Starting phenix.real_space_refine on Fri Jul 3 04:59:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ly4_23587/07_2026/7ly4_23587.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ly4_23587/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7ly4_23587/07_2026/7ly4_23587.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ly4_23587/07_2026/7ly4_23587.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ly4_23587/07_2026/7ly4_23587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ly4_23587/07_2026/7ly4_23587.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ly4_23587/07_2026/7ly4_23587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ly4_23587/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.87, per 1000 atoms: 0.24 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: 1.34 Conformation dependent library (CDL) restraints added in 553.0 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: 0.43 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: 2.36 Time building geometry restraints manager: 1.69 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=" C10 FMN D 401 " pdb=" C4A FMN D 401 " ideal model delta sigma weight residual 1.390 1.549 -0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C10 FMN A 401 " pdb=" C4A FMN A 401 " ideal model delta sigma weight residual 1.390 1.542 -0.152 2.00e-02 2.50e+03 5.80e+01 bond pdb=" C4 FMN D 401 " pdb=" C4A FMN D 401 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.21e+01 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 ... (remaining 12217 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 15581 3.33 - 6.66: 936 6.66 - 9.99: 75 9.99 - 13.32: 4 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 - 32.91: 7192 32.91 - 65.82: 85 65.82 - 98.73: 9 98.73 - 131.63: 1 131.63 - 164.54: 3 Dihedral angle restraints: 7290 sinusoidal: 2967 harmonic: 4323 Sorted by residual: dihedral pdb=" C10 FMN A 401 " pdb=" C1' FMN A 401 " pdb=" N10 FMN A 401 " pdb=" C2' FMN A 401 " ideal model delta sinusoidal sigma weight residual 257.59 93.05 164.54 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C5' FMN A 401 " pdb=" O5' FMN A 401 " pdb=" P FMN A 401 " pdb=" O1P FMN A 401 " ideal model delta sinusoidal sigma weight residual 75.26 -120.91 -163.83 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C10 FMN D 401 " pdb=" C1' FMN D 401 " pdb=" N10 FMN D 401 " pdb=" C2' FMN D 401 " ideal model delta sinusoidal sigma weight residual 257.59 102.93 154.66 1 2.00e+01 2.50e-03 4.57e+01 ... (remaining 7287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1306 0.103 - 0.206: 429 0.206 - 0.309: 73 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: 2145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN A 401 " 0.683 2.00e-02 2.50e+03 2.38e-01 2.69e+03 pdb=" C10 FMN A 401 " 0.026 2.00e-02 2.50e+03 pdb=" C2 FMN A 401 " -0.240 2.00e-02 2.50e+03 pdb=" C4 FMN A 401 " 0.128 2.00e-02 2.50e+03 pdb=" C4A FMN A 401 " 0.105 2.00e-02 2.50e+03 pdb=" C5A FMN A 401 " 0.073 2.00e-02 2.50e+03 pdb=" C6 FMN A 401 " 0.004 2.00e-02 2.50e+03 pdb=" C7 FMN A 401 " -0.085 2.00e-02 2.50e+03 pdb=" C7M FMN A 401 " -0.148 2.00e-02 2.50e+03 pdb=" C8 FMN A 401 " -0.123 2.00e-02 2.50e+03 pdb=" C8M FMN A 401 " -0.235 2.00e-02 2.50e+03 pdb=" C9 FMN A 401 " -0.051 2.00e-02 2.50e+03 pdb=" C9A FMN A 401 " 0.056 2.00e-02 2.50e+03 pdb=" N1 FMN A 401 " -0.150 2.00e-02 2.50e+03 pdb=" N10 FMN A 401 " 0.151 2.00e-02 2.50e+03 pdb=" N3 FMN A 401 " 0.022 2.00e-02 2.50e+03 pdb=" N5 FMN A 401 " 0.132 2.00e-02 2.50e+03 pdb=" O2 FMN A 401 " -0.555 2.00e-02 2.50e+03 pdb=" O4 FMN A 401 " 0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN D 401 " -0.777 2.00e-02 2.50e+03 2.29e-01 2.50e+03 pdb=" C10 FMN D 401 " 0.033 2.00e-02 2.50e+03 pdb=" C2 FMN D 401 " 0.220 2.00e-02 2.50e+03 pdb=" C4 FMN D 401 " -0.086 2.00e-02 2.50e+03 pdb=" C4A FMN D 401 " -0.079 2.00e-02 2.50e+03 pdb=" C5A FMN D 401 " -0.076 2.00e-02 2.50e+03 pdb=" C6 FMN D 401 " -0.049 2.00e-02 2.50e+03 pdb=" C7 FMN D 401 " 0.049 2.00e-02 2.50e+03 pdb=" C7M FMN D 401 " 0.050 2.00e-02 2.50e+03 pdb=" C8 FMN D 401 " 0.143 2.00e-02 2.50e+03 pdb=" C8M FMN D 401 " 0.245 2.00e-02 2.50e+03 pdb=" C9 FMN D 401 " 0.123 2.00e-02 2.50e+03 pdb=" C9A FMN D 401 " 0.001 2.00e-02 2.50e+03 pdb=" N1 FMN D 401 " 0.187 2.00e-02 2.50e+03 pdb=" N10 FMN D 401 " -0.055 2.00e-02 2.50e+03 pdb=" N3 FMN D 401 " 0.076 2.00e-02 2.50e+03 pdb=" N5 FMN D 401 " -0.148 2.00e-02 2.50e+03 pdb=" O2 FMN D 401 " 0.342 2.00e-02 2.50e+03 pdb=" O4 FMN D 401 " -0.200 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 2142 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: 9.