Starting phenix.real_space_refine on Fri Jul 3 10:58:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oxe_70974/07_2026/9oxe_70974.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oxe_70974/07_2026/9oxe_70974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oxe_70974/07_2026/9oxe_70974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oxe_70974/07_2026/9oxe_70974.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oxe_70974/07_2026/9oxe_70974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oxe_70974/07_2026/9oxe_70974.map" } resolution = 2.53 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= 0.043 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 7 5.49 5 S 89 5.16 5 C 8528 2.51 5 N 2325 2.21 5 O 2407 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13359 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9281 Classifications: {'peptide': 1169} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1102} Chain breaks: 13 Chain: "B" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3035 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 15, 'TRANS': 360} Chain: "C" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 905 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "E" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 135 Classifications: {'DNA': 1, 'RNA': 6} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 1} Link IDs: {'rna2p': 6} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12622 SG CYS C 41 30.579 88.950 97.306 1.00 56.62 S ATOM 12686 SG CYS C 49 27.818 89.395 99.927 1.00 69.89 S ATOM 12721 SG CYS C 55 28.971 85.918 99.099 1.00 47.63 S ATOM 12823 SG CYS C 68 45.966 80.781 108.472 1.00 53.65 S ATOM 12893 SG CYS C 76 42.267 79.736 108.509 1.00 56.45 S ATOM 12938 SG CYS C 82 43.348 83.345 109.450 1.00 55.03 S ATOM 13059 SG CYS C 96 62.502 78.222 111.127 1.00 80.56 S ATOM 13139 SG CYS C 105 64.524 75.252 109.813 1.00 97.85 S ATOM 13177 SG CYS C 110 61.718 76.785 107.672 1.00 69.74 S Time building chain proxies: 2.71, per 1000 atoms: 0.20 Number of scatterers: 13359 At special positions: 0 Unit cell: (87.5136, 104.851, 134.573, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 89 16.00 P 7 15.00 O 2407 8.00 N 2325 7.00 C 8528 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: 0.98 Conformation dependent library (CDL) restraints added in 634.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 59 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 49 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 55 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 41 " pdb=" ZN C 302 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS C 86 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 68 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 82 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 76 " pdb=" ZN C 303 " pdb="ZN ZN C 303 " - pdb=" NE2 HIS C 114 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 96 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 110 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 105 " Number of angles added : 9 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3106 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 29 sheets defined 10.7% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.789A pdb=" N ASP A 130 " --> pdb=" O GLU A 127 " (cutoff:3.500A) 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: 3.751A pdb=" N VAL A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.944A pdb=" N THR A 304 " --> pdb=" O ASN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 491 removed outlier: 3.561A pdb=" N GLN A 491 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.556A pdb=" N GLN A 858 " --> pdb=" O GLY A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1156 Processing helix chain 'A' and resid 1352 through 1370 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: 4.032A pdb=" N ARG A1406 " --> pdb=" O GLU A1402 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR A1407 " --> pdb=" O LEU A1403 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A1408 " --> pdb=" O LEU A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1422 Processing helix chain 'A' and resid 1425 through 1440 removed outlier: 3.786A pdb=" N THR A1436 " --> pdb=" O ASP A1432 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A1437 " --> pdb=" O LEU A1433 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR A1440 " --> pdb=" O THR A1436 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 73 removed outlier: 3.866A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TRP B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.760A pdb=" N LEU B 92 " --> pdb=" O TYR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 96 through 102 Processing sheet with id=AA1, first strand: chain 'A' and resid 1308 through 1315 removed outlier: 4.178A pdb=" N THR A1310 " --> pdb=" O ALA A1339 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N HIS A1334 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE A1345 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR A 2 " --> pdb=" O MET A1351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 20 removed outlier: 