: 85.0386 Evaluate side-chains 151 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 3.129 ------------------------------------------------------------------------------- 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 205 MET Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 59 optimal weight: 5.9990 chunk 277 optimal weight: 0.0980 chunk 258 optimal weight: 0.9990 chunk 268 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 255 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 315 optimal weight: 4.9990 chunk 293 optimal weight: 20.0000 chunk 301 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.066412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.047812 restraints weight = 108284.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.049476 restraints weight = 52703.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.050559 restraints weight = 33442.174| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26795 Z= 0.116 Angle : 0.576 26.593 36465 Z= 0.287 Chirality : 0.050 1.893 4169 Planarity : 0.004 0.047 4551 Dihedral : 13.712 143.421 4246 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.44 % Allowed : 10.90 % Favored : 87.66 % 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: -0.58 (0.15), residues: 3169 helix: 1.48 (0.16), residues: 1145 sheet: -0.80 (0.27), residues: 380 loop : -1.71 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 580 HIS 0.005 0.001 HIS B 132 PHE 0.011 0.001 PHE C 514 TYR 0.012 0.001 TYR D 631 ARG 0.004 0.000 ARG E 3 Details of bonding type rmsd hydrogen bonds : bond 0.04584 ( 1145) hydrogen bonds : angle 4.20629 ( 3096) metal coordination : bond 0.00616 ( 7) metal coordination : angle 3.48759 ( 6) covalent geometry : bond 0.00260 (26788) covalent geometry : angle 0.57464 (36459) *********************** 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 168 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASN cc_start: 0.9024 (t0) cc_final: 0.8761 (t0) REVERT: B 186 ASN cc_start: 0.8604 (t0) cc_final: 0.8251 (t0) REVERT: C 265 LYS cc_start: 0.8073 (mmtt) cc_final: 0.7643 (mmpt) REVERT: C 464 PHE cc_start: 0.9202 (t80) cc_final: 0.8900 (t80) REVERT: C 488 MET cc_start: 0.8740 (tpp) cc_final: 0.8454 (tpp) REVERT: C 515 MET cc_start: 0.8555 (ttm) cc_final: 0.8192 (ttp) REVERT: C 800 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8129 (mtp) REVERT: C 1131 MET cc_start: 0.8897 (ttm) cc_final: 0.8618 (ttm) REVERT: D 479 GLU cc_start: 0.8763 (tt0) cc_final: 0.8369 (tt0) REVERT: D 604 MET cc_start: 0.9112 (tmm) cc_final: 0.8846 (tmm) REVERT: D 724 MET cc_start: 0.8960 (mtp) cc_final: 0.8598 (ttm) REVERT: D 802 ASP cc_start: 0.8052 (t0) cc_final: 0.7819 (t0) REVERT: D 822 MET cc_start: 0.9108 (mmm) cc_final: 0.8298 (mmm) REVERT: D 1040 MET cc_start: 0.5615 (mtp) cc_final: 0.5362 (mtp) REVERT: E 8 ASP cc_start: 0.8961 (m-30) cc_final: 0.8444 (p0) REVERT: E 72 GLN cc_start: 0.9005 (tt0) cc_final: 0.8756 (pt0) outliers start: 39 outliers final: 27 residues processed: 159 average time/residue: 0.3319 time to fit residues: 89.8228 Evaluate side-chains 148 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 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 674 THR Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 1080 ILE 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.3931 > 50: distance: 54 - 59: 13.687 distance: 59 - 60: 19.188 distance: 60 - 61: 23.589 distance: 60 - 63: 15.067 distance: 61 - 62: 19.294 distance: 61 - 64: 28.199 distance: 64 - 65: 44.739 distance: 64 - 160: 23.253 distance: 65 - 66: 47.764 distance: 65 - 68: 18.737 distance: 66 - 67: 37.533 distance: 66 - 72: 24.662 distance: 67 - 157: 15.485 distance: 68 - 69: 23.150 distance: 69 - 70: 14.206 distance: 69 - 71: 10.772 distance: 72 - 73: 28.121 distance: 73 - 74: 46.912 distance: 73 - 76: 49.390 distance: 74 - 75: 44.356 distance: 74 - 81: 35.845 distance: 76 - 77: 15.077 distance: 77 - 78: 23.469 distance: 78 - 79: 23.559 distance: 79 - 80: 19.445 distance: 81 - 82: 29.277 distance: 82 - 83: 36.325 distance: 82 - 85: 31.065 distance: 83 - 84: 39.399 distance: 83 - 89: 40.086 distance: 85 - 86: 21.591 distance: 85 - 87: 18.968 distance: 86 - 88: 8.189 distance: 89 - 90: 40.028 distance: 90 - 91: 53.102 distance: 90 - 93: 13.264 distance: 91 - 92: 40.646 distance: 91 - 96: 39.614 distance: 93 - 94: 19.225 distance: 93 - 95: 12.008 distance: 96 - 97: 22.315 distance: 97 - 98: 13.458 distance: 97 - 100: 22.727 distance: 98 - 99: 29.638 distance: 98 - 104: 27.735 distance: 100 - 101: 26.972 distance: 101 - 102: 31.673 distance: 101 - 103: 26.067 distance: 104 - 105: 35.206 distance: 105 - 106: 29.915 distance: 105 - 108: 40.457 distance: 106 - 107: 18.603 distance: 106 - 109: 32.149 distance: 109 - 110: 22.260 distance: 110 - 111: 23.631 distance: 110 - 113: 6.643 distance: 111 - 112: 27.756 distance: 111 - 118: 32.437 distance: 113 - 114: 15.446 distance: 114 - 115: 14.359 distance: 115 - 116: 21.038 distance: 115 - 117: 20.129 distance: 118 - 119: 11.050 distance: 119 - 120: 14.095 distance: 120 - 121: 15.813 distance: 120 - 122: 10.838 distance: 122 - 123: 3.368 distance: 123 - 124: 27.283 distance: 123 - 126: 10.680 distance: 124 - 125: 38.483 distance: 124 - 130: 15.869 distance: 126 - 127: 15.216 distance: 127 - 128: 15.493 distance: 127 - 129: 3.482