Starting phenix.real_space_refine on Thu Jul 2 22:52:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ky9_23072/07_2026/7ky9_23072.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ky9_23072/07_2026/7ky9_23072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ky9_23072/07_2026/7ky9_23072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ky9_23072/07_2026/7ky9_23072.map" model { file = "/net/cci-nas-00/data/ceres_data/7ky9_23072/07_2026/7ky9_23072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ky9_23072/07_2026/7ky9_23072.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ky9_23072/07_2026/7ky9_23072.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ky9_23072/07_2026/7ky9_23072.cif" } resolution = 4.05 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= 0.002 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 2 5.49 5 Mg 2 5.21 5 S 53 5.16 5 C 6646 2.51 5 N 1690 2.21 5 O 1956 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10354 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 7229 Classifications: {'peptide': 910} Link IDs: {'PTRANS': 25, 'TRANS': 884} Chain breaks: 2 Chain: "B" Number of atoms: 2959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2959 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.97, per 1000 atoms: 0.19 Number of scatterers: 10354 At special positions: 0 Unit cell: (129.682, 114.814, 130.508, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 53 16.00 P 2 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 1956 8.00 N 1690 7.00 C 6646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.03 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=1, symmetry=0 Links applied ALPHA1-4 " NAG C 2 " - " MAN C 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B1001 " - " ASN B 298 " " NAG C 1 " - " ASN B 240 " " NAG D 1 " - " ASN B 256 " " NAG E 1 " - " ASN B 332 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 280.1 milliseconds 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2384 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 51.5% alpha, 10.4% 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 282 through 301 removed outlier: 3.600A pdb=" N SER A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 619 removed outlier: 3.682A pdb=" N ARG A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY A 617 " --> pdb=" O GLY A 613 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 654 Processing helix chain 'A' and resid 661 through 679 removed outlier: 5.005A pdb=" N GLU A 667 " --> pdb=" O TYR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 684 Processing helix chain 'A' and resid 700 through 705 removed outlier: 3.694A pdb=" N GLY A 704 " --> pdb=" O ASP A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 Processing helix chain 'A' and resid 754 through 779 removed outlier: 3.511A pdb=" N SER A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 799 removed outlier: 3.873A pdb=" N VAL A 797 " --> pdb=" O SER A 793 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 798 " --> pdb=" O LYS A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 821 Processing helix chain 'A' and resid 843 through 857 Processing helix chain 'A' and resid 918 through 925 removed outlier: 4.200A pdb=" N ARG A 925 " --> pdb=" O VAL A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 949 Processing helix chain 'A' and resid 962 through 977 Processing helix chain 'A' and resid 983 through 995 Processing helix chain 'A' and resid 1013 through 1024 removed outlier: 3.796A pdb=" N SER A1017 " --> pdb=" O GLY A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1046 Processing helix chain 'A' and resid 1063 through 1069 removed outlier: 4.038A pdb=" N GLU A1067 " --> pdb=" O GLU A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1087 removed outlier: 3.930A pdb=" N VAL A1075 " --> pdb=" O ASP A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1104 Processing helix chain 'A' and resid 1116 through 1124 removed outlier: 3.782A pdb=" N LEU A1124 " --> pdb=" O LEU A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1137 Processing helix chain 'A' and resid 1149 through 1163 Processing helix chain 'A' and resid 1177 through 1183 Processing helix chain 'A' and resid 1193 through 1200 removed outlier: 3.792A pdb=" N GLN A1197 " --> pdb=" O GLU A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1210 No H-bonds generated for 'chain 'A' and resid 1208 through 1210' Processing helix chain 'A' and resid 1211 through 1218 removed outlier: 3.505A pdb=" N LEU A1217 " --> pdb=" O THR A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1249 Proline residue: A1232 - end of helix removed outlier: 3.712A pdb=" N