Starting phenix.real_space_refine on Wed Feb 4 20:16:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t3x_55519/02_2026/9t3x_55519.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t3x_55519/02_2026/9t3x_55519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9t3x_55519/02_2026/9t3x_55519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t3x_55519/02_2026/9t3x_55519.map" model { file = "/net/cci-nas-00/data/ceres_data/9t3x_55519/02_2026/9t3x_55519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t3x_55519/02_2026/9t3x_55519.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 7995 2.51 5 N 2172 2.21 5 O 2246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12487 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1205, 9469 Classifications: {'peptide': 1205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 4, 'PTRANS': 62, 'TRANS': 1138} Chain breaks: 10 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2886 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 343} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 132 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 17} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 2.93, per 1000 atoms: 0.23 Number of scatterers: 12487 At special positions: 0 Unit cell: (87.6736, 103.846, 137.894, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 2246 8.00 N 2172 7.00 C 7995 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: 0.94 Conformation dependent library (CDL) restraints added in 386.2 milliseconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2962 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 29 sheets defined 8.7% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.699A pdb=" N VAL A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.963A pdb=" N THR A 304 " --> pdb=" O ASN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 491 Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 810 through 814 removed outlier: 3.539A pdb=" N VAL A 813 " --> pdb=" O ASN A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1156 Processing helix chain 'A' and resid 1352 through 1370 removed outlier: 3.691A pdb=" N THR A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A1369 " --> pdb=" O ALA A1365 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A1370 " --> pdb=" O LEU A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1376 Processing helix chain 'A' and resid 1377 through 1382 Processing helix chain 'A' and resid 1401 through 1410 removed outlier: 4.135A pdb=" N ARG A1406 " --> pdb=" O GLU A1402 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR A1407 " --> pdb=" O LEU A1403 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A1408 " --> pdb=" O LEU A1404 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A1409 " --> pdb=" O ASN A1405 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A1410 " --> pdb=" O ARG A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1422 Processing helix chain 'A' and resid 1425 through 1440 removed outlier: 3.679A pdb=" N ILE A1429 " --> pdb=" O THR A1425 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A1440 " --> pdb=" O THR A1436 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 70 Processing helix chain 'B' and resid 75 through 79 Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.759A pdb=" N ASP B 91 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU B 92 " --> pdb=" O TYR B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 92' Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.555A pdb=" N ASN B 104 " --> pdb=" O ASN B 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1308 through 1315 removed outlier: 4.414A pdb=" N THR A1310 " --> pdb=" O ALA A1339 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A1339 " --> pdb=" O THR A1310 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N HIS A1334 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE A1345 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR A 2 " --> pdb=" O MET A1351 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA A 3 " --> pdb=" O LEU A1399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 20 removed outlier: 6.741A pdb=" N LEU A 38 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER A 71 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 40 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 84 removed outlier: 6.616A pdb=" N SER A 97 " --> pdb=" O MET A 79 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N MET A 81 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU A 95 " --> pdb=" O MET A 81 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER A 83 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA A 93 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU A 107 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N THR A 117 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASP A 109 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU A 115 " --> pdb=" O ASP A 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 143 Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 208 removed outlier: 3.662A pdb=" N ASP A 205 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 240 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N THR A 259 