6.527A pdb=" N LEU A 38 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER A 71 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 40 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 84 removed outlier: 3.803A pdb=" N SER A 80 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU A 103 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU A 120 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A 105 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP A 114 " --> 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: 6.728A pdb=" N LEU A 220 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU A 206 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 218 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE A 208 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR A 216 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N CYS A 238 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR A 259 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 240 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER A 257 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.693A pdb=" N PHE A 281 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 279 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.881A 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: 7.213A pdb=" N ILE A 344 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LYS A 364 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 346 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE A 362 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR A 348 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE A 360 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 6.806A 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: 3.508A pdb=" N SER A 391 " --> pdb=" O ILE A 469 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 467 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS A 395 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL A 465 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR A 397 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE A 463 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 477 through 481 removed outlier: 4.122A pdb=" N ASN A 477 " --> pdb=" O CYS A 503 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 522 through 528 removed outlier: 5.363A pdb=" N VAL A 523 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A1000 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A 989 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 3.983A 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: 3.651A pdb=" N ASP A 534 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 574 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 4.561A 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: 3.528A pdb=" N PHE A 608 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 646 through 651 Processing sheet with id=AB5, first strand: chain 'A' and resid 695 through 703 removed outlier: 6.596A pdb=" N MET A 794 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU A 807 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE A 796 " --> pdb=" O VAL A 805 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 817 through 818 removed outlier: 4.557A pdb=" N ILE A 873 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ARG A 860 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA A 853 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR A 862 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU A 851 " --> pdb=" O TYR A 862 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 864 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL A 849 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.532A 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: 3.572A pdb=" N ASP A 936 " --> pdb=" O TYR A 940 " (cutoff:3.500A) removed outlier: 5.861A 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: 5.672A pdb=" N ALA A1022 " --> pdb=" O SER A1039 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N SER A1039 " --> pdb=" O ALA A1022 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR A1024 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 13.373A pdb=" N GLU A1072 " --> pdb=" O GLU A1093 " (cutoff:3.500A) removed outlier: 11.720A pdb=" N GLU A1093 " --> pdb=" O GLU A1072 " (cutoff:3.500A) removed outlier: 11.068A pdb=" N PHE A1074 " --> pdb=" O ARG A1091 " (cutoff:3.500A) removed outlier: 10.206A pdb=" N ARG A1091 " --> pdb=" O PHE A1074 " (cutoff:3.500A) removed outlier: 10.882A pdb=" N ILE A1076 " --> pdb=" O ASN A1089 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N ASN A1089 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU A1078 " --> pdb=" O ILE A1087 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU A1085 " --> pdb=" O SER A1080 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1046 through 1048 Processing sheet with id=AC1, first strand: chain 'A' and resid 1098 through 1106 removed outlier: 5.308A pdb=" N VAL A1100 " --> pdb=" O CYS A1126 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS A1126 " --> pdb=" O VAL A1100 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE A1139 