VAL A1239 " --> pdb=" O PHE A1235 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE A1240 " --> pdb=" O TYR A1236 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N PHE A1241 " --> pdb=" O LYS A1237 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR A1242 " --> pdb=" O ASN A1238 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A1245 " --> pdb=" O PHE A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1255 removed outlier: 4.622A pdb=" N ASN A1253 " --> pdb=" O ILE A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1271 removed outlier: 3.775A pdb=" N PHE A1267 " --> pdb=" O THR A1263 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR A1268 " --> pdb=" O TYR A1264 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ASN A1269 " --> pdb=" O LEU A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1274 through 1283 removed outlier: 3.931A pdb=" N ILE A1278 " --> pdb=" O SER A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1295 Processing helix chain 'A' and resid 1296 through 1298 No H-bonds generated for 'chain 'A' and resid 1296 through 1298' Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1309 through 1334 removed outlier: 3.502A pdb=" N PHE A1313 " --> pdb=" O ASN A1309 " (cutoff:3.500A) Proline residue: A1331 - end of helix Processing helix chain 'A' and resid 1350 through 1374 Processing helix chain 'A' and resid 1380 through 1399 removed outlier: 3.622A pdb=" N PHE A1384 " --> pdb=" O PHE A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1406 Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1418 through 1447 removed outlier: 4.107A pdb=" N TRP A1422 " --> pdb=" O GLN A1418 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A1427 " --> pdb=" O ALA A1423 " (cutoff:3.500A) Proline residue: A1435 - end of helix Processing helix chain 'A' and resid 1449 through 1461 removed outlier: 3.733A pdb=" N GLY A1461 " --> pdb=" O MET A1457 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 71 through 98 Proline residue: B 77 - end of helix Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 267 through 273 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.879A pdb=" N GLU B 290 " --> pdb=" O PRO B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 removed outlier: 4.055A pdb=" N TRP B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.683A pdb=" N PHE B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 399 Processing helix chain 'B' and resid 405 through 409 Processing sheet with id=AA1, first strand: chain 'A' and resid 1055 through 1057 removed outlier: 6.473A pdb=" N VAL A1113 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL A1143 " --> pdb=" O LEU A1028 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A1030 " --> pdb=" O VAL A1143 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS A1145 " --> pdb=" O VAL A1030 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE A 709 " --> pdb=" O TRP A1029 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU A1031 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER A 711 " --> pdb=" O LEU A1031 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR A 708 " --> pdb=" O LEU A1169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 732 through 734 removed outlier: 5.520A pdb=" N VAL A 721 " --> pdb=" O ARG A1009 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A1009 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS A 725 " --> pdb=" O ALA A1005 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ALA A1005 " --> pdb=" O LYS A 725 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N CYS A 727 " --> pdb=" O GLY A1003 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY A1003 " --> pdb=" O CYS A 727 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE A 729 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N LEU A1001 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 956 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY A1003 " --> pdb=" O LEU A 954 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A 954 " --> pdb=" O GLY A1003 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA A1005 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG A 952 " --> pdb=" O ALA A1005 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 858 through 860 Processing sheet with id=AA4, first strand: chain 'A' and resid 1188 through 1190 Processing sheet with id=AA5, first strand: chain 'A' and resid 1377 through 1378 Processing sheet with id=AA6, first strand: chain 'B' and resid 126 through 129 removed outlier: 6.897A pdb=" N VAL B 173 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE B 329 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 175 " --> pdb=" O ILE B 327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 119 through 120 removed outlier: 4.035A pdb=" N GLN B 341 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR B 248 " --> pdb=" O GLN B 341 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP B 343 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N GLN B 246 " --> pdb=" O ASP B 343 " (cutoff:3.500A) 493 hydrogen bonds defined for protein. 