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ALA A 242 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N SER A 257 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N SER A 244 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE A 255 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 270 removed outlier: 3.803A pdb=" N GLN A 267 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 329 removed outlier: 7.342A pdb=" N ILE A 344 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LYS A 364 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 346 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE A 362 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR A 348 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE A 360 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE A 350 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 373 through 376 removed outlier: 3.612A pdb=" N SER A 373 " --> pdb=" O GLY A 385 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER A 391 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A 468 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU A 393 " --> pdb=" O CYS A 466 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 478 through 481 Processing sheet with id=AB1, first strand: chain 'A' and resid 522 through 528 removed outlier: 5.293A pdb=" N VAL A 523 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A1000 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU A 995 " --> pdb=" O ASN A 991 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASN A 980 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER A 974 " --> pdb=" O PHE A 990 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 534 through 539 removed outlier: 3.935A pdb=" N ASP A 534 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 574 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY A 573 " --> pdb=" O THR A 588 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 608 through 612 removed outlier: 6.342A pdb=" N GLU A 630 " --> pdb=" O GLN A 634 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN A 634 " --> pdb=" O GLU A 630 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 646 through 652 Processing sheet with id=AB5, first strand: chain 'A' and resid 695 through 703 removed outlier: 6.905A pdb=" N VAL A 788 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU A 698 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 786 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 700 " --> pdb=" O TRP A 784 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TRP A 784 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG A 702 " --> pdb=" O THR A 782 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR A 782 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 806 " --> pdb=" O ILE A 796 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN A 798 " --> pdb=" O LEU A 804 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU A 804 " --> pdb=" O GLN A 798 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 817 through 818 removed outlier: 3.628A pdb=" N PHE A 892 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ARG A 860 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA A 853 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR A 862 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU A 851 " --> pdb=" O TYR A 862 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 864 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL A 849 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N HIS A 866 " --> pdb=" O LYS A 847 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 931 through 937 removed outlier: 3.578A pdb=" N ASP A 936 " --> pdb=" O TYR A 940 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1021 through 1028 removed outlier: 6.693A pdb=" N ALA A1037 " --> pdb=" O HIS A1023 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A1025 " --> pdb=" O ALA A1035 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA A1035 " --> pdb=" O VAL A1025 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TYR A1027 " --> pdb=" O VAL A1033 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A1033 " --> pdb=" O TYR A1027 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A1078 " --> pdb=" O ALA A1090 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA A1090 " --> pdb=" O LEU A1078 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N SER A1080 " --> pdb=" O PRO A1088 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1046 through 1049 Processing sheet with id=AC1, first strand: chain 'A' and resid 1098 through 1109 removed outlier: 6.674A pdb=" N GLY A1124 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET A1103 " --> pdb=" O ALA A1122 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA A1122 " --> pdb=" O MET A1103 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR A1105 " --> pdb=" O TYR A1120 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TYR A1120 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER A1107 " --> pdb=" O LYS A1118 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LYS A1118 " --> pdb=" O SER A1107 " (cutoff:3.500A) removed outlier: 19.991A pdb=" N LEU A1117 " --> pdb=" O GLU A1146 " (cutoff:3.500A) removed outlier: 