Starting phenix.real_space_refine on Wed Mar 4 08:37:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ly4_23587/03_2026/7ly4_23587.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ly4_23587/03_2026/7ly4_23587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ly4_23587/03_2026/7ly4_23587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ly4_23587/03_2026/7ly4_23587.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ly4_23587/03_2026/7ly4_23587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ly4_23587/03_2026/7ly4_23587.map" } resolution = 3.8 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= 0.011 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 51 5.16 5 C 7647 2.51 5 N 1989 2.21 5 O 2245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11934 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2599 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain: "D" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2599 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain: "E" Number of atoms: 6674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 6674 Classifications: {'peptide': 828} Link IDs: {'PTRANS': 48, 'TRANS': 779} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.48, per 1000 atoms: 0.21 Number of scatterers: 11934 At special positions: 0 Unit cell: (90.06, 103.74, 182.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 2 15.00 O 2245 8.00 N 1989 7.00 C 7647 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: 0.91 Conformation dependent library (CDL) restraints added in 512.3 milliseconds 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2778 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 17 sheets defined 44.2% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 removed outlier: 4.261A pdb=" N ILE A 32 " --> pdb=" O THR A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 removed outlier: 4.049A pdb=" N TYR A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 60 through 74 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.522A pdb=" N ILE A 103 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 158 through 168 removed outlier: 3.691A pdb=" N SER A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.911A pdb=" N LEU A 187 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 272 through 286 removed outlier: 3.813A pdb=" N THR A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.543A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 35 Processing helix chain 'D' and resid 35 through 46 removed outlier: 3.694A pdb=" N PHE D 39 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR D 40 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR D 45 " --> pdb=" O PHE D 41 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY D 46 " --> pdb=" O PHE D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 60 through 74 Processing helix chain 'D' and resid 83 through 88 Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 106 through 118 Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 158 through 168 removed outlier: 3.729A pdb=" N SER D 168 " --> pdb=" O ASN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 236 through 243 Processing helix chain 'D' and resid 253 through 261 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 262 through 286 removed outlier: 4.248A pdb=" N GLY D 273 " --> pdb=" O CYS D 269 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 Processing helix chain 'E' and resid 853 through 862 Processing helix chain 'E' and resid 885 through 900 Processing helix chain 'E' and resid 901 through 903 No H-bonds generated for 'chain 'E' and resid 901 through 903' Processing helix chain 'E' and resid 933 through 951 Processing helix chain 'E' and resid 982 through 984 No H-bonds generated for 'chain 'E' and resid 982 through 984' Processing helix chain 'E' and resid 985 through 1002 Processing helix chain 'E' and resid 1013 through 1025 Processing helix chain 'E' and resid 1027 through 1041 Processing helix chain 'E' and resid 1042 through 1044 No H-bonds generated for 'chain 'E' and resid 1042 through 1044' Processing helix chain 'E' and resid 1055 through 1059 Processing helix chain 'E' and resid 1072 through 1086 Processing helix chain 'E' and resid 1089 through 1107 Processing helix chain 'E' and resid 1126 through 1130 Processing helix chain 'E' and resid 1149 through 1165 Processing helix chain 'E' and resid 1171 through 1183 Processing helix chain 'E' and resid 1205 through 1211 Processing helix chain 'E' and resid 1245 through 1247 No H-bonds generated for 'chain 'E' and resid 1245 through 1247' Processing helix chain 'E' and resid 1248 through 1269 Processing helix chain 'E' and resid 1278 through 1289 removed outlier: 4.081A pdb=" N ALA E1283 " --> pdb=" O GLN E1279 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU E1284 " --> pdb=" O LYS E1280 " (cutoff:3.500A) Processing helix chain 'E' and resid 1299 through 1311 removed outlier: 3.526A pdb=" N PHE E1304 " --> pdb=" O LEU E1300 " (cutoff:3.500A) Processing helix chain 'E' and resid 1326 through 1342 Processing helix chain 'E' and resid 1358 through 1371 removed outlier: 4.155A pdb=" N ILE E1362 " --> pdb=" O GLN E1358 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E1363 " --> pdb=" O VAL E1359 " (cutoff:3.500A) Processing helix chain 'E' and resid 1383 through 1394 Processing helix chain 'E' and resid 1409 through 1413 Processing helix chain 'E' and resid 1447 through 1461 Processing helix chain 'E' and resid 1478 through 1489 removed outlier: 3.985A pdb=" N TYR E1482 " --> pdb=" O ASP E1478 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP E1483 " --> pdb=" O LEU E1479 " (cutoff:3.500A) Processing helix chain 'E' and resid 1502 through 1514 Processing helix chain 'E' and resid 1521 through 1529 removed outlier: 4.018A pdb=" N MET E1525 " --> pdb=" O VAL E1521 " (cutoff:3.500A) Processing helix chain 'E' and resid 1530 through 1532 No H-bonds generated for 'chain 'E' and resid 1530 through 1532' Processing helix chain 'E' and resid 1554 through 1563 removed outlier: 4.007A pdb=" N LYS E1558 " --> pdb=" O PRO E1554 " (cutoff:3.500A) Processing helix chain 'E' and resid 1639 through 1646 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 131 removed outlier: 6.794A pdb=" N PHE D 208 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL D 192 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR D 251 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE D 313 " --> pdb=" O TYR D 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 173 Processing sheet with id=AA5, first strand: chain 'A' and resid 288 through 293 removed outlier: 4.121A pdb=" N ALA A 316 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE A 313 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR A 251 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL A 192 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE A 208 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 47 through 48 Processing sheet with id=AA7, first strand: chain 'D' and resid 14 through 16 Processing sheet with id=AA8, first strand: chain 'D' and resid 172 through 173 Processing sheet with id=AA9, first strand: chain 'E' and resid 849 through 850 Processing sheet with id=AB1, first strand: chain 'E' and resid 925 through 928 removed outlier: 6.000A pdb=" N GLU E 925 " --> pdb=" O ALA E 965 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN E 967 " --> pdb=" O GLU E 925 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLU E 927 " --> pdb=" O GLN E 967 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLN E 969 " --> pdb=" O GLU E 927 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR E 972 " --> pdb=" O LEU E 968 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU E 881 " --> pdb=" O LEU E1213 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU E1213 " --> pdb=" O GLU E 881 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 1064 through 1071 removed outlier: 12.392A pdb=" N ILE E1193 " --> pdb=" O ARG E1110 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ALA E1112 " --> pdb=" O ILE E1193 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N PHE E1195 " --> pdb=" O ALA E1112 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN E1114 " --> pdb=" O PHE E1195 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N SER E1197 " --> pdb=" O ASN E1114 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR E1116 " --> pdb=" O SER E1197 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 1323 through 1325 removed outlier: 6.625A pdb=" N LEU E1324 " --> pdb=" O ALA E1316 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 1374 through 1378 removed outlier: 6.520A pdb=" N VAL E1351 " --> pdb=" O VAL E1376 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE E1378 " --> pdb=" O VAL E1351 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL E1353 " --> pdb=" O ILE E1378 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ARG E1350 " --> pdb=" O ILE E1398 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N LEU E1400 " --> pdb=" O ARG E1350 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY E1352 " --> pdb=" O LEU E1400 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 1427 through 1433 removed outlier: 7.215A pdb=" N ILE E1445 " --> pdb=" O ALA E1428 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL E1430 " --> pdb=" O VAL E1443 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL E1443 " --> pdb=" O VAL E1430 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR E1432 " --> pdb=" O LYS E1441 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LYS E1441 " --> pdb=" O TYR E1432 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY E1442 " --> pdb=" O LEU E1637 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 1517 through 1520 removed outlier: 6.443A pdb=" N TRP E1518 " --> pdb=" O LEU E1545 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N SER E1547 " --> pdb=" O TRP E1518 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR E1520 " --> pdb=" O SER E1547 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 1605 through 1610 removed outlier: 6.667A pdb=" N GLY E1623 " --> pdb=" O ASP E1661 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP E1661 " --> pdb=" O GLY E1623 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU E1625 " --> pdb=" O THR E1659 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY E1629 " --> pdb=" O PRO E1655 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 1605 through 1610 removed outlier: 6.667A pdb=" N GLY E1623 " --> pdb=" O ASP E1661 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP E1661 " --> pdb=" O GLY E1623 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU E1625 " --> pdb=" O THR E1659 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY E1629 " --> pdb=" O PRO E1655 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1530 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: 2.04 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2775 1.32 - 1.46: 3728 1.46 - 1.59: 5616 1.59 - 1.72: 16 1.72 - 1.85: 87 Bond restraints: 12222 Sorted by residual: bond pdb=" CB HIS E1301 " pdb=" CG HIS E1301 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.20e+01 bond pdb=" CG ARG E1120 " pdb=" CD ARG E1120 " ideal model delta sigma weight residual 1.520 1.327 0.193 3.00e-02 