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 13.210 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 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= 1.026 Angle : 1.728 16.647 16598 Z= 1.183 Chirality : 0.097 0.515 1810 Planarity : 0.012 0.238 2145 Dihedral : 11.371 164.542 4512 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/Z covalent geometry : bond 0.01916 / 1.03 (12222) covalent geometry : angle 1.72758 / 1.18 (16598) hydrogen bonds : bond 0.17843 / 11.62 ( 547) hydrogen bonds : angle 7.68096 / 5.25 ( 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 : 0.482 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: 0.1183 time to fit residues: 34.3415 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 : 0.449 ------------------------------------------------------------------------------- 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... 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 = 0.3894 r_free = 0.3894 target = 0.091657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.078179 restraints weight = 49068.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.079962 restraints weight = 26769.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.081117 restraints weight = 17857.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.081924 restraints weight = 13553.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.082445 restraints weight = 11106.547| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2871 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= 0.170 Angle : 0.691 8.851 16598 Z= 0.370 Chirality : 0.046 0.174 1810 Planarity : 0.005 0.058 2145 Dihedral : 8.810 172.299 1637 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.39 % Favored : 97.41 % Rotamer: Outliers : 1.40 % Allowed : 5.05 % 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: 1.01 (0.21), residues: 1466 helix: 1.10 (0.22), residues: 522 sheet: 0.55 (0.31), residues: 285 loop : 0.56 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 55 TYR 0.015 0.002 TYR E1036 PHE 0.024 0.002 PHE E1150 TRP 0.016 0.002 TRP E1076 HIS 0.009 0.001 HIS E1382 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (12222) covalent geometry : angle 0.69069 / 0.37 (16598) hydrogen bonds : bond 0.05611 / 3.61 ( 547) hydrogen bonds : angle 5.60502 / 3.86 ( 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 143 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7965 (tp) cc_final: 0.7734 (tt) REVERT: D 103 ILE cc_start: 0.8731 (pt) cc_final: 0.8381 (mm) REVERT: D 297 ASN cc_start: 0.7316 (t0) cc_final: 0.6960 (t0) REVERT: E 932 MET cc_start: 0.3919 (mtm) cc_final: 0.3066 (mmt) REVERT: E 984 MET cc_start: 0.5244 (ptm) cc_final: 0.4778 (ppp) REVERT: E 1118 PHE cc_start: 0.6165 (m-80) cc_final: 0.5725 (m-80) REVERT: E 1185 MET cc_start: 0.7409 (tpp) cc_final: 0.6985 (ttm) REVERT: E 1281 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6769 (m-30) REVERT: E 1366 MET cc_start: 0.8712 (mmm) cc_final: 0.8452 (mmm) outliers start: 18 outliers final: 10 residues processed: 137 average time/residue: 0.0927 time to fit residues: 19.4485 Evaluate side-chains 95 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 161 THR 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 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: 2.9990 chunk 101 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN A 280 ASN D 216 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.088913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.075589 restraints weight = 49762.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.077298 restraints weight = 26894.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.078446 restraints weight = 17956.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.079175 restraints weight = 13596.