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU A1165 " --> pdb=" O ILE A1139 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A1141 " --> pdb=" O LEU A1163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1172 through 1178 removed outlier: 3.707A pdb=" N ALA A1174 " --> pdb=" O ALA A1185 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE A1190 " --> pdb=" O PHE A1205 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE A1205 " --> pdb=" O ILE A1190 " (cutoff:3.500A) removed outlier: 6.730A 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: 3.780A pdb=" N GLN A1214 " --> pdb=" O ALA A1225 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG A1235 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU A1245 " --> pdb=" O ARG A1235 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLN A1237 " --> pdb=" O LEU A1243 " (cutoff:3.500A) removed outlier: 5.682A 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: 4.199A pdb=" N SER A1257 " --> pdb=" O SER A1272 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET A1282 " --> pdb=" O ARG A1298 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ARG A1298 " --> pdb=" O MET A1282 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 109 through 114 removed outlier: 5.415A pdb=" N PHE B 110 " --> pdb=" O THR B 403 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR B 403 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 3.815A 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: 4.378A pdb=" N GLU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR B 155 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASN B 147 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 7.009A 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: 4.600A pdb=" N TYR B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 3.970A 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: 3.894A pdb=" N GLU B 207 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 238 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP B 230 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU B 236 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 250 through 252 removed outlier: 6.823A pdb=" N ILE B 270 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR B 283 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 6.509A 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: 3.596A pdb=" N GLY B 368 " --> pdb=" O PHE B 358 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1146 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: 3.13 Time building geometry restraints manager: 1.35 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: 4302 1.34 - 1.46: 2955 1.46 - 1.58: 6285 1.58 - 1.70: 13 1.70 - 1.82: 141 Bond restraints: 13696 Sorted by residual: bond pdb=" CA VAL B 106 " pdb=" CB VAL B 106 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 8.08e-01 bond pdb=" CB PRO A 654 " pdb=" CG PRO A 654 " ideal model delta sigma weight residual 1.506 1.541 -0.035 3.90e-02 6.57e+02 7.97e-01 bond pdb=" C LEU A 799 " pdb=" N PRO A 800 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.59e-01 bond pdb=" N PRO A 294 " pdb=" CA PRO A 294 " ideal model delta sigma weight residual 1.459 1.470 -0.011 1.40e-02 5.10e+03 5.82e-01 bond pdb=" CA VAL A 293 " pdb=" CB VAL A 293 " ideal model delta sigma weight residual 1.537 1.547 -0.009 1.29e-02 6.01e+03 5.33e-01 ... (remaining 13691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 18181 1.31 - 2.62: 299 2.62 - 3.93: 93 3.93 - 5.24: 14 5.24 - 6.55: 4 Bond angle restraints: 18591 Sorted by residual: angle pdb=" N LEU A 799 " pdb=" CA LEU A 799 " pdb=" C LEU A 799 " ideal model delta sigma weight residual 109.81 115.56 -5.75 2.21e+00 2.05e-01 6.77e+00 angle pdb=" CA PRO C 29 " pdb=" C PRO C 29 " pdb=" N PHE C 30 " ideal model delta sigma weight residual 114.72 118.00 -3.28 1.27e+00 6.20e-01 6.67e+00 angle pdb=" N PRO C 31 " pdb=" CA PRO C 31 " pdb=" C PRO C 31 " ideal model delta sigma weight residual 112.47 117.56 -5.09 2.06e+00 2.36e-01 6.10e+00 angle pdb=" N GLY A 111 " pdb=" CA GLY A 111 " pdb=" C GLY A 111 " ideal model delta sigma weight residual 113.18 107.37 5.81 2.37e+00 1.78e-01 6.02e+00 angle pdb=" N VAL B 106 " pdb=" CA VAL B 106 " pdb=" C VAL B 106 " ideal model delta sigma weight residual 109.34 104.46 4.88 2.08e+00 2.31e-01 5.51e+00 ... (remaining 18586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 7626 16.36 - 32.73: 408 32.73 - 49.09: 90 49.09 - 65.45: 24 65.45 - 81.82: 5 Dihedral angle restraints: 8153 sinusoidal: 3348 harmonic: 4805 Sorted by residual: dihedral pdb=" CA LYS A1229 " pdb=" C LYS A1229 " pdb=" N SER A1230 " pdb=" CA SER A1230 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLY A 706 " pdb=" C GLY A 706 " pdb=" N MET A 707 " pdb=" CA MET A 707 " ideal model delta harmonic sigma weight residual 180.00 160.41 19.59 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA LEU A 258 " pdb=" C LEU A 258 " pdb=" N THR A 259 " pdb=" CA THR A 259 " ideal model delta harmonic sigma weight residual 180.00 -160.45 -19.55 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 8150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1302 