1.11e+03 4.13e+01 bond pdb=" CB HIS A 216 " pdb=" CG HIS A 216 " ideal model delta sigma weight residual 1.497 1.409 0.088 1.40e-02 5.10e+03 3.92e+01 bond pdb=" C10 FMN D 401 " pdb=" C4A FMN D 401 " ideal model delta sigma weight residual 1.443 1.549 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" CG GLN E1158 " pdb=" CD GLN E1158 " ideal model delta sigma weight residual 1.516 1.390 0.126 2.50e-02 1.60e+03 2.54e+01 ... (remaining 12217 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 15561 3.33 - 6.66: 950 6.66 - 9.99: 80 9.99 - 13.32: 5 13.32 - 16.65: 2 Bond angle restraints: 16598 Sorted by residual: angle pdb=" N LEU E1602 " pdb=" CA LEU E1602 " pdb=" C LEU E1602 " ideal model delta sigma weight residual 111.03 125.16 -14.13 1.11e+00 8.12e-01 1.62e+02 angle pdb=" N ILE A 274 " pdb=" CA ILE A 274 " pdb=" C ILE A 274 " ideal model delta sigma weight residual 110.21 97.64 12.57 1.13e+00 7.83e-01 1.24e+02 angle pdb=" N SER E 873 " pdb=" CA SER E 873 " pdb=" C SER E 873 " ideal model delta sigma weight residual 109.83 97.67 12.16 1.27e+00 6.20e-01 9.16e+01 angle pdb=" C ARG E1666 " pdb=" N PRO E1667 " pdb=" CA PRO E1667 " ideal model delta sigma weight residual 119.82 128.29 -8.47 9.80e-01 1.04e+00 7.46e+01 angle pdb=" C ASP E1499 " pdb=" N PRO E1500 " pdb=" CA PRO E1500 " ideal model delta sigma weight residual 119.56 128.13 -8.57 1.02e+00 9.61e-01 7.06e+01 ... (remaining 16593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 7013 17.79 - 35.57: 194 35.57 - 53.35: 54 53.35 - 71.14: 27 71.14 - 88.92: 6 Dihedral angle restraints: 7294 sinusoidal: 2971 harmonic: 4323 Sorted by residual: dihedral pdb=" C PHE A 36 " pdb=" N PHE A 36 " pdb=" CA PHE A 36 " pdb=" CB PHE A 36 " ideal model delta harmonic sigma weight residual -122.60 -136.94 14.34 0 2.50e+00 1.60e-01 3.29e+01 dihedral pdb=" C ARG E1120 " pdb=" N ARG E1120 " pdb=" CA ARG E1120 " pdb=" CB ARG E1120 " ideal model delta harmonic sigma weight residual -122.60 -132.05 9.45 0 2.50e+00 1.60e-01 1.43e+01 dihedral pdb=" CA PHE A 36 " pdb=" C PHE A 36 " pdb=" N PRO A 37 " pdb=" CA PRO A 37 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 7291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1305 0.103 - 0.206: 431 0.206 - 0.309: 72 0.309 - 0.412: 0 0.412 - 0.515: 2 Chirality restraints: 1810 Sorted by residual: chirality pdb=" CA PHE A 36 " pdb=" N PHE A 36 " pdb=" C PHE A 36 " pdb=" CB PHE A 36 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.62e+00 chirality pdb=" CA ARG E1120 " pdb=" N ARG E1120 " pdb=" C ARG E1120 " pdb=" CB ARG E1120 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.23e+00 chirality pdb=" CA LEU E1041 " pdb=" N LEU E1041 " pdb=" C LEU E1041 " pdb=" CB LEU E1041 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 1807 not shown) Planarity restraints: 2147 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN A 401 " 0.637 2.00e-02 2.50e+03 2.37e-01 2.54e+03 pdb=" C10 FMN A 401 " 0.033 2.00e-02 2.50e+03 pdb=" C2 FMN A 401 " -0.219 2.00e-02 2.50e+03 pdb=" C4 FMN A 401 " 0.190 2.00e-02 2.50e+03 pdb=" C4A FMN A 401 " 0.145 2.00e-02 2.50e+03 pdb=" C5A FMN A 401 " 0.100 2.00e-02 2.50e+03 pdb=" C6 FMN A 401 " 0.041 2.00e-02 2.50e+03 pdb=" C7 FMN A 401 " -0.069 2.00e-02 2.50e+03 pdb=" C7M FMN A 401 " -0.120 2.00e-02 2.50e+03 pdb=" C8 FMN A 401 " -0.139 2.00e-02 2.50e+03 pdb=" C8M FMN A 401 " -0.274 2.00e-02 2.50e+03 pdb=" C9 FMN A 401 " -0.076 2.00e-02 2.50e+03 pdb=" C9A FMN A 401 " 0.051 2.00e-02 2.50e+03 pdb=" N1 FMN A 401 " -0.150 2.00e-02 2.50e+03 pdb=" N10 FMN A 401 " 0.136 2.00e-02 2.50e+03 pdb=" N3 FMN A 401 " 0.073 2.00e-02 2.50e+03 pdb=" N5 FMN A 401 " 0.180 2.00e-02 2.50e+03 pdb=" O2 FMN A 401 " -0.540 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN D 401 " -0.734 2.00e-02 2.50e+03 2.29e-01 2.36e+03 pdb=" C10 FMN D 401 " 0.027 2.00e-02 2.50e+03 pdb=" C2 FMN D 401 " 0.199 2.00e-02 2.50e+03 pdb=" C4 FMN D 401 " -0.145 2.00e-02 2.50e+03 pdb=" C4A FMN D 401 " -0.118 2.00e-02 2.50e+03 pdb=" C5A FMN D 401 " -0.102 2.00e-02 2.50e+03 pdb=" C6 FMN D 401 " -0.084 2.00e-02 2.50e+03 pdb=" C7 FMN D 401 " 0.033 2.00e-02 2.50e+03 pdb=" C7M FMN D 401 " 0.023 2.00e-02 2.50e+03 pdb=" C8 FMN D 401 " 0.158 2.00e-02 2.50e+03 pdb=" C8M FMN D 401 " 0.282 2.00e-02 2.50e+03 pdb=" C9 FMN D 401 " 0.148 2.00e-02 2.50e+03 pdb=" C9A FMN D 401 " 0.006 2.00e-02 2.50e+03 pdb=" N1 FMN D 401 " 0.186 2.00e-02 2.50e+03 pdb=" N10 FMN D 401 " -0.039 2.00e-02 2.50e+03 pdb=" N3 FMN D 401 " 0.026 2.00e-02 2.50e+03 pdb=" N5 FMN D 401 " -0.194 2.00e-02 2.50e+03 pdb=" O2 FMN D 401 " 0.328 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 265 " -0.076 2.00e-02 2.50e+03 4.12e-02 3.40e+01 pdb=" CG TYR D 265 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR D 265 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR D 265 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR D 265 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR D 265 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR D 265 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR D 265 " -0.065 2.00e-02 2.50e+03 ... (remaining 2144 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3449 2.81 - 3.34: 11340 3.34 - 3.86: 20008 3.86 - 4.38: 24770 4.38 - 4.90: 38841 Nonbonded interactions: 98408 Sorted by model distance: nonbonded pdb=" N ILE A 274 " pdb=" O ILE A 274 " model vdw 2.293 2.496 nonbonded pdb=" N ASP E1478 " pdb=" OD1 ASP E1478 " model vdw 2.377 3.120 nonbonded pdb=" NZ LYS E1147 " pdb=" OD1 ASP E1613 " model vdw 2.382 3.120 nonbonded pdb=" OD2 ASP E1074 " pdb=" NZ LYS E1078 " model vdw 2.391 3.120 nonbonded pdb=" N LYS E1147 " pdb=" N GLN E1148 " model vdw 2.402 2.560 ... (remaining 