1386 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: 1.71 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3265 1.34 - 1.46: 2385 1.46 - 1.58: 4853 1.58 - 1.69: 3 1.69 - 1.81: 80 Bond restraints: 10586 Sorted by residual: bond pdb=" F1 ALF A1702 " pdb="AL ALF A1702 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" F2 ALF A1702 " pdb="AL ALF A1702 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" F4 ALF A1702 " pdb="AL ALF A1702 " ideal model delta sigma weight residual 1.686 1.785 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" F3 ALF A1702 " pdb="AL ALF A1702 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C5 MAN C 3 " pdb=" O5 MAN C 3 " ideal model delta sigma weight residual 1.418 1.461 -0.043 2.00e-02 2.50e+03 4.61e+00 ... (remaining 10581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.24: 14356 14.24 - 28.48: 5 28.48 - 42.71: 0 42.71 - 56.95: 0 56.95 - 71.19: 2 Bond angle restraints: 14363 Sorted by residual: angle pdb=" F1 ALF A1702 " pdb="AL ALF A1702 " pdb=" F2 ALF A1702 " ideal model delta sigma weight residual 108.68 179.87 -71.19 3.00e+00 1.11e-01 5.63e+02 angle pdb=" F3 ALF A1702 " pdb="AL ALF A1702 " pdb=" F4 ALF A1702 " ideal model delta sigma weight residual 109.63 179.94 -70.31 3.00e+00 1.11e-01 5.49e+02 angle pdb=" F2 ALF A1702 " pdb="AL ALF A1702 " pdb=" F4 ALF A1702 " ideal model delta sigma weight residual 110.21 90.13 20.08 3.00e+00 1.11e-01 4.48e+01 angle pdb=" F2 ALF A1702 " pdb="AL ALF A1702 " pdb=" F3 ALF A1702 " ideal model delta sigma weight residual 109.59 89.89 19.70 3.00e+00 1.11e-01 4.31e+01 angle pdb=" F1 ALF A1702 " pdb="AL ALF A1702 " pdb=" F3 ALF A1702 " ideal model delta sigma weight residual 109.69 90.00 19.69 3.00e+00 1.11e-01 4.31e+01 ... (remaining 14358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.79: 5988 28.79 - 57.58: 188 57.58 - 86.38: 10 86.38 - 115.17: 2 115.17 - 143.96: 1 Dihedral angle restraints: 6189 sinusoidal: 2472 harmonic: 3717 Sorted by residual: dihedral pdb=" CB CYS B 110 " pdb=" SG CYS B 110 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual -86.00 -157.60 71.60 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" O1B ADP A1701 " pdb=" O3A ADP A1701 " pdb=" PB ADP A1701 " pdb=" PA ADP A1701 " ideal model delta sinusoidal sigma weight residual -60.00 83.96 -143.96 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" O2A ADP A1701 " pdb=" O3A ADP A1701 " pdb=" PA ADP A1701 " pdb=" PB ADP A1701 " ideal model delta sinusoidal sigma weight residual -60.00 -150.44 90.44 1 2.00e+01 2.50e-03 2.42e+01 ... (remaining 6186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 1622 0.165 - 0.329: 2 0.329 - 0.494: 0 0.494 - 0.659: 0 0.659 - 0.824: 1 Chirality restraints: 1625 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN B 240 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.70e+01 chirality pdb=" C1 MAN C 3 " pdb=" O4 NAG C 2 " pdb=" C2 MAN C 3 " pdb=" O5 MAN C 3 " both_signs ideal model delta sigma weight residual False 2.40 2.36 0.04 2.00e-02 2.50e+03 4.03e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.09e+00 ... (remaining 1622 not shown) Planarity restraints: 1806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 648 " 0.023 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP A 648 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP A 648 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 648 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 648 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 648 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 648 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 648 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 648 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 648 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 240 " -0.002 2.00e-02 2.50e+03 2.93e-02 1.07e+01 pdb=" CG ASN B 240 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 240 " -0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN B 240 " 0.037 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 240 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.80e+00 pdb=" C ASN B 240 " -0.042 2.00e-02 2.50e+03 pdb=" O ASN B 240 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP B 241 " 