15.641A pdb=" N GLU A1146 " --> pdb=" O LEU A1117 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N GLY A1119 " --> pdb=" O VAL A1144 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL A1144 " --> pdb=" O GLY A1119 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP A1143 " --> pdb=" O VAL A1162 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL A1162 " --> pdb=" O ASP A1143 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE A1145 " --> pdb=" O PHE A1160 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N PHE A1160 " --> pdb=" O ILE A1145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1172 through 1178 removed outlier: 3.976A pdb=" N ALA A1174 " --> pdb=" O ALA A1185 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE A1190 " --> pdb=" O PHE A1205 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE A1205 " --> pdb=" O ILE A1190 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A1192 " --> pdb=" O MET A1203 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1212 through 1218 removed outlier: 3.696A pdb=" N GLN A1214 " --> pdb=" O ALA A1225 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A1247 " --> pdb=" O LEU A1233 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ARG A1235 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU A1245 " --> pdb=" O ARG A1235 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N GLN A1237 " --> pdb=" O LEU A1243 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU A1243 " --> pdb=" O GLN A1237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1255 through 1262 removed outlier: 6.936A pdb=" N SER A1272 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A1258 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU A1270 " --> pdb=" O VAL A1258 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE A1260 " --> pdb=" O GLY A1268 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLY A1268 " --> pdb=" O PHE A1260 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A1273 " --> pdb=" O ASN A1277 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A1278 " --> pdb=" O ASP A1301 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP A1301 " --> pdb=" O LEU A1278 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A1280 " --> pdb=" O ARG A1299 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 109 through 114 removed outlier: 5.324A pdb=" N PHE B 110 " --> pdb=" O THR B 403 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THR B 403 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 112 " --> pdb=" O PHE B 401 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 122 through 127 removed outlier: 3.706A pdb=" N ALA B 138 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B 155 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ASN B 147 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE B 153 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 164 through 169 removed outlier: 6.712A pdb=" N ALA B 179 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET B 167 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU B 177 " --> pdb=" O MET B 167 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS B 196 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 205 through 210 removed outlier: 7.027A pdb=" N CYS B 220 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA B 208 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA B 218 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE B 210 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS B 216 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 221 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG B 238 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP B 230 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU B 236 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 247 through 252 removed outlier: 6.831A pdb=" N GLY B 262 " --> pdb=" O LYS B 248 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL B 250 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 260 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 270 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR B 283 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE B 272 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 291 through 296 Processing sheet with id=AD2, first strand: chain 'B' and resid 334 through 339 removed outlier: 3.884A pdb=" N GLY B 368 " --> pdb=" O PHE B 358 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4064 1.34 - 1.46: 2704 1.46 - 1.58: 5901 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 12789 Sorted by residual: bond pdb=" N SER A1230 " pdb=" CA SER A1230 " ideal model delta sigma weight residual 1.457 1.484 -0.026 1.29e-02 6.01e+03 4.12e+00 bond pdb=" C TRP B 339 " pdb=" N HIS B 340 " ideal model delta sigma weight residual 1.329 1.351 -0.022 1.60e-02 3.91e+03 1.94e+00 bond pdb=" C LEU A 384 " pdb=" N GLY A 385 " ideal model delta sigma weight residual 1.330 1.349 -0.019 1.58e-02 4.01e+03 1.41e+00 bond pdb=" CA SER A1230 " pdb=" C SER A1230 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.34e-02 5.57e+03 1.07e+00 bond pdb=" C SER A1257 " pdb=" N VAL A1258 " ideal model delta sigma weight residual 1.332 1.342 -0.010 1.20e-02 6.94e+03 7.08e-01 ... (remaining 12784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 16786 1.48 - 2.97: 500 2.97 - 4.45: 74 4.45 - 5.93: 6 5.93 - 7.41: 1 Bond angle restraints: 17367 Sorted by residual: angle pdb=" C SER A1230 " pdb=" CA SER A1230 " pdb=" CB SER A1230 " ideal model delta sigma weight residual 110.42 115.05 -4.63 1.99e+00 2.53e-01 5.41e+00 angle pdb=" C ALA A 652 " pdb=" N ASP A 653 " pdb=" CA ASP A 653 " ideal model delta sigma weight residual 121.80 127.46 -5.66 2.44e+00 1.68e-01 5.38e+00 angle pdb=" CA TRP B 339 " pdb=" CB TRP B 339 " pdb=" CG TRP B 339 " ideal model delta sigma weight residual 113.60 117.84 -4.24 1.90e+00 2.77e-01 4.98e+00 angle pdb=" C ILE A 469 " pdb=" N LEU A 470 " pdb=" CA LEU A 470 " ideal model delta sigma weight residual 121.42 124.47 -3.05 1.43e+00 4.89e-01 4.55e+00 angle pdb=" CA LEU B 145 " pdb=" CB LEU B 145 " pdb=" CG LEU B 145 " ideal model delta sigma weight residual 116.30 123.71 -7.41 3.50e+00 8.16e-02 4.49e+00 ... (remaining 17362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 7154 17.75 - 35.51: 341 35.51 - 53.26: 79 53.26 - 71.02: 17 71.02 - 88.77: 12 Dihedral angle restraints: 7603 sinusoidal: 3021 harmonic: 4582 Sorted by residual: dihedral pdb=" CA LYS A 99 " pdb=" C LYS A 99 " pdb=" N ASP A 100 " pdb=" CA ASP A 100 " ideal model delta harmonic sigma weight residual 180.00 -154.26 -25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA GLY B 362 " pdb=" C GLY B 362 " pdb=" N VAL B 363 " pdb=" CA VAL B 363 " ideal model delta harmonic sigma weight residual 180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA GLY B 393 " pdb=" C GLY B 393 " pdb=" N SER B 394 " pdb=" CA SER B 394 " ideal model delta harmonic sigma weight residual 180.00 -161.40 -18.60 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 7600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1187 0.034 - 0.068: 505 0.068 - 0.102: 138 0.102 - 0.136: 114 0.136 - 0.171: 7 Chirality restraints: 1951 Sorted by residual: chirality pdb=" CA ILE A 998 " pdb=" N ILE A 998 " pdb=" C ILE A 998 " pdb=" CB ILE A 998 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA ILE A1335 " pdb=" N ILE A1335 " pdb=" C ILE A1335 " pdb=" CB ILE A1335 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA VAL B 185 " pdb=" N VAL B 185 " pdb=" C VAL B 185 " pdb=" CB VAL B 185 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 1948 not shown) Planarity restraints: 2217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 860 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.60e+00 pdb=" N PRO A 861 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 861 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 861 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 94 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO B 95 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 653 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO A 654 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 654 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 654 " 0.019 5.00e-02 4.00e+02 ... (remaining 2214 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 7017 3.06 - 3.52: 10999 3.52 - 3.98: 19308 3.98 - 4.44: 22210 4.44 - 4.90: 37148 Nonbonded interactions: 96682 Sorted by model distance: nonbonded pdb=" O TYR B 187 " pdb=" ND2 ASN B 194 " model vdw 2.605 3.120 nonbonded pdb=" N SER B 162 " pdb=" O SER B 162 " model vdw 2.616 2.496 nonbonded pdb=" N SER A 331 " pdb=" O SER A 331 " model vdw 2.620 2.496 nonbonded pdb=" NE2 GLN B 325 " pdb=" O VAL B 361 " model vdw 2.625 3.120 nonbonded pdb=" N ALA A 282 " pdb=" O ALA A 282 " model vdw 2.625 2.496 ... (remaining 96677 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.160 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 0.003 0.026 12789 Z= 0.162 Angle : 0.612 7.414 17367 Z= 0.335 Chirality : 0.046 0.171 1951 Planarity : 0.004 0.047 2217 Dihedral : 11.974 88.770 4641 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.81 % Allowed : 4.07 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.20), residues: 1554 helix: 1.49 (0.62), residues: 68 sheet: 0.85 (0.20), residues: 593 loop : -0.72 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 80 TYR 0.011 0.002 TYR A1066 PHE 0.017 0.002 PHE A1311 TRP 0.017 0.002 TRP B 383 HIS 0.004 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00275 (12789) covalent geometry : angle 0.61175 (17367) hydrogen bonds : bond 0.12609 ( 398) hydrogen bonds : angle 5.99052 ( 1035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.528 Fit side-chains outliers start: 11 outliers final: 1 residues processed: 106 average time/residue: 0.7320 time to fit residues: 83.4626 Evaluate side-chains 77 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.0010 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS A 692 GLN B 181 HIS B 325 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.067913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.048607 restraints weight = 21570.815| |-----------------------------------------------------------------------------| r_work (start): 0.2524 rms_B_bonded: 2.53 r_work: 0.2380 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2265 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9194 