98403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.500 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 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 : 0.019 0.193 12222 Z= 1.020 Angle : 1.741 16.647 16598 Z= 1.185 Chirality : 0.097 0.515 1810 Planarity : 0.012 0.237 2147 Dihedral : 10.550 88.924 4516 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.34 % Allowed : 1.84 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.20), residues: 1466 helix: 0.01 (0.20), residues: 517 sheet: 0.91 (0.31), residues: 279 loop : 0.81 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 120 TYR 0.076 0.010 TYR D 265 PHE 0.034 0.007 PHE D 162 TRP 0.045 0.009 TRP E1323 HIS 0.010 0.002 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.01903 (12222) covalent geometry : angle 1.74142 (16598) hydrogen bonds : bond 0.17843 ( 547) hydrogen bonds : angle 7.68096 ( 1530) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 MET cc_start: 0.8226 (mtt) cc_final: 0.7940 (mtt) REVERT: D 103 ILE cc_start: 0.8368 (pt) cc_final: 0.7982 (mt) REVERT: D 257 MET cc_start: 0.8811 (mmm) cc_final: 0.8443 (mmm) REVERT: E 984 MET cc_start: 0.5465 (ptm) cc_final: 0.4356 (ppp) REVERT: E 999 TYR cc_start: 0.6503 (m-80) cc_final: 0.6302 (t80) REVERT: E 1018 MET cc_start: 0.7223 (mmm) cc_final: 0.6796 (tpp) REVERT: E 1079 LEU cc_start: 0.8598 (mt) cc_final: 0.8146 (pp) REVERT: E 1175 PHE cc_start: 0.9220 (t80) cc_final: 0.8962 (t80) REVERT: E 1207 TRP cc_start: 0.6880 (m100) cc_final: 0.6316 (m100) REVERT: E 1241 ASN cc_start: 0.8061 (m-40) cc_final: 0.7492 (m-40) REVERT: E 1366 MET cc_start: 0.8683 (mmm) cc_final: 0.8458 (mmm) REVERT: E 1525 MET cc_start: 0.8731 (tpp) cc_final: 0.8381 (tpp) REVERT: E 1665 MET cc_start: 0.8302 (ttt) cc_final: 0.7848 (tpp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1229 time to fit residues: 35.4744 Evaluate side-chains 97 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 0.0020 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 GLN ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1169 HIS E1382 HIS E1560 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.091788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.078399 restraints weight = 49040.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.080167 restraints weight = 26761.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.081334 restraints weight = 17896.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.082073 restraints weight = 13560.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.082614 restraints weight = 11182.315| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12222 Z= 0.168 Angle : 0.683 8.967 16598 Z= 0.366 Chirality : 0.047 0.168 1810 Planarity : 0.005 0.059 2147 Dihedral : 5.262 31.545 1641 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.32 % Favored : 97.48 % Rotamer: Outliers : 1.55 % Allowed : 4.90 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.21), residues: 1466 helix: 1.06 (0.22), residues: 522 sheet: 0.59 (0.31), residues: 283 loop : 0.56 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 55 TYR 0.017 0.002 TYR E1036 PHE 0.023 0.002 PHE E1150 TRP 0.016 0.002 TRP E1518 HIS 0.010 0.001 HIS E1382 Details of bonding type rmsd covalent geometry : bond 0.00361 (12222) covalent geometry : angle 0.68267 (16598) hydrogen bonds : bond 0.05567 ( 547) hydrogen bonds : angle 5.60894 ( 1530) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7943 (tp) cc_final: 0.7725 (tt) REVERT: A 63 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7794 (mt-10) REVERT: A 141 ILE cc_start: 0.8561 (tt) cc_final: 0.8322 (pt) REVERT: D 103 ILE cc_start: 0.8731 (pt) cc_final: 0.8376 (mm) REVERT: D 297 ASN cc_start: 0.7364 (t0) cc_final: 0.7049 (t0) REVERT: E 932 MET cc_start: 0.3902 (mtm) cc_final: 0.3041 (mmt) REVERT: E 984 MET cc_start: 0.5274 (ptm) cc_final: 0.4778 (ppp) REVERT: E 1018 MET cc_start: 0.6829 (mmm) cc_final: 0.6289 (tpp) REVERT: E 1118 PHE cc_start: 0.6178 (m-80) cc_final: 0.5728 (m-80) REVERT: E 1175 PHE cc_start: 0.8732 (t80) cc_final: 0.8362 (t80) REVERT: E 1185 MET cc_start: 0.7418 (tpp) cc_final: 0.6978 (ttm) REVERT: E 1366 MET cc_start: 0.8713 (mmm) cc_final: 0.8448 (mmm) outliers start: 20 outliers final: 12 residues processed: 141 average time/residue: 0.0924 time to fit residues: 19.8671 Evaluate side-chains 100 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain E residue 1011 SER Chi-restraints excluded: chain E residue 1101 VAL Chi-restraints excluded: chain E residue 1117 VAL Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1226 ASP Chi-restraints excluded: chain E residue 1281 ASP Chi-restraints excluded: chain E residue 1396 CYS Chi-restraints excluded: chain E residue 1418 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 120 optimal weight: 0.9980 chunk 101 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 280 ASN ** E 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.089352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.075966 restraints weight = 49822.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.077722 restraints weight = 27069.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.078879 restraints weight = 17995.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.079613 restraints weight = 13571.