0.014 2.00e-02 2.50e+03 ... (remaining 1803 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1142 2.74 - 3.28: 11225 3.28 - 3.82: 17779 3.82 - 4.36: 20162 4.36 - 4.90: 33082 Nonbonded interactions: 83390 Sorted by model distance: nonbonded pdb=" OD1 ASP B 304 " pdb=" N ILE B 305 " model vdw 2.206 3.120 nonbonded pdb=" OE1 GLU A1193 " pdb=" F3 ALF A1702 " model vdw 2.216 2.990 nonbonded pdb=" OG1 THR A 718 " pdb=" O ARG A1009 " model vdw 2.218 3.040 nonbonded pdb=" O ARG B 188 " pdb=" OG SER B 192 " model vdw 2.224 3.040 nonbonded pdb=" CG2 THR A1342 " pdb=" O LEU A1346 " model vdw 2.244 3.460 ... (remaining 83385 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 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 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 : 0.004 0.101 10597 Z= 0.186 Angle : 1.150 71.188 14391 Z= 0.476 Chirality : 0.049 0.824 1625 Planarity : 0.003 0.042 1802 Dihedral : 13.328 143.959 3799 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: -1.25 (0.24), residues: 1267 helix: 0.13 (0.22), residues: 568 sheet: -0.22 (0.42), residues: 143 loop : -2.01 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A1130 TYR 0.022 0.002 TYR B 79 PHE 0.027 0.002 PHE A1437 TRP 0.060 0.002 TRP A 648 HIS 0.008 0.001 HIS B 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.19 (10586) covalent geometry : angle 1.14022 / 0.47 (14363) SS BOND : bond 0.00185 / 0.09 ( 2) SS BOND : angle 0.95191 / 0.43 ( 4) hydrogen bonds : bond 0.14355 / 9.11 ( 493) hydrogen bonds : angle 6.30171 / 4.35 ( 1386) Misc. bond : bond 0.00031 / 0.02 ( 1) link_ALPHA1-4 : bond 0.00110 / 0.06 ( 1) link_ALPHA1-4 : angle 1.91195 / 0.99 ( 3) link_BETA1-4 : bond 0.00176 / 0.09 ( 3) link_BETA1-4 : angle 1.15013 / 0.86 ( 9) link_NAG-ASN : bond 0.00409 / 0.21 ( 4) link_NAG-ASN : angle 5.27647 / 4.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 MET cc_start: -0.0507 (tmm) cc_final: -0.0782 (tmm) REVERT: A 784 PHE cc_start: 0.8947 (p90) cc_final: 0.8497 (t80) REVERT: A 1130 ARG cc_start: 0.9604 (ptp90) cc_final: 0.9308 (ptp90) REVERT: A 1200 MET cc_start: 0.9229 (mpp) cc_final: 0.8903 (mpp) REVERT: A 1213 THR cc_start: 0.8914 (m) cc_final: 0.8662 (t) REVERT: A 1421 TYR cc_start: 0.7916 (t80) cc_final: 0.7499 (t80) REVERT: A 1457 MET cc_start: 0.9097 (ppp) cc_final: 0.8592 (ppp) REVERT: B 179 LEU cc_start: 0.8636 (mp) cc_final: 0.8370 (mp) REVERT: B 182 PHE cc_start: 0.8496 (t80) cc_final: 0.7809 (t80) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.0762 time to fit residues: 23.8358 Evaluate side-chains 171 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 30.0000 chunk 123 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1041 ASN ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 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 = 0.3944 r_free = 0.3944 target = 0.100006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.076116 restraints weight = 43804.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.078667 restraints weight = 26405.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.080463 restraints weight = 18467.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.081607 restraints weight = 14290.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.082564 restraints weight = 11935.756| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 10597 Z= 0.276 Angle : 0.776 15.442 14391 Z= 0.393 Chirality : 0.047 0.185 1625 Planarity : 0.005 0.048 1802 Dihedral : 6.781 126.879 1399 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.18 % Allowed : 9.43 % Favored : 90.39 % 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: -1.50 (0.23), residues: 1267 helix: -0.18 (0.21), residues: 585 sheet: -0.63 (0.41), residues: 146 loop : -2.00 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 162 TYR 0.022 0.003 TYR A1332 PHE 0.023 0.003 PHE A1330 TRP 0.025 0.003 TRP A 648 HIS 0.008 0.002 HIS A1350 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.28 (10586) covalent geometry : angle 0.76615 / 0.39 (14363) SS BOND : bond 0.00227 / 0.12 ( 2) SS BOND : angle 0.92172 / 0.42 ( 4) hydrogen bonds : bond 0.04497 / 2.82 ( 493) hydrogen bonds : angle 5.46108 / 3.83 ( 1386) Misc. bond : bond 0.00039 / 0.02 ( 1) link_ALPHA1-4 : bond 0.00369 / 0.19 ( 1) link_ALPHA1-4 : angle 1.90174 / 0.96 ( 3) link_BETA1-4 : bond 0.00244 / 0.13 ( 3) link_BETA1-4 : angle 1.66275 / 1.10 ( 9) link_NAG-ASN : bond 0.00495 / 0.25 ( 4) link_NAG-ASN : angle 4.07367 / 4.