0.032 - 0.064: 507 0.064 - 0.096: 125 0.096 - 0.127: 124 0.127 - 0.159: 9 Chirality restraints: 2067 Sorted by residual: chirality pdb=" CA PRO C 31 " pdb=" N PRO C 31 " pdb=" C PRO C 31 " pdb=" CB PRO C 31 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CB ILE A1231 " pdb=" CA ILE A1231 " pdb=" CG1 ILE A1231 " pdb=" CG2 ILE A1231 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE A 472 " pdb=" N ILE A 472 " pdb=" C ILE A 472 " pdb=" CB ILE A 472 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 2064 not shown) Planarity restraints: 2345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 94 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+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 VAL A 271 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO A 272 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 293 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.88e+00 pdb=" N PRO A 294 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 294 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 294 " -0.019 5.00e-02 4.00e+02 ... (remaining 2342 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1056 2.75 - 3.29: 11949 3.29 - 3.82: 22794 3.82 - 4.36: 29070 4.36 - 4.90: 49545 Nonbonded interactions: 114414 Sorted by model distance: nonbonded pdb=" O HIS A1177 " pdb=" OG SER A1217 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASP B 396 " pdb=" OG1 THR B 398 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASN A 24 " pdb=" OG SER A 26 " model vdw 2.235 3.040 nonbonded pdb=" OG1 THR B 150 " pdb=" OD1 ASN B 152 " model vdw 2.236 3.040 nonbonded pdb=" N ASP B 246 " pdb=" OD1 ASP B 246 " model vdw 2.239 3.120 ... (remaining 114409 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: 1.500 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.860 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 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 : 0.002 0.035 13708 Z= 0.106 Angle : 0.499 6.549 18600 Z= 0.261 Chirality : 0.043 0.159 2067 Planarity : 0.004 0.045 2345 Dihedral : 11.176 81.818 5047 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.24 % Allowed : 4.35 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.27 (0.20), residues: 1628 helix: -0.46 (0.47), residues: 125 sheet: 0.79 (0.21), residues: 605 loop : -0.82 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.008 0.001 TYR A 288 PHE 0.012 0.001 PHE A1311 TRP 0.012 0.001 TRP A 227 HIS 0.003 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (13696) covalent geometry : angle 0.49747 / 0.26 (18591) hydrogen bonds : bond 0.21902 / 14.18 ( 434) hydrogen bonds : angle 8.39337 / 5.61 ( 1146) metal coordination : bond 0.00620 / 0.37 ( 12) metal coordination : angle 1.64021 / 0.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 0.489 Fit side-chains REVERT: A 395 LYS cc_start: 0.8722 (ttpp) cc_final: 0.8293 (ttpp) REVERT: A 488 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7085 (mm-30) REVERT: A 815 GLN cc_start: 0.8025 (mt0) cc_final: 0.7721 (mp10) REVERT: A 1118 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.6997 (tmtp) REVERT: B 103 MET cc_start: 0.8707 (mmp) cc_final: 0.8396 (mmp) REVERT: B 255 THR cc_start: 0.8300 (m) cc_final: 0.7908 (p) REVERT: B 321 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7891 (mmpt) REVERT: B 414 ARG cc_start: 0.7598 (ptm160) cc_final: 0.7380 (tmm-80) REVERT: C 89 ASP cc_start: 0.8500 (t0) cc_final: 0.8175 (t0) outliers start: 18 outliers final: 6 residues processed: 222 average time/residue: 0.6360 time to fit residues: 152.5473 Evaluate side-chains 184 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 177 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1413 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 246 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 GLN A 471 ASN A 636 HIS A 664 HIS ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1264 ASN A1266 GLN A1334 HIS B 100 ASN B 194 ASN B 268 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.148898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126063 restraints weight = 12579.350| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.19 r_work: 0.3335 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13708 Z= 0.123 Angle : 0.569 8.286 18600 Z= 0.303 Chirality : 0.045 0.192 2067 Planarity : 0.004 0.041 2345 Dihedral : 7.020 63.714 1893 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.45 % Allowed : 9.46 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.23 (0.20), residues: 1628 helix: -0.18 (0.46), residues: 125 sheet: 0.73 (0.20), residues: 613 loop : -0.78 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 997 TYR 0.010 0.001 TYR A 189 PHE 0.015 0.001 PHE A1311 TRP 0.011 0.001 TRP A 227 HIS 0.005 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (13696) covalent geometry : angle 0.56854 / 0.30 (18591) hydrogen bonds : bond 0.05304 / 3.33 ( 434) hydrogen bonds : angle 6.40915 / 4.30 ( 1146) metal coordination : bond 0.00620 / 0.32 ( 12) metal coordination : angle 1.22802 / 0.59 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.505 Fit side-chains REVERT: A 395 LYS cc_start: 0.8796 (ttpp) cc_final: 