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.080128 restraints weight = 11185.444| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12222 Z= 0.156 Angle : 0.629 8.238 16598 Z= 0.332 Chirality : 0.045 0.148 1810 Planarity : 0.005 0.060 2147 Dihedral : 4.804 29.299 1641 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.93 % Favored : 96.86 % Rotamer: Outliers : 1.24 % Allowed : 7.46 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.22), residues: 1466 helix: 1.23 (0.23), residues: 521 sheet: 0.63 (0.32), residues: 270 loop : 0.31 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1120 TYR 0.033 0.002 TYR E 999 PHE 0.018 0.002 PHE E1150 TRP 0.015 0.002 TRP E1076 HIS 0.008 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00338 (12222) covalent geometry : angle 0.62895 (16598) hydrogen bonds : bond 0.04854 ( 547) hydrogen bonds : angle 5.21820 ( 1530) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LYS cc_start: 0.7402 (pttt) cc_final: 0.7090 (mmmm) REVERT: D 31 MET cc_start: 0.6563 (mtp) cc_final: 0.5634 (ttp) REVERT: D 103 ILE cc_start: 0.8810 (pt) cc_final: 0.8507 (mm) REVERT: D 281 MET cc_start: 0.6436 (ttm) cc_final: 0.6213 (ttm) REVERT: E 932 MET cc_start: 0.4571 (mtm) cc_final: 0.3490 (mmt) REVERT: E 984 MET cc_start: 0.5670 (ptm) cc_final: 0.4634 (ptp) REVERT: E 1079 LEU cc_start: 0.8535 (mt) cc_final: 0.8117 (pp) REVERT: E 1185 MET cc_start: 0.7473 (tpp) cc_final: 0.7063 (ttm) REVERT: E 1366 MET cc_start: 0.8751 (mmm) cc_final: 0.8492 (mmm) REVERT: E 1418 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8166 (tt) REVERT: E 1607 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.8447 (m-80) outliers start: 16 outliers final: 9 residues processed: 107 average time/residue: 0.1046 time to fit residues: 16.9479 Evaluate side-chains 83 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain E residue 1011 SER Chi-restraints excluded: chain E residue 1117 VAL Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1226 ASP Chi-restraints excluded: chain E residue 1396 CYS Chi-restraints excluded: chain E residue 1418 LEU Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1607 TYR Chi-restraints excluded: chain E residue 1643 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 43 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 49 optimal weight: 0.0040 chunk 116 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 HIS D 216 HIS ** E 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1063 ASN ** E1227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.084077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.070689 restraints weight = 49876.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.072368 restraints weight = 26999.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.073476 restraints weight = 18092.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.074197 restraints weight = 13775.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.074642 restraints weight = 11419.857| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12222 Z= 0.268 Angle : 0.749 8.411 16598 Z= 0.395 Chirality : 0.048 0.148 1810 Planarity : 0.005 0.068 2147 Dihedral : 5.320 32.653 1641 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.02 % Favored : 95.70 % Rotamer: Outliers : 1.79 % Allowed : 8.08 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.21), residues: 1466 helix: 0.74 (0.22), residues: 523 sheet: 0.06 (0.32), residues: 268 loop : -0.16 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 978 TYR 0.022 0.002 TYR E1036 PHE 0.024 0.002 PHE E 850 TRP 0.027 0.003 TRP E1518 HIS 0.006 0.002 HIS E1447 Details of bonding type rmsd covalent geometry : bond 0.00600 (12222) covalent geometry : angle 0.74941 (16598) hydrogen bonds : bond 0.05639 ( 547) hydrogen bonds : angle 5.55967 ( 1530) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.490 Fit side-chains REVERT: A 21 VAL cc_start: 0.7906 (t) cc_final: 0.7645 (m) REVERT: D 31 MET cc_start: 0.7303 (mtp) cc_final: 0.6561 (ttm) REVERT: D 103 ILE cc_start: 0.8827 (pt) cc_final: 0.8544 (mm) REVERT: D 257 MET cc_start: 0.8796 (mmm) cc_final: 0.8575 (mmm) REVERT: E 984 MET cc_start: 0.6205 (ptm) cc_final: 0.5724 (ptp) REVERT: E 1018 MET cc_start: 0.6742 (tpp) cc_final: 0.6311 (tpp) REVERT: E 1150 PHE cc_start: 0.7380 (t80) cc_final: 0.7145 (t80) REVERT: E 1252 MET cc_start: 0.7262 (tpp) cc_final: 0.7049 (tpt) REVERT: E 1366 MET cc_start: 0.8676 (mmm) cc_final: 0.8271 (mmm) REVERT: E 1408 MET cc_start: 0.8504 (mmm) cc_final: 0.8287 (tpt) REVERT: E 1418 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8375 (tt) REVERT: E 1488 LEU cc_start: 0.9352 (mm) cc_final: 0.9097 (mp) REVERT: E 1593 TRP cc_start: 0.8090 (OUTLIER) cc_final: 0.6919 (p90) outliers start: 23 outliers final: 15 residues processed: 97 average time/residue: 0.0833 time to fit residues: 13.1324 Evaluate side-chains 81 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 1011 SER Chi-restraints excluded: chain E residue 1094 LEU Chi-restraints excluded: chain E residue 1117 VAL Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1396 CYS Chi-restraints excluded: chain E residue 1418 LEU Chi-restraints excluded: chain E residue 1476 CYS Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1593 TRP Chi-restraints excluded: chain E residue 1643 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.085566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.072618 restraints weight = 50535.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.074268 restraints weight = 27532.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.075346 restraints weight = 18468.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.076025 restraints weight = 14066.