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.079688 restraints weight = 11242.714| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12222 Z= 0.164 Angle : 0.641 8.219 16598 Z= 0.339 Chirality : 0.045 0.147 1810 Planarity : 0.005 0.059 2145 Dihedral : 8.453 169.096 1637 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.80 % Favored : 96.93 % Rotamer: Outliers : 1.63 % Allowed : 7.15 % Favored : 91.22 % 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: 0.91 (0.22), residues: 1466 helix: 1.18 (0.23), residues: 521 sheet: 0.63 (0.32), residues: 270 loop : 0.28 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1120 TYR 0.024 0.002 TYR E 999 PHE 0.018 0.002 PHE E1150 TRP 0.015 0.002 TRP E1518 HIS 0.010 0.001 HIS E 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (12222) covalent geometry : angle 0.64149 / 0.34 (16598) hydrogen bonds : bond 0.04941 / 3.14 ( 547) hydrogen bonds : angle 5.21688 / 3.60 ( 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: 21 poor density : 89 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LYS cc_start: 0.7434 (pttt) cc_final: 0.7219 (mmmm) REVERT: D 31 MET cc_start: 0.7018 (mtp) cc_final: 0.5904 (ttm) REVERT: D 103 ILE cc_start: 0.8818 (pt) cc_final: 0.8510 (mm) REVERT: E 932 MET cc_start: 0.4726 (mtm) cc_final: 0.3567 (mmt) REVERT: E 984 MET cc_start: 0.5695 (ptm) cc_final: 0.4487 (ptp) REVERT: E 1079 LEU cc_start: 0.8570 (mt) cc_final: 0.8144 (pp) REVERT: E 1366 MET cc_start: 0.8737 (mmm) cc_final: 0.8485 (mmm) REVERT: E 1418 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8227 (tt) REVERT: E 1607 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.8495 (m-80) outliers start: 21 outliers final: 14 residues processed: 105 average time/residue: 0.0887 time to fit residues: 14.1037 Evaluate side-chains 87 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 169 LEU 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 161 THR 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 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: 0.9980 chunk 75 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 HIS ** E 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1063 ASN ** 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 = 0.3714 r_free = 0.3714 target = 0.083010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.069741 restraints weight = 49940.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.071409 restraints weight = 27080.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.072500 restraints weight = 18121.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.073176 restraints weight = 13802.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.073672 restraints weight = 11539.842| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 12222 Z= 0.319 Angle : 0.818 9.431 16598 Z= 0.433 Chirality : 0.050 0.163 1810 Planarity : 0.006 0.079 2145 Dihedral : 8.621 160.289 1637 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.02 % Favored : 95.70 % Rotamer: Outliers : 1.94 % Allowed : 7.77 % Favored : 90.29 % 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: -0.11 (0.21), residues: 1466 helix: 0.37 (0.22), residues: 533 sheet: 0.00 (0.32), residues: 268 loop : -0.33 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E1168 TYR 0.045 0.002 TYR E 999 PHE 0.026 0.003 PHE E 850 TRP 0.031 0.003 TRP E1518 HIS 0.006 0.002 HIS E1019 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.32 (12222) covalent geometry : angle 0.81765 / 0.43 (16598) hydrogen bonds : bond 0.06118 / 3.90 ( 547) hydrogen bonds : angle 5.80501 / 3.99 ( 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 104 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.306 Fit side-chains REVERT: A 21 VAL cc_start: 0.7834 (t) cc_final: 0.7592 (m) REVERT: D 31 MET cc_start: 0.7395 (mtp) cc_final: 0.6664 (ttm) REVERT: D 103 ILE cc_start: 0.8846 (pt) cc_final: 0.8583 (mm) REVERT: E 1018 MET cc_start: 0.6524 (tpp) cc_final: 0.6271 (tpp) REVERT: E 1150 PHE cc_start: 0.7555 (t80) cc_final: 0.7317 (t80) REVERT: E 1252 MET cc_start: 0.7341 (tpp) cc_final: 0.7061 (tpt) REVERT: E 1366 MET cc_start: 0.8689 (mmm) cc_final: 0.8347 (mmm) REVERT: E 1418 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8399 (tt) REVERT: E 1593 TRP cc_start: 0.8189 (OUTLIER) cc_final: 0.7014 (p90) outliers start: 25 outliers final: 16 residues processed: 98 average time/residue: 0.0748 time to fit residues: 11.7129 Evaluate side-chains 82 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 118 LEU 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 1226 ASP Chi-restraints excluded: chain E residue 1396 CYS Chi-restraints excluded: chain E residue 1418 LEU Chi-restraints excluded: chain E residue 1463 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3773 r_free = 0.3773 target = 0.085650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.072706 restraints weight = 50097.