0.8479 (ttpp) REVERT: A 488 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7266 (mm-30) REVERT: A 616 ARG cc_start: 0.7619 (ttt90) cc_final: 0.7419 (ttp80) REVERT: B 54 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7530 (ptp-110) REVERT: B 103 MET cc_start: 0.8509 (mmp) cc_final: 0.8176 (mmp) REVERT: B 255 THR cc_start: 0.8346 (m) cc_final: 0.7959 (p) REVERT: B 321 LYS cc_start: 0.8289 (mmtt) cc_final: 0.7992 (mmpt) REVERT: B 414 ARG cc_start: 0.7627 (ptm160) cc_final: 0.7420 (tmm-80) REVERT: C 21 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7618 (mt0) REVERT: C 89 ASP cc_start: 0.8640 (t0) cc_final: 0.8380 (t0) outliers start: 21 outliers final: 5 residues processed: 194 average time/residue: 0.6094 time to fit residues: 128.6629 Evaluate side-chains 179 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 172 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain C residue 21 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 43 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 516 GLN A 636 HIS A 866 HIS A1442 HIS B 268 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.141647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.118466 restraints weight = 12637.629| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.18 r_work: 0.3212 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 13708 Z= 0.327 Angle : 0.788 10.003 18600 Z= 0.412 Chirality : 0.054 0.257 2067 Planarity : 0.006 0.054 2345 Dihedral : 7.663 64.032 1880 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.35 % Allowed : 9.88 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.20), residues: 1628 helix: -0.59 (0.45), residues: 131 sheet: 0.46 (0.20), residues: 616 loop : -1.11 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 997 TYR 0.025 0.003 TYR A 155 PHE 0.025 0.003 PHE B 347 TRP 0.016 0.003 TRP B 273 HIS 0.009 0.002 HIS A 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00782 / 0.33 (13696) covalent geometry : angle 0.78599 / 0.41 (18591) hydrogen bonds : bond 0.06213 / 3.97 ( 434) hydrogen bonds : angle 6.39920 / 4.30 ( 1146) metal coordination : bond 0.00973 / 0.61 ( 12) metal coordination : angle 2.40821 / 1.11 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.533 Fit side-chains REVERT: A 249 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.7910 (mm110) REVERT: A 488 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7274 (mm-30) REVERT: A 517 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.7831 (tmtt) REVERT: A 630 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7080 (tm-30) REVERT: A 869 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8092 (mt0) REVERT: A 1131 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7967 (tp30) REVERT: A 1159 LYS cc_start: 0.8457 (ttmm) cc_final: 0.8253 (tttm) REVERT: A 1274 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7966 (tmt90) REVERT: B 103 MET cc_start: 0.8704 (mmp) cc_final: 0.8421 (mmp) REVERT: B 189 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8645 (mt0) REVERT: B 414 ARG cc_start: 0.7796 (ptm160) cc_final: 0.7484 (tmm-80) REVERT: C 21 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7721 (mt0) outliers start: 34 outliers final: 13 residues processed: 198 average time/residue: 0.6457 time to fit residues: 138.6854 Evaluate side-chains 187 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1131 GLU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 40 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 42 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 136 optimal weight: 0.0670 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 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 = 0.3677 r_free = 0.3677 target = 0.147279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124624 restraints weight = 12581.544| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.18 r_work: 0.3292 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13708 Z= 0.116 Angle : 0.559 8.149 18600 Z= 0.298 Chirality : 0.045 0.178 2067 Planarity : 0.004 0.047 2345 Dihedral : 7.143 63.731 1880 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.59 % Allowed : 11.95 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.52 (0.20), residues: 1628 helix: -0.42 (0.45), residues: 131 sheet: 0.56 (0.20), residues: 612 loop : -0.99 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1274 TYR 0.010 0.001 TYR A 617 PHE 0.016 0.001 PHE A1311 TRP 0.012 0.001 TRP B 273 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (13696) covalent geometry : angle 0.55817 / 0.30 (18591) hydrogen bonds : bond 0.04322 / 2.77 ( 434) hydrogen bonds : angle 5.95377 / 4.01 ( 1146) metal coordination : bond 0.00641 / 0.30 ( 12) metal coordination : angle 1.50864 / 0.