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.076534 restraints weight = 11725.667| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12222 Z= 0.190 Angle : 0.640 9.739 16598 Z= 0.336 Chirality : 0.046 0.162 1810 Planarity : 0.004 0.061 2147 Dihedral : 5.122 30.543 1641 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.82 % Favored : 95.84 % Rotamer: Outliers : 1.94 % Allowed : 9.32 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.21), residues: 1466 helix: 0.92 (0.23), residues: 521 sheet: 0.01 (0.31), residues: 284 loop : -0.27 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E1168 TYR 0.035 0.002 TYR E 999 PHE 0.015 0.002 PHE A 208 TRP 0.020 0.002 TRP E1518 HIS 0.005 0.001 HIS E 900 Details of bonding type rmsd covalent geometry : bond 0.00423 (12222) covalent geometry : angle 0.63972 (16598) hydrogen bonds : bond 0.04745 ( 547) hydrogen bonds : angle 5.26463 ( 1530) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 VAL cc_start: 0.8042 (t) cc_final: 0.7725 (m) REVERT: D 31 MET cc_start: 0.7169 (mtp) cc_final: 0.6607 (ttm) REVERT: D 103 ILE cc_start: 0.8856 (pt) cc_final: 0.8581 (mm) REVERT: E 984 MET cc_start: 0.6248 (ptm) cc_final: 0.5758 (ptp) REVERT: E 1079 LEU cc_start: 0.8675 (mt) cc_final: 0.8214 (pp) REVERT: E 1150 PHE cc_start: 0.7664 (t80) cc_final: 0.7434 (t80) REVERT: E 1366 MET cc_start: 0.8753 (mmm) cc_final: 0.8311 (mmm) REVERT: E 1593 TRP cc_start: 0.8163 (OUTLIER) cc_final: 0.7083 (p90) outliers start: 25 outliers final: 16 residues processed: 91 average time/residue: 0.0749 time to fit residues: 11.6626 Evaluate side-chains 82 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain E residue 1011 SER Chi-restraints excluded: chain E residue 1094 LEU Chi-restraints excluded: chain E residue 1111 LEU Chi-restraints excluded: chain E residue 1117 VAL Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1226 ASP Chi-restraints excluded: chain E residue 1476 CYS Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1593 TRP Chi-restraints excluded: chain E residue 1643 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 31 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 0.0170 chunk 3 optimal weight: 0.6980 chunk 107 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.087173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.074313 restraints weight = 50194.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.075984 restraints weight = 27123.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.077052 restraints weight = 17966.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.077735 restraints weight = 13650.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.078253 restraints weight = 11368.086| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12222 Z= 0.116 Angle : 0.585 9.780 16598 Z= 0.299 Chirality : 0.044 0.154 1810 Planarity : 0.004 0.055 2147 Dihedral : 4.790 27.208 1641 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.41 % Favored : 96.32 % Rotamer: Outliers : 1.40 % Allowed : 9.71 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.22), residues: 1466 helix: 1.04 (0.23), residues: 524 sheet: 0.10 (0.31), residues: 282 loop : -0.17 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1561 TYR 0.021 0.001 TYR E 999 PHE 0.024 0.001 PHE A 36 TRP 0.016 0.002 TRP E1518 HIS 0.003 0.001 HIS E 900 Details of bonding type rmsd covalent geometry : bond 0.00248 (12222) covalent geometry : angle 0.58485 (16598) hydrogen bonds : bond 0.04016 ( 547) hydrogen bonds : angle 4.94409 ( 1530) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 VAL cc_start: 0.7981 (t) cc_final: 0.7682 (m) REVERT: D 31 MET cc_start: 0.6831 (mtp) cc_final: 0.6302 (ttp) REVERT: D 103 ILE cc_start: 0.8875 (pt) cc_final: 0.8570 (mm) REVERT: E 984 MET cc_start: 0.6181 (ptm) cc_final: 0.5624 (ptp) REVERT: E 997 MET cc_start: 0.7664 (ppp) cc_final: 0.7313 (ppp) REVERT: E 1004 ASP cc_start: 0.9162 (p0) cc_final: 0.8855 (p0) REVERT: E 1018 MET cc_start: 0.6315 (tpp) cc_final: 0.5987 (tpp) REVERT: E 1150 PHE cc_start: 0.7416 (t80) cc_final: 0.7210 (t80) REVERT: E 1185 MET cc_start: 0.7978 (tpp) cc_final: 0.7573 (ttm) REVERT: E 1191 MET cc_start: 0.8712 (mmm) cc_final: 0.8328 (mmm) REVERT: E 1366 MET cc_start: 0.8722 (mmm) cc_final: 0.8280 (mmm) REVERT: E 1593 TRP cc_start: 0.8045 (OUTLIER) cc_final: 0.7027 (p90) outliers start: 18 outliers final: 12 residues processed: 92 average time/residue: 0.0773 time to fit residues: 12.1290 Evaluate side-chains 81 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 1011 SER Chi-restraints excluded: chain E residue 1117 VAL Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1226 ASP Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1418 LEU Chi-restraints excluded: chain E residue 1476 CYS Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1593 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 119 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 125 optimal weight: 0.0980 chunk 70 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1001 HIS E1560 ASN E1588 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.082830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.069708 restraints weight = 49892.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.071324 restraints weight = 27297.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.072378 restraints weight = 18316.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.073078 restraints weight = 13975.