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12789 Z= 0.220 Angle : 0.659 8.157 17367 Z= 0.356 Chirality : 0.049 0.163 1951 Planarity : 0.005 0.046 2217 Dihedral : 4.872 27.653 1712 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.70 % Allowed : 5.70 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.20), residues: 1554 helix: 0.97 (0.59), residues: 74 sheet: 0.73 (0.20), residues: 617 loop : -0.81 (0.19), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 932 TYR 0.014 0.002 TYR A1066 PHE 0.018 0.002 PHE A1311 TRP 0.016 0.002 TRP B 339 HIS 0.005 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00540 (12789) covalent geometry : angle 0.65919 (17367) hydrogen bonds : bond 0.06236 ( 398) hydrogen bonds : angle 5.52779 ( 1035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.533 Fit side-chains REVERT: A 694 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8426 (ptmt) REVERT: A 988 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9149 (pp) outliers start: 23 outliers final: 4 residues processed: 93 average time/residue: 0.7077 time to fit residues: 71.5288 Evaluate side-chains 79 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1439 VAL Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 106 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.067726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.048540 restraints weight = 21389.072| |-----------------------------------------------------------------------------| r_work (start): 0.2534 rms_B_bonded: 2.49 r_work: 0.2391 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2277 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9236 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12789 Z= 0.204 Angle : 0.627 7.826 17367 Z= 0.340 Chirality : 0.048 0.161 1951 Planarity : 0.005 0.045 2217 Dihedral : 4.822 28.234 1712 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.41 % Allowed : 6.96 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.20), residues: 1554 helix: 0.97 (0.59), residues: 74 sheet: 0.74 (0.20), residues: 625 loop : -0.86 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 997 TYR 0.013 0.002 TYR A1066 PHE 0.018 0.002 PHE A1311 TRP 0.017 0.002 TRP B 339 HIS 0.004 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00499 (12789) covalent geometry : angle 0.62728 (17367) hydrogen bonds : bond 0.05988 ( 398) hydrogen bonds : angle 5.45626 ( 1035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.548 Fit side-chains REVERT: A 988 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9174 (pp) REVERT: A 1167 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7508 (tp30) outliers start: 19 outliers final: 7 residues processed: 89 average time/residue: 0.6460 time to fit residues: 62.6336 Evaluate side-chains 80 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1439 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.067352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.048187 restraints weight = 21352.456| |-----------------------------------------------------------------------------| r_work (start): 0.2529 rms_B_bonded: 2.49 r_work: 0.2387 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2274 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9244 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12789 Z= 0.217 Angle : 0.637 7.923 17367 Z= 0.345 Chirality : 0.049 0.163 1951 Planarity : 0.005 0.046 2217 Dihedral : 4.856 28.199 1712 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.48 % Allowed : 7.25 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.20), residues: 1554 helix: 0.98 (0.59), residues: 74 sheet: 0.73 (0.20), residues: 625 loop : -0.91 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 997 TYR 0.012 0.002 TYR A1066 PHE 0.018 0.002 PHE A1311 TRP 0.018 0.002 TRP B 339 HIS 0.004 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00534 (12789) covalent geometry : angle 0.63730 (17367) hydrogen bonds : bond 0.06115 ( 398) hydrogen bonds : angle 5.46969 ( 1035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.532 Fit side-chains REVERT: A 988 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9186 (pp) REVERT: A 1167 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7523 (tp30) outliers start: 20 outliers final: 10 residues processed: 90 average time/residue: 0.6664 time to fit residues: 65.5557 Evaluate side-chains 83 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1439 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 3 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.068722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.049416 restraints weight = 21675.231| |-----------------------------------------------------------------------------| r_work (start): 0.2558 rms_B_bonded: 2.53 r_work: 0.2416 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2303 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9221 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12789 Z= 0.135 Angle : 0.551 7.120 17367 Z= 0.298 Chirality : 0.045 0.158 1951 Planarity : 0.004 0.043 2217 Dihedral : 4.571 25.577 1712 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.11 % Allowed : 8.36 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.20), residues: 1554 helix: 1.06 (0.59), residues: 74 sheet: 0.80 (0.20), residues: 626 loop : -0.82 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 997 TYR 0.010 0.001 TYR A1066 PHE 0.014 0.001 PHE A1311 TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00319 (12789) covalent geometry : angle 0.55101 (17367) hydrogen bonds : bond 0.04879 ( 398) hydrogen bonds : angle 5.19468 ( 1035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.518 Fit side-chains REVERT: A 988 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9161 (pp) REVERT: A 1167 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7417 (tp30) outliers start: 15 outliers final: 7 residues processed: 86 average time/residue: 0.6488 time to fit residues: 60.9078 Evaluate side-chains 79 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1439 VAL Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.068963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.049689 restraints weight = 21553.640| |-----------------------------------------------------------------------------| r_work (start): 0.2566 rms_B_bonded: 2.52 r_work: 0.2424 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2311 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9213 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12789 Z= 0.129 Angle : 0.539 6.965 17367 Z= 0.291 Chirality : 0.045 0.160 1951 Planarity : 0.004 0.042 2217 Dihedral : 4.465 23.448 1712 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.18 % Allowed : 8.66 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.20), residues: 1554 helix: 1.17 (0.59), residues: 74 sheet: 0.83 (0.20), residues: 627 loop : -0.78 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 997 TYR 0.010 0.001 TYR A1066 PHE 0.014 0.001 PHE A1311 TRP 0.013 0.001 TRP B 339 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00301 (12789) covalent geometry : angle 0.53881 (17367) hydrogen bonds : bond 0.04727 ( 398) hydrogen bonds : angle 5.10561 ( 1035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.521 Fit side-chains REVERT: A 988 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9155 (pp) REVERT: A 1167 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7419 (tp30) outliers start: 16 outliers final: 8 residues processed: 87 average time/residue: 0.6574 time to fit residues: 62.4720 Evaluate side-chains 81 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1439 VAL Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 53 optimal weight: 0.0040 chunk 102 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 121 optimal weight: 0.0070 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.0470 overall best weight: 0.3310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS B 310 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.071645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.052659 restraints weight = 21540.583| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 2.51 r_work: 0.2497 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2387 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9163 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12789 Z= 0.078 Angle : 0.459 5.856 17367 Z= 0.247 Chirality : 0.043 0.145 1951 Planarity : 0.003 0.039 2217 Dihedral : 4.043 19.224 1712 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.96 % Allowed : 9.18 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1554 helix: 1.31 (0.60), residues: 74 sheet: 0.94 (0.20), residues: 634 loop : -0.65 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 406 TYR 0.008 0.001 TYR A 189 PHE 0.011 0.001 PHE B 217 TRP 0.012 0.001 TRP A1337 HIS 0.003 0.000 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00160 (12789) covalent geometry : angle 0.45931 (17367) hydrogen bonds : bond 0.03369 ( 398) hydrogen bonds : angle 4.70506 ( 1035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.538 Fit side-chains REVERT: A 1167 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7177 (tp30) outliers start: 13 outliers final: 6 residues processed: 86 average time/residue: 0.6687 time to fit residues: 62.7330 Evaluate side-chains 80 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1439 VAL Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.068107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.048829 restraints weight = 21363.763| |-----------------------------------------------------------------------------| r_work (start): 0.2545 rms_B_bonded: 2.51 r_work: 0.2404 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2290 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9232 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12789 Z= 0.183 Angle : 0.592 7.248 17367 Z= 0.320 Chirality : 0.047 0.165 1951 Planarity : 0.004 0.041 2217 Dihedral : 4.585 23.362 1712 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.04 % Allowed : 9.47 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.20), residues: 1554 helix: 1.22 (0.60), residues: 74 sheet: 0.85 (0.20), residues: 627 loop : -0.77 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 997 TYR 0.012 0.001 TYR A1066 PHE 0.018 0.002 PHE A 975 TRP 0.014 0.001 TRP B 339 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00446 (12789) covalent geometry : angle 0.59177 (17367) hydrogen bonds : bond 0.05484 ( 