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.074362 restraints weight = 27176.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.075450 restraints weight = 18163.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.076151 restraints weight = 13842.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.076660 restraints weight = 11492.253| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12222 Z= 0.151 Angle : 0.619 10.378 16598 Z= 0.323 Chirality : 0.045 0.153 1810 Planarity : 0.004 0.060 2145 Dihedral : 8.362 167.143 1637 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.09 % Favored : 95.63 % Rotamer: Outliers : 1.71 % Allowed : 9.56 % 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: 0.87 (0.23), residues: 527 sheet: 0.06 (0.31), residues: 282 loop : -0.26 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1504 TYR 0.024 0.001 TYR E 999 PHE 0.031 0.001 PHE D 56 TRP 0.016 0.002 TRP E1076 HIS 0.004 0.001 HIS E 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (12222) covalent geometry : angle 0.61949 / 0.32 (16598) hydrogen bonds : bond 0.04616 / 2.97 ( 547) hydrogen bonds : angle 5.21094 / 3.61 ( 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: 22 poor density : 73 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 VAL cc_start: 0.8053 (t) cc_final: 0.7745 (m) REVERT: D 31 MET cc_start: 0.7175 (mtp) cc_final: 0.6370 (ttm) REVERT: D 103 ILE cc_start: 0.8823 (pt) cc_final: 0.8542 (mm) REVERT: E 997 MET cc_start: 0.7650 (ppp) cc_final: 0.7286 (ppp) REVERT: E 1150 PHE cc_start: 0.7619 (t80) cc_final: 0.7398 (t80) REVERT: E 1199 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7640 (pp) REVERT: E 1366 MET cc_start: 0.8765 (mmm) cc_final: 0.8466 (mmm) REVERT: E 1593 TRP cc_start: 0.8159 (OUTLIER) cc_final: 0.7050 (p90) outliers start: 22 outliers final: 13 residues processed: 91 average time/residue: 0.0709 time to fit residues: 10.8289 Evaluate side-chains 80 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 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 1199 LEU 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 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: 2.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3756 r_free = 0.3756 target = 0.084979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.071826 restraints weight = 49270.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.073484 restraints weight = 26717.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.074576 restraints weight = 17844.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.075284 restraints weight = 13565.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.075776 restraints weight = 11238.206| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12222 Z= 0.139 Angle : 0.602 9.802 16598 Z= 0.311 Chirality : 0.045 0.152 1810 Planarity : 0.004 0.059 2145 Dihedral : 8.209 167.871 1637 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.82 % Favored : 95.84 % Rotamer: Outliers : 1.32 % Allowed : 10.41 % Favored : 88.27 % 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: 0.32 (0.22), residues: 1466 helix: 0.95 (0.23), residues: 524 sheet: 0.05 (0.31), residues: 280 loop : -0.20 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 978 TYR 0.019 0.001 TYR E 999 PHE 0.022 0.001 PHE A 36 TRP 0.022 0.002 TRP E1518 HIS 0.004 0.001 HIS E 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (12222) covalent geometry : angle 0.60211 / 0.31 (16598) hydrogen bonds : bond 0.04268 / 2.76 ( 547) hydrogen bonds : angle 5.06730 / 3.51 ( 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 91 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 VAL cc_start: 0.8041 (t) cc_final: 0.7760 (m) REVERT: D 31 MET cc_start: 0.7110 (mtp) cc_final: 0.6458 (ttm) REVERT: D 103 ILE cc_start: 0.8896 (pt) cc_final: 0.8585 (mm) REVERT: E 984 MET cc_start: 0.4513 (ppp) cc_final: 0.4001 (ppp) REVERT: E 997 MET