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.073542 restraints weight = 11598.414| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12222 Z= 0.225 Angle : 0.680 11.131 16598 Z= 0.352 Chirality : 0.047 0.189 1810 Planarity : 0.005 0.065 2147 Dihedral : 5.067 29.744 1641 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.12 % Favored : 94.54 % Rotamer: Outliers : 1.63 % Allowed : 10.64 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.22), residues: 1466 helix: 0.78 (0.23), residues: 522 sheet: -0.07 (0.32), residues: 268 loop : -0.30 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1168 TYR 0.021 0.002 TYR E1036 PHE 0.023 0.002 PHE D 56 TRP 0.020 0.002 TRP E1518 HIS 0.006 0.001 HIS E 900 Details of bonding type rmsd covalent geometry : bond 0.00506 (12222) covalent geometry : angle 0.68050 (16598) hydrogen bonds : bond 0.04890 ( 547) hydrogen bonds : angle 5.28150 ( 1530) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 21 VAL cc_start: 0.7968 (t) cc_final: 0.7738 (m) REVERT: D 31 MET cc_start: 0.7229 (mtp) cc_final: 0.6765 (ttm) REVERT: D 103 ILE cc_start: 0.8999 (pt) cc_final: 0.8727 (mm) REVERT: E 997 MET cc_start: 0.7634 (ppp) cc_final: 0.7308 (ppp) REVERT: E 1004 ASP cc_start: 0.9136 (p0) cc_final: 0.8784 (p0) REVERT: E 1018 MET cc_start: 0.6261 (tpp) cc_final: 0.5856 (tpp) REVERT: E 1366 MET cc_start: 0.8774 (mmm) cc_final: 0.8378 (mmm) REVERT: E 1525 MET cc_start: 0.8571 (mmm) cc_final: 0.8368 (tpp) REVERT: E 1593 TRP cc_start: 0.8218 (OUTLIER) cc_final: 0.7151 (p90) outliers start: 21 outliers final: 14 residues processed: 85 average time/residue: 0.0821 time to fit residues: 11.4588 Evaluate side-chains 79 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 1011 SER Chi-restraints excluded: chain E residue 1094 LEU Chi-restraints excluded: chain E residue 1111 LEU Chi-restraints excluded: chain E residue 1117 VAL Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1226 ASP Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1418 LEU Chi-restraints excluded: chain E residue 1476 CYS Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1593 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 2 optimal weight: 0.6980 chunk 132 optimal weight: 0.0170 chunk 79 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 chunk 124 optimal weight: 2.9990 chunk 80 optimal weight: 0.1980 chunk 90 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 chunk 140 optimal weight: 0.0170 overall best weight: 0.1456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 856 GLN ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1560 ASN E1588 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.087871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.074972 restraints weight = 50780.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.076656 restraints weight = 27617.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.077743 restraints weight = 18330.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.078464 restraints weight = 13879.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.078968 restraints weight = 11429.012| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12222 Z= 0.107 Angle : 0.576 10.760 16598 Z= 0.292 Chirality : 0.044 0.213 1810 Planarity : 0.004 0.051 2147 Dihedral : 4.599 23.974 1641 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.73 % Favored : 96.93 % Rotamer: Outliers : 0.78 % Allowed : 11.73 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.22), residues: 1466 helix: 1.11 (0.23), residues: 515 sheet: 0.26 (0.31), residues: 272 loop : -0.07 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E1508 TYR 0.013 0.001 TYR E 999 PHE 0.012 0.001 PHE D 56 TRP 0.013 0.001 TRP E1076 HIS 0.003 0.001 HIS E 951 Details of bonding type rmsd covalent geometry : bond 0.00217 (12222) covalent geometry : angle 0.57624 (16598) hydrogen bonds : bond 0.03546 ( 547) hydrogen bonds : angle 4.76269 ( 1530) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 21 VAL cc_start: 0.7831 (t) cc_final: 0.7598 (m) REVERT: A 282 VAL cc_start: 0.9009 (t) cc_final: 0.8747 (m) REVERT: D 31 MET cc_start: 0.6514 (mtp) cc_final: 0.6290 (ttp) REVERT: D 103 ILE cc_start: 0.8942 (pt) cc_final: 0.8657 (mm) REVERT: D 217 SER cc_start: 0.9549 (p) cc_final: 0.9311 (t) REVERT: E 932 MET cc_start: 0.2647 (ptt) cc_final: -0.0116 (mmt) REVERT: E 984 MET cc_start: 0.5885 (ptp) cc_final: 0.5161 (ptp) REVERT: E 997 MET cc_start: 0.7586 (ppp) cc_final: 0.7224 (ppp) REVERT: E 1004 ASP cc_start: 0.9045 (p0) cc_final: 0.8802 (p0) REVERT: E 1024 MET cc_start: 0.7178 (ptt) cc_final: 0.6976 (ptm) REVERT: E 1142 MET cc_start: 0.7819 (tpt) cc_final: 0.7529 (tpt) REVERT: E 1185 MET cc_start: 0.8000 (tpp) cc_final: 0.7596 (ttm) REVERT: E 1191 MET cc_start: 0.8625 (mmm) cc_final: 0.8321 (mmm) REVERT: E 1593 TRP cc_start: 0.8048 (OUTLIER) cc_final: 0.7084 (p90) outliers start: 10 outliers final: 8 residues processed: 85 average time/residue: 0.0730 time to fit residues: 10.6024 Evaluate side-chains 81 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 1094 LEU Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1226 ASP Chi-restraints excluded: chain E residue 1418 LEU Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1593 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 117 optimal weight: 0.0470 chunk 56 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1560 ASN E1588 GLN 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 = 0.082010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.068906 restraints weight = 50118.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.070509 restraints weight = 27544.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.071526 restraints weight = 18509.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.072243 restraints weight = 14231.