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.546 Fit side-chains REVERT: A 488 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7297 (mm-30) REVERT: A 630 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: A 648 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: B 54 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7476 (ptp-110) REVERT: B 103 MET cc_start: 0.8540 (mmp) cc_final: 0.8271 (mmp) REVERT: B 321 LYS cc_start: 0.8258 (mmpt) cc_final: 0.7881 (mmpt) REVERT: B 414 ARG cc_start: 0.7669 (ptm160) cc_final: 0.7362 (tmm-80) REVERT: C 21 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7689 (mt0) outliers start: 23 outliers final: 6 residues processed: 194 average time/residue: 0.6171 time to fit residues: 130.7182 Evaluate side-chains 185 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain C residue 21 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 72 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 0.0470 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 HIS A1266 GLN B 310 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.122991 restraints weight = 12478.364| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.17 r_work: 0.3271 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13708 Z= 0.151 Angle : 0.586 7.373 18600 Z= 0.310 Chirality : 0.046 0.183 2067 Planarity : 0.004 0.049 2345 Dihedral : 7.200 63.793 1880 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.73 % Allowed : 12.29 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.56 (0.20), residues: 1628 helix: -0.38 (0.45), residues: 131 sheet: 0.49 (0.20), residues: 615 loop : -1.00 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1109 TYR 0.011 0.001 TYR A 288 PHE 0.015 0.002 PHE A1311 TRP 0.013 0.001 TRP B 273 HIS 0.004 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (13696) covalent geometry : angle 0.58543 / 0.31 (18591) hydrogen bonds : bond 0.04491 / 2.88 ( 434) hydrogen bonds : angle 5.90735 / 3.98 ( 1146) metal coordination : bond 0.00707 / 0.41 ( 12) metal coordination : angle 1.69599 / 0.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.543 Fit side-chains REVERT: A 517 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.7753 (tmtt) REVERT: A 630 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: A 648 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: B 54 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7435 (ptp-110) REVERT: B 103 MET cc_start: 0.8600 (mmp) cc_final: 0.8314 (mmp) REVERT: B 321 LYS cc_start: 0.8289 (mmpt) cc_final: 0.7981 (mmpt) REVERT: B 414 ARG cc_start: 0.7731 (ptm160) cc_final: 0.7431 (tmm-80) REVERT: C 21 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7697 (mt0) outliers start: 25 outliers final: 9 residues processed: 195 average time/residue: 0.6218 time to fit residues: 132.0541 Evaluate side-chains 187 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 21 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 109 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 9 optimal weight: 0.0570 chunk 115 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.147555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124827 restraints weight = 12474.261| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.18 r_work: 0.3292 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 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 0.033 13708 Z= 0.120 Angle : 0.547 6.251 18600 Z= 0.290 Chirality : 0.045 0.173 2067 Planarity : 0.004 0.047 2345 Dihedral : 7.047 63.753 1880 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.73 % Allowed : 12.98 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.20), residues: 1628 helix: -0.27 (0.46), residues: 130 sheet: 0.56 (0.20), residues: 607 loop : -0.99 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 902 TYR 0.010 0.001 TYR A 989 PHE 0.015 0.001 PHE A1311 TRP 0.012 0.001 TRP B 273 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (13696) covalent geometry : angle 0.54629 / 0.29 (18591) hydrogen bonds : bond 0.04093 / 2.62 ( 434) hydrogen bonds : angle 5.74519 / 3.87 ( 1146) metal coordination : bond 0.00643 / 0.36 ( 12) metal coordination : angle 1.48302 / 0.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.496 Fit side-chains REVERT: A 125 GLU cc_start: 0.7638 (mp0) cc_final: 0.7436 (mp0) REVERT: A 630 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7152 (tm-30) REVERT: A 648 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: A 1118 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.6914 (tmtp) REVERT: B 54 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7453 (ptp-110) REVERT: B 103 MET cc_start: 0.8559 (mmp) cc_final: 0.8175 (mmp) REVERT: B 134 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8738 (tt) REVERT: B 321 LYS cc_start: 0.8360 (mmpt) cc_final: 0.8057 (mmpt) REVERT: B 414 ARG cc_start: 0.7666 (ptm160) cc_final: 0.7374 (tmm-80) REVERT: C 21 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7684 (mt0) outliers start: 25 outliers final: 10 residues processed: 196 average time/residue: 0.5764 time to fit residues: 123.4784 Evaluate side-chains 189 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1160 PHE Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain C residue 21 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 68 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 136 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 310 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122660 restraints weight = 12500.483| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.17 