cc_start: 0.7702 (ppp) cc_final: 0.7273 (ppp) REVERT: E 1199 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7702 (pp) REVERT: E 1385 GLU cc_start: 0.6935 (pm20) cc_final: 0.6712 (pp20) REVERT: E 1593 TRP cc_start: 0.8144 (OUTLIER) cc_final: 0.7110 (p90) outliers start: 17 outliers final: 14 residues processed: 87 average time/residue: 0.0701 time to fit residues: 10.1765 Evaluate side-chains 87 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 1199 LEU 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: 0.2980 chunk 74 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.083490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.070253 restraints weight = 49828.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.071864 restraints weight = 27420.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.072933 restraints weight = 18428.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.073637 restraints weight = 14098.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.074094 restraints weight = 11731.208| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12222 Z= 0.179 Angle : 0.641 10.138 16598 Z= 0.332 Chirality : 0.045 0.151 1810 Planarity : 0.004 0.064 2145 Dihedral : 8.174 166.597 1637 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.84 % Favored : 94.82 % Rotamer: Outliers : 1.86 % Allowed : 10.57 % Favored : 87.57 % 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: 0.08 (0.22), residues: 1466 helix: 0.68 (0.23), residues: 535 sheet: -0.05 (0.31), residues: 282 loop : -0.30 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1168 TYR 0.020 0.002 TYR E1036 PHE 0.019 0.002 PHE D 56 TRP 0.015 0.002 TRP E1076 HIS 0.005 0.001 HIS E 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (12222) covalent geometry : angle 0.64058 / 0.33 (16598) hydrogen bonds : bond 0.04680 / 3.02 ( 547) hydrogen bonds : angle 5.18805 / 3.58 ( 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 98 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 VAL cc_start: 0.7942 (t) cc_final: 0.7732 (m) REVERT: D 31 MET cc_start: 0.7143 (mtp) cc_final: 0.6577 (ttm) REVERT: D 103 ILE cc_start: 0.8983 (pt) cc_final: 0.8714 (mm) REVERT: E 984 MET cc_start: 0.4210 (ppp) cc_final: 0.3897 (ppp) REVERT: E 997 MET cc_start: 0.7618 (ppp) cc_final: 0.7239 (ppp) REVERT: E 1004 ASP cc_start: 0.9171 (p0) cc_final: 0.8825 (p0) REVERT: E 1018 MET cc_start: 0.5939 (tpp) cc_final: 0.5632 (tpp) REVERT: E 1191 MET cc_start: 0.8646 (mmm) cc_final: 0.8296 (mmm) REVERT: E 1593 TRP cc_start: 0.8209 (OUTLIER) cc_final: 0.7155 (p90) outliers start: 24 outliers final: 20 residues processed: 93 average time/residue: 0.0703 time to fit residues: 10.8144 Evaluate side-chains 90 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain A residue 142 ILE 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 161 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain E residue 977 PHE 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 1183 HIS 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: 0.2980 chunk 79 optimal weight: 2.9990 chunk 9 optimal weight: 0.0970 chunk 124 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 chunk 130 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 140 optimal weight: 0.0770 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.086533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.073309 restraints weight = 50175.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.074947 restraints weight = 27403.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.076029 restraints weight = 18329.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.076754 restraints weight = 13952.