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.072642 restraints weight = 11799.701| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12222 Z= 0.260 Angle : 0.732 13.071 16598 Z= 0.378 Chirality : 0.049 0.556 1810 Planarity : 0.005 0.068 2147 Dihedral : 5.091 29.576 1641 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.05 % Favored : 94.61 % Rotamer: Outliers : 1.24 % Allowed : 11.50 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.22), residues: 1466 helix: 0.58 (0.23), residues: 536 sheet: -0.17 (0.31), residues: 284 loop : -0.32 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E1168 TYR 0.022 0.002 TYR E1036 PHE 0.021 0.002 PHE D 39 TRP 0.024 0.003 TRP E1518 HIS 0.008 0.001 HIS E 900 Details of bonding type rmsd covalent geometry : bond 0.00586 (12222) covalent geometry : angle 0.73156 (16598) hydrogen bonds : bond 0.05074 ( 547) hydrogen bonds : angle 5.30169 ( 1530) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 31 MET cc_start: 0.7406 (mtp) cc_final: 0.6856 (ttm) REVERT: D 103 ILE cc_start: 0.9073 (pt) cc_final: 0.8769 (mm) REVERT: E 932 MET cc_start: 0.3266 (ptt) cc_final: 0.0182 (tpt) REVERT: E 997 MET cc_start: 0.7659 (ppp) cc_final: 0.7355 (ppp) REVERT: E 1018 MET cc_start: 0.5874 (tpp) cc_final: 0.5522 (tpp) REVERT: E 1185 MET cc_start: 0.8000 (tpp) cc_final: 0.7597 (ttm) REVERT: E 1191 MET cc_start: 0.8636 (mmm) cc_final: 0.8290 (mmm) REVERT: E 1408 MET cc_start: 0.8570 (mmm) cc_final: 0.8326 (tpt) REVERT: E 1593 TRP cc_start: 0.8356 (OUTLIER) cc_final: 0.7239 (p90) outliers start: 16 outliers final: 10 residues processed: 78 average time/residue: 0.0741 time to fit residues: 9.6398 Evaluate side-chains 74 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 1011 SER Chi-restraints excluded: chain E residue 1183 HIS Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1593 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 0.0670 chunk 121 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1560 ASN E1588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.084353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.071152 restraints weight = 49437.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.072810 restraints weight = 26731.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.073908 restraints weight = 17732.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.074619 restraints weight = 13446.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.075051 restraints weight = 11121.163| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.6031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12222 Z= 0.130 Angle : 0.621 14.355 16598 Z= 0.312 Chirality : 0.044 0.171 1810 Planarity : 0.004 0.061 2147 Dihedral : 4.794 27.537 1641 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.55 % Favored : 96.11 % Rotamer: Outliers : 0.85 % Allowed : 11.89 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.22), residues: 1466 helix: 0.92 (0.23), residues: 526 sheet: -0.05 (0.31), residues: 282 loop : -0.22 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1508 TYR 0.015 0.001 TYR E 999 PHE 0.017 0.001 PHE E1304 TRP 0.014 0.001 TRP E1076 HIS 0.003 0.001 HIS E 900 Details of bonding type rmsd covalent geometry : bond 0.00285 (12222) covalent geometry : angle 0.62122 (16598) hydrogen bonds : bond 0.04100 ( 547) hydrogen bonds : angle 4.89307 ( 1530) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 31 MET cc_start: 0.6952 (mtp) cc_final: 0.6478 (ttp) REVERT: D 103 ILE cc_start: 0.9062 (pt) cc_final: 0.8752 (mm) REVERT: D 257 MET cc_start: 0.8928 (tpp) cc_final: 0.8705 (mmm) REVERT: E 932 MET cc_start: 0.3098 (ptt) cc_final: 0.0005 (tpt) REVERT: E 984 MET cc_start: 0.5800 (OUTLIER) cc_final: 0.5055 (ptp) REVERT: E 1018 MET cc_start: 0.5658 (tpp) cc_final: 0.5347 (tpp) REVERT: E 1185 MET cc_start: 0.7919 (tpp) cc_final: 0.7616 (ttm) REVERT: E 1191 MET cc_start: 0.8648 (mmm) cc_final: 0.8339 (mmm) REVERT: E 1525 MET cc_start: 0.8611 (mmm) cc_final: 0.8399 (tpp) REVERT: E 1593 TRP cc_start: 0.8218 (OUTLIER) cc_final: 0.7226 (p90) outliers start: 11 outliers final: 9 residues processed: 72 average time/residue: 0.0801 time to fit residues: 9.5632 Evaluate side-chains 75 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 984 MET Chi-restraints excluded: chain E residue 1183 HIS Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1299 THR Chi-restraints excluded: chain E residue 1418 LEU Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1593 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 8 optimal weight: 0.0270 chunk 25 optimal weight: 0.7980 chunk 106 optimal weight: 0.0000 chunk 131 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.086760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.073897 restraints weight = 50079.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.075557 restraints weight = 27039.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.076660 restraints weight = 18021.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.077360 restraints weight = 13617.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.077854 restraints weight = 11265.534| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12222 Z= 0.105 Angle : 0.574 13.114 16598 Z= 0.288 Chirality : 0.044 0.169 1810 Planarity : 0.004 0.055 2147 Dihedral : 4.407 24.677 1641 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.82 % Favored : 95.84 % Rotamer: Outliers : 0.85 % Allowed : 11.81 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.22), residues: 1466 helix: 1.22 (0.23), residues: 514 sheet: 0.07 (0.31), residues: 278 loop : -0.07 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1508 TYR 0.012 0.001 TYR E 999 PHE 0.031 0.001 PHE E1151 TRP 0.014 0.001 TRP E1076 HIS 0.003 0.001 HIS E1019 Details of bonding type rmsd covalent geometry : bond 0.00221 (12222) covalent geometry : angle 0.57391 (16598) hydrogen bonds : bond 0.03585 ( 547) hydrogen bonds : angle 4.62299 ( 1530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1989.61 seconds wall clock time: 35 minutes 3.67 seconds (2103.67 seconds total)