r_work: 0.3264 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13708 Z= 0.166 Angle : 0.598 6.393 18600 Z= 0.315 Chirality : 0.046 0.190 2067 Planarity : 0.004 0.048 2345 Dihedral : 7.210 63.816 1880 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.21 % Allowed : 12.78 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.58 (0.20), residues: 1628 helix: -0.36 (0.46), residues: 131 sheet: 0.52 (0.20), residues: 608 loop : -1.05 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 997 TYR 0.012 0.002 TYR A1024 PHE 0.015 0.002 PHE A1311 TRP 0.014 0.002 TRP B 273 HIS 0.005 0.001 HIS A 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (13696) covalent geometry : angle 0.59714 / 0.32 (18591) hydrogen bonds : bond 0.04482 / 2.88 ( 434) hydrogen bonds : angle 5.83045 / 3.93 ( 1146) metal coordination : bond 0.00730 / 0.44 ( 12) metal coordination : angle 1.76925 / 0.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.513 Fit side-chains REVERT: A 125 GLU cc_start: 0.7659 (mp0) cc_final: 0.7414 (mp0) REVERT: A 517 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.7767 (tmtt) REVERT: A 630 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: A 648 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7796 (tt0) REVERT: A 1274 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7740 (tmt90) REVERT: B 54 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7473 (ptp-110) REVERT: B 103 MET cc_start: 0.8592 (mmp) cc_final: 0.8304 (mmp) REVERT: B 308 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7631 (mtt180) REVERT: B 321 LYS cc_start: 0.8339 (mmpt) cc_final: 0.8062 (mmpt) REVERT: B 414 ARG cc_start: 0.7712 (ptm160) cc_final: 0.7422 (tmm-80) REVERT: C 21 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7694 (mt0) outliers start: 32 outliers final: 12 residues processed: 198 average time/residue: 0.5716 time to fit residues: 123.6565 Evaluate side-chains 194 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1160 PHE Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain C residue 21 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 146 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 83 optimal weight: 0.2980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 310 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.121131 restraints weight = 12420.781| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.17 r_work: 0.3244 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13708 Z= 0.207 Angle : 0.651 7.069 18600 Z= 0.342 Chirality : 0.048 0.209 2067 Planarity : 0.005 0.051 2345 Dihedral : 7.407 63.877 1880 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.00 % Allowed : 13.05 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.20), residues: 1628 helix: -0.43 (0.46), residues: 130 sheet: 0.47 (0.20), residues: 603 loop : -1.13 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1109 TYR 0.015 0.002 TYR A1024 PHE 0.018 0.002 PHE B 347 TRP 0.016 0.002 TRP B 273 HIS 0.006 0.001 HIS A 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (13696) covalent geometry : angle 0.64988 / 0.34 (18591) hydrogen bonds : bond 0.04822 / 3.09 ( 434) hydrogen bonds : angle 5.94775 / 4.01 ( 1146) metal coordination : bond 0.00792 / 0.47 ( 12) metal coordination : angle 2.04354 / 0.98 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.317 Fit side-chains REVERT: A 517 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.7845 (tmtt) REVERT: A 630 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: A 648 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: A 1131 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7891 (tp30) REVERT: A 1274 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7736 (tmt90) REVERT: A 1354 LYS cc_start: 0.8075 (mppt) cc_final: 0.7817 (mtmm) REVERT: B 54 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7588 (ptp-110) REVERT: B 103 MET cc_start: 0.8626 (mmp) cc_final: 0.8344 (mmp) REVERT: B 321 LYS cc_start: 0.8362 (mmpt) cc_final: 0.8093 (mmpt) REVERT: B 414 ARG cc_start: 0.7768 (ptm160) cc_final: 0.7467 (tmm-80) REVERT: C 21 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7703 (mt0) outliers start: 29 outliers final: 12 residues processed: 198 average time/residue: 0.5805 time to fit residues: 124.9572 Evaluate side-chains 195 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1131 GLU Chi-restraints excluded: chain A residue 1160 PHE Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain C residue 21 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 94 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 310 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.145695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122831 restraints weight = 12504.447| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.18 r_work: 0.3268 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13708 Z= 0.149 Angle : 0.589 7.167 18600 Z= 0.311 Chirality : 0.046 0.190 2067 Planarity : 0.004 0.049 2345 Dihedral : 7.246 63.787 1880 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.93 % Allowed : 13.40 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.61 (0.20), residues: 1628 helix: -0.41 (0.46), residues: 131 sheet: 0.50 (0.20), residues: 613 loop : -1.07 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 997 TYR 0.011 0.001 TYR A1004 PHE 0.015 0.002 PHE A1311 TRP 0.014 0.002 TRP B 273 HIS 0.004 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (13696) covalent geometry : angle 0.58789 / 0.31 (18591) hydrogen bonds : bond 0.04320 / 2.78 ( 434) hydrogen bonds : angle 5.83621 / 3.93 ( 1146) metal coordination : bond 0.00764 / 0.43 ( 12) metal coordination : angle 1.72736 / 0.