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.077222 restraints weight = 11556.976| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5800 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= 0.108 Angle : 0.570 10.994 16598 Z= 0.290 Chirality : 0.044 0.257 1810 Planarity : 0.004 0.054 2145 Dihedral : 7.939 170.092 1637 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.86 % Favored : 96.79 % Rotamer: Outliers : 1.01 % Allowed : 11.81 % Favored : 87.18 % 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: 0.46 (0.22), residues: 1466 helix: 1.12 (0.23), residues: 514 sheet: 0.03 (0.31), residues: 281 loop : -0.10 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 978 TYR 0.013 0.001 TYR E 999 PHE 0.015 0.001 PHE E1304 TRP 0.014 0.001 TRP E1076 HIS 0.003 0.001 HIS E 951 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (12222) covalent geometry : angle 0.57018 / 0.29 (16598) hydrogen bonds : bond 0.03649 / 2.38 ( 547) hydrogen bonds : angle 4.82248 / 3.35 ( 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 94 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 VAL cc_start: 0.7955 (t) cc_final: 0.7749 (m) REVERT: D 31 MET cc_start: 0.6767 (mtp) cc_final: 0.6306 (ttp) REVERT: D 103 ILE cc_start: 0.8974 (pt) cc_final: 0.8688 (mm) REVERT: D 217 SER cc_start: 0.9540 (p) cc_final: 0.9302 (t) REVERT: E 932 MET cc_start: 0.2953 (ptt) cc_final: 0.0089 (mmt) REVERT: E 984 MET cc_start: 0.4870 (ppp) cc_final: 0.4313 (ppp) REVERT: E 997 MET cc_start: 0.7662 (ppp) cc_final: 0.7332 (ppp) REVERT: E 1004 ASP cc_start: 0.9223 (p0) cc_final: 0.9014 (p0) REVERT: E 1018 MET cc_start: 0.5935 (tpp) cc_final: 0.5683 (tpp) REVERT: E 1185 MET cc_start: 0.7883 (tpp) cc_final: 0.7484 (ttm) REVERT: E 1191 MET cc_start: 0.8599 (mmm) cc_final: 0.8356 (mmm) REVERT: E 1593 TRP cc_start: 0.8096 (OUTLIER) cc_final: 0.7116 (p90) outliers start: 13 outliers final: 9 residues processed: 92 average time/residue: 0.0707 time to fit residues: 10.7773 Evaluate side-chains 82 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain A 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 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: 0.9990 chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 117 optimal weight: 0.0470 chunk 56 optimal weight: 3.9990 chunk 120 optimal weight: 0.0870 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN ** E 875 GLN ** 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 = 0.3765 r_free = 0.3765 target = 0.085425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.072092 restraints weight = 49617.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.073757 restraints weight = 27281.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.074849 restraints weight = 18280.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.075552 restraints weight = 13925.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.076062 restraints weight = 11556.352| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12222 Z= 0.119 Angle : 0.590 12.564 16598 Z= 0.298 Chirality : 0.045 0.404 1810 Planarity : 0.004 0.056 2145 Dihedral : 7.814 169.035 1637 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.82 % Favored : 95.84 % Rotamer: Outliers : 1.01 % Allowed : 12.20 % Favored : 86.79 % 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: 0.47 (0.22), residues: 1466 helix: 1.05 (0.23), residues: 526 sheet: 0.20 (0.32), residues: 271 loop : -0.12 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1168 TYR 0.014 0.001 TYR E1036 PHE 0.013 0.001 PHE E1304 TRP 0.014 0.001 TRP E1076 HIS 0.003 0.001 HIS E 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (12222) covalent geometry : angle 0.59024 / 0.30 (16598) hydrogen bonds : bond 0.03845 / 2.49 ( 547) hydrogen bonds : angle 4.80197 / 3.34 ( 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 94 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 VAL cc_start: 0.8017 (t) cc_final: 0.7804 (m) REVERT: D 31 MET cc_start: 0.6944 (mtp) cc_final: 0.6472 (ttp) REVERT: D 103 ILE cc_start: 0.9002 (pt) cc_final: 0.8682 (mm) REVERT: E 852 LEU cc_start: 0.5828 (mt) cc_final: 0.5587 (tp) REVERT: E 932 MET cc_start: 0.3065 (ptt) cc_final: 0.0142 (mmt) REVERT: E 984 MET cc_start: 0.4918 (ppp) cc_final: 0.4344 (ppp) REVERT: E 997 MET cc_start: 0.7617 (ppp) cc_final: 0.7302 (ppp) REVERT: E 1004 ASP cc_start: 0.9107 (p0) cc_final: 0.8895 (p0) REVERT: E 1185 MET cc_start: 0.7866 (tpp) cc_final: 0.7552 (ttm) REVERT: E 1408 MET cc_start: 0.8485 (mmm) cc_final: 0.8255 (tpt) REVERT: E 1593 TRP cc_start: 0.8098 (OUTLIER) cc_final: 0.7158 (p90) outliers start: 13 outliers final: 10 residues processed: 91 average time/residue: 0.0710 time to fit residues: 10.6012 Evaluate side-chains 85 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 1011 SER Chi-restraints excluded: chain E residue 1094 LEU Chi-restraints excluded: chain E residue 1111 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 121 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 139 optimal weight: 0.3980 chunk 124 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 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 = 0.3721 r_free = 0.3721 target = 0.083327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.070121 restraints weight = 50128.