398) hydrogen bonds : angle 5.24990 ( 1035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.572 Fit side-chains REVERT: A 988 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9162 (pp) REVERT: A 1167 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7460 (tp30) outliers start: 14 outliers final: 8 residues processed: 85 average time/residue: 0.6779 time to fit residues: 62.9338 Evaluate side-chains 80 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1439 VAL Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 58 optimal weight: 4.9990 chunk 141 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.069463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.050104 restraints weight = 21712.806| |-----------------------------------------------------------------------------| r_work (start): 0.2575 rms_B_bonded: 2.54 r_work: 0.2433 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2321 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9208 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12789 Z= 0.114 Angle : 0.522 6.582 17367 Z= 0.282 Chirality : 0.044 0.158 1951 Planarity : 0.004 0.040 2217 Dihedral : 4.371 21.928 1712 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.18 % Allowed : 9.47 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1554 helix: 1.28 (0.60), residues: 74 sheet: 0.89 (0.20), residues: 627 loop : -0.73 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 997 TYR 0.009 0.001 TYR A1066 PHE 0.014 0.001 PHE A1311 TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00261 (12789) covalent geometry : angle 0.52207 (17367) hydrogen bonds : bond 0.04410 ( 398) hydrogen bonds : angle 5.01865 ( 1035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.553 Fit side-chains REVERT: A 988 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9153 (pp) REVERT: A 1167 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7358 (tp30) outliers start: 16 outliers final: 8 residues processed: 85 average time/residue: 0.6710 time to fit residues: 62.2428 Evaluate side-chains 81 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1439 VAL Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.069225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.049990 restraints weight = 21543.427| |-----------------------------------------------------------------------------| r_work (start): 0.2571 rms_B_bonded: 2.52 r_work: 0.2430 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2317 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9211 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12789 Z= 0.126 Angle : 0.537 6.968 17367 Z= 0.289 Chirality : 0.045 0.160 1951 Planarity : 0.004 0.040 2217 Dihedral : 4.387 21.754 1712 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.81 % Allowed : 9.92 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1554 helix: 1.28 (0.60), residues: 74 sheet: 0.89 (0.20), residues: 627 loop : -0.73 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 997 TYR 0.010 0.001 TYR A1066 PHE 0.014 0.001 PHE A1311 TRP 0.013 0.001 TRP B 339 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00294 (12789) covalent geometry : angle 0.53656 (17367) hydrogen bonds : bond 0.04605 ( 398) hydrogen bonds : angle 5.04396 ( 1035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.461 Fit side-chains REVERT: A 988 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9163 (pp) REVERT: A 1167 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7390 (tp30) outliers start: 11 outliers final: 8 residues processed: 81 average time/residue: 0.6824 time to fit residues: 60.2420 Evaluate side-chains 80 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1439 VAL Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 26 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 133 optimal weight: 0.1980 chunk 128 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 chunk 149 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS B 310 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.070771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.051537 restraints weight = 21729.791| |-----------------------------------------------------------------------------| r_work (start): 0.2609 rms_B_bonded: 2.54 r_work: 0.2470 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2359 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9181 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12789 Z= 0.090 Angle : 0.486 7.187 17367 Z= 0.261 Chirality : 0.043 0.150 1951 Planarity : 0.004 0.039 2217 Dihedral : 4.128 19.383 1712 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.74 % Allowed : 10.14 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.21), residues: 1554 helix: 1.39 (0.61), residues: 74 sheet: 1.00 (0.20), residues: 626 loop : -0.66 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 406 TYR 0.008 0.001 TYR A 189 PHE 0.012 0.001 PHE B 217 TRP 0.011 0.001 TRP A1337 HIS 0.004 0.000 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00195 (12789) covalent geometry : angle 0.48571 (17367) hydrogen bonds : bond 0.03723 ( 398) hydrogen bonds : angle 4.78842 ( 1035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5327.98 seconds wall clock time: 91 minutes 19.10 seconds (5479.10 seconds total)