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.523 Fit side-chains REVERT: A 125 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: A 517 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.7747 (tmtt) REVERT: A 648 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: A 1274 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7705 (tmt90) REVERT: A 1354 LYS cc_start: 0.8050 (mppt) cc_final: 0.7788 (mtmm) REVERT: B 54 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7437 (ptp-110) REVERT: B 103 MET cc_start: 0.8577 (mmp) cc_final: 0.8286 (mmp) REVERT: B 414 ARG cc_start: 0.7751 (ptm160) cc_final: 0.7456 (tmm-80) REVERT: C 21 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7673 (mt0) outliers start: 28 outliers final: 14 residues processed: 197 average time/residue: 0.5742 time to fit residues: 123.8790 Evaluate side-chains 198 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1160 PHE Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 9 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 189 GLN B 310 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.144291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120932 restraints weight = 12557.611| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.20 r_work: 0.3245 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13708 Z= 0.200 Angle : 0.643 7.180 18600 Z= 0.338 Chirality : 0.048 0.216 2067 Planarity : 0.005 0.052 2345 Dihedral : 7.389 63.870 1880 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.07 % Allowed : 13.26 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.69 (0.20), residues: 1628 helix: -0.48 (0.46), residues: 131 sheet: 0.45 (0.20), residues: 610 loop : -1.11 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1109 TYR 0.014 0.002 TYR A 288 PHE 0.017 0.002 PHE B 347 TRP 0.015 0.002 TRP B 273 HIS 0.005 0.001 HIS A 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (13696) covalent geometry : angle 0.64186 / 0.34 (18591) hydrogen bonds : bond 0.04718 / 3.03 ( 434) hydrogen bonds : angle 5.93054 / 4.00 ( 1146) metal coordination : bond 0.00791 / 0.46 ( 12) metal coordination : angle 1.94165 / 0.92 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.533 Fit side-chains REVERT: A 125 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: A 517 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.7834 (tmtt) REVERT: A 648 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: A 1274 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7733 (tmt90) REVERT: A 1354 LYS cc_start: 0.8087 (mppt) cc_final: 0.7811 (mttm) REVERT: B 54 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7521 (ptp-110) REVERT: B 103 MET cc_start: 0.8622 (mmp) cc_final: 0.8335 (mmp) REVERT: B 134 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8719 (tt) REVERT: B 414 ARG cc_start: 0.7767 (ptm160) cc_final: 0.7478 (tmm-80) REVERT: C 21 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7704 (mt0) outliers start: 30 outliers final: 13 residues processed: 194 average time/residue: 0.6400 time to fit residues: 135.4315 Evaluate side-chains 193 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1160 PHE Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 7 optimal weight: 0.0050 chunk 62 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 0.0470 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 overall best weight: 0.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 189 GLN B 310 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.148639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125885 restraints weight = 12585.935| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.19 r_work: 0.3332 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13708 Z= 0.104 Angle : 0.538 6.819 18600 Z= 0.285 Chirality : 0.044 0.195 2067 Planarity : 0.004 0.047 2345 Dihedral : 6.996 63.731 1880 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.31 % Allowed : 14.02 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.50 (0.20), residues: 1628 helix: -0.29 (0.46), residues: 131 sheet: 0.57 (0.20), residues: 610 loop : -1.00 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1274 TYR 0.011 0.001 TYR A1004 PHE 0.014 0.001 PHE A1311 TRP 0.013 0.001 TRP A 227 HIS 0.004 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (13696) covalent geometry : angle 0.53731 / 0.28 (18591) hydrogen bonds : bond 0.03758 / 2.42 ( 434) hydrogen bonds : angle 5.62004 / 3.78 ( 1146) metal coordination : bond 0.00764 / 0.41 ( 12) metal coordination : angle 1.27066 / 0.64 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4540.82 seconds wall clock time: 78 minutes 12.32 seconds (4692.32 seconds total)