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.071736 restraints weight = 27518.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.072754 restraints weight = 18468.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.073470 restraints weight = 14190.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.073938 restraints weight = 11770.017| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12222 Z= 0.189 Angle : 0.656 13.484 16598 Z= 0.337 Chirality : 0.046 0.407 1810 Planarity : 0.004 0.065 2145 Dihedral : 7.925 166.447 1637 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.77 % Favored : 94.88 % Rotamer: Outliers : 0.85 % Allowed : 12.51 % Favored : 86.64 % 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: 0.16 (0.22), residues: 1466 helix: 0.74 (0.23), residues: 536 sheet: 0.08 (0.32), residues: 271 loop : -0.29 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1168 TYR 0.019 0.002 TYR E1036 PHE 0.022 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/Z covalent geometry : bond 0.00426 / 0.19 (12222) covalent geometry : angle 0.65611 / 0.34 (16598) hydrogen bonds : bond 0.04474 / 2.88 ( 547) hydrogen bonds : angle 5.05463 / 3.50 ( 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 86 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 21 VAL cc_start: 0.7990 (t) cc_final: 0.7777 (m) REVERT: A 78 VAL cc_start: 0.9550 (m) cc_final: 0.9325 (p) REVERT: D 31 MET cc_start: 0.7181 (mtp) cc_final: 0.6756 (ttm) REVERT: D 103 ILE cc_start: 0.9067 (pt) cc_final: 0.8750 (mm) REVERT: E 932 MET cc_start: 0.3087 (ptt) cc_final: 0.0003 (tpt) REVERT: E 984 MET cc_start: 0.4870 (ppp) cc_final: 0.4566 (ppp) REVERT: E 997 MET cc_start: 0.7633 (ppp) cc_final: 0.7259 (ppp) REVERT: E 1004 ASP cc_start: 0.9124 (p0) cc_final: 0.8912 (p0) REVERT: E 1185 MET cc_start: 0.7964 (tpp) cc_final: 0.7634 (ttm) REVERT: E 1408 MET cc_start: 0.8565 (mmm) cc_final: 0.8331 (tpt) REVERT: E 1593 TRP cc_start: 0.8257 (OUTLIER) cc_final: 0.7264 (p90) outliers start: 11 outliers final: 10 residues processed: 85 average time/residue: 0.0750 time to fit residues: 10.6165 Evaluate side-chains 82 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 1011 SER Chi-restraints excluded: chain E residue 1094 LEU Chi-restraints excluded: chain E residue 1111 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 111 optimal weight: 0.5980 chunk 13 optimal weight: 0.0670 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3760 r_free = 0.3760 target = 0.085158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.071872 restraints weight = 49894.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.073460 restraints weight = 27380.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.074557 restraints weight = 18497.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.075247 restraints weight = 14109.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.075739 restraints weight = 11756.278| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.6164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12222 Z= 0.116 Angle : 0.614 14.031 16598 Z= 0.305 Chirality : 0.044 0.219 1810 Planarity : 0.004 0.057 2145 Dihedral : 7.811 168.966 1637 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.21 % Favored : 96.45 % Rotamer: Outliers : 0.78 % Allowed : 12.67 % Favored : 86.56 % 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: 0.38 (0.22), residues: 1466 helix: 1.02 (0.23), residues: 526 sheet: 0.09 (0.31), residues: 272 loop : -0.19 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 55 TYR 0.013 0.001 TYR E1036 PHE 0.013 0.001 PHE D 56 TRP 0.014 0.001 TRP E1076 HIS 0.003 0.001 HIS E 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (12222) covalent geometry : angle 0.61419 / 0.31 (16598) hydrogen bonds : bond 0.03819 / 2.48 ( 547) hydrogen bonds : angle 4.77029 / 3.32 ( 1530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1868.83 seconds wall clock time: 33 minutes 1.76 seconds (1981.76 seconds total)