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 PHE cc_start: 0.9009 (p90) cc_final: 0.8504 (t80) REVERT: A 1141 LYS cc_start: 0.7458 (mmtt) cc_final: 0.7248 (pttt) REVERT: A 1213 THR cc_start: 0.9146 (m) cc_final: 0.8905 (t) REVERT: A 1238 ASN cc_start: 0.8564 (t0) cc_final: 0.8360 (t0) REVERT: A 1303 ILE cc_start: 0.9374 (mm) cc_final: 0.9133 (mt) REVERT: A 1341 VAL cc_start: 0.8002 (m) cc_final: 0.7717 (p) REVERT: A 1457 MET cc_start: 0.9111 (ppp) cc_final: 0.8816 (ppp) REVERT: B 182 PHE cc_start: 0.8814 (t80) cc_final: 0.8194 (t80) REVERT: B 199 ARG cc_start: 0.8670 (mpp-170) cc_final: 0.8098 (mmt180) REVERT: B 304 ASP cc_start: 0.7386 (t0) cc_final: 0.7090 (t0) REVERT: B 333 ASP cc_start: 0.8683 (m-30) cc_final: 0.8396 (m-30) outliers start: 2 outliers final: 1 residues processed: 201 average time/residue: 0.0814 time to fit residues: 24.2141 Evaluate side-chains 163 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 77 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 114 optimal weight: 0.0170 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 942 HIS ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 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 = 0.4002 r_free = 0.4002 target = 0.103554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.079327 restraints weight = 42555.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.082159 restraints weight = 24980.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.084058 restraints weight = 17098.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.085502 restraints weight = 13025.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.086383 restraints weight = 10627.716| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10597 Z= 0.140 Angle : 0.649 10.260 14391 Z= 0.327 Chirality : 0.044 0.153 1625 Planarity : 0.004 0.043 1802 Dihedral : 6.374 122.123 1399 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: -1.29 (0.24), residues: 1267 helix: -0.02 (0.22), residues: 581 sheet: -0.36 (0.42), residues: 142 loop : -1.91 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1130 TYR 0.019 0.002 TYR A 678 PHE 0.025 0.002 PHE A1426 TRP 0.019 0.001 TRP A1308 HIS 0.004 0.001 HIS A 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (10586) covalent geometry : angle 0.63956 / 0.32 (14363) SS BOND : bond 0.00319 / 0.15 ( 2) SS BOND : angle 1.12787 / 0.47 ( 4) hydrogen bonds : bond 0.03849 / 2.45 ( 493) hydrogen bonds : angle 5.13810 / 3.66 ( 1386) Misc. bond : bond 0.00006 / 0.00 ( 1) link_ALPHA1-4 : bond 0.00802 / 0.42 ( 1) link_ALPHA1-4 : angle 1.65768 / 0.87 ( 3) link_BETA1-4 : bond 0.00285 / 0.14 ( 3) link_BETA1-4 : angle 1.16862 / 0.73 ( 9) link_NAG-ASN : bond 0.00198 / 0.10 ( 4) link_NAG-ASN : angle 3.61234 / 3.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 PHE cc_start: 0.9009 (p90) cc_final: 0.8493 (t80) REVERT: A 1199 VAL cc_start: 0.8822 (m) cc_final: 0.8522 (m) REVERT: A 1301 VAL cc_start: 0.8755 (p) cc_final: 0.8549 (m) REVERT: A 1359 THR cc_start: 0.8499 (p) cc_final: 0.8229 (p) REVERT: A 1457 MET cc_start: 0.9029 (ppp) cc_final: 0.8473 (ppp) REVERT: B 180 GLU cc_start: 0.8232 (tp30) cc_final: 0.7510 (tm-30) REVERT: B 181 LYS cc_start: 0.8851 (tmmt) cc_final: 0.8362 (tmtt) REVERT: B 182 PHE cc_start: 0.8685 (t80) cc_final: 0.8154 (t80) REVERT: B 304 ASP cc_start: 0.7420 (t0) cc_final: 0.7074 (t0) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.0798 time to fit residues: 24.5734 Evaluate side-chains 165 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 76 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN B 347 HIS ** B 412 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 = 0.4020 r_free = 0.4020 target = 0.104999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.080547 restraints weight = 41293.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.083367 restraints weight = 24357.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.085305 restraints weight = 16808.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.086728 restraints weight = 12852.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.087608 restraints weight = 10517.223| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10597 Z= 0.111 Angle : 0.611 9.979 14391 Z= 0.304 Chirality : 0.043 0.149 1625 Planarity : 0.003 0.038 1802 Dihedral : 5.928 115.164 1399 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % 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: -1.17 (0.24), residues: 1267 helix: 0.06 (0.22), residues: 584 sheet: -0.33 (0.42), residues: 142 loop : -1.82 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1300 TYR 0.020 0.001 TYR A1299 PHE 0.014 0.001 PHE A1408 TRP 0.014 0.001 TRP A1458 HIS 0.005 0.001 HIS B 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (10586) covalent geometry : angle 0.60363 / 0.30 (14363) SS BOND : bond 0.00349 / 0.17 ( 2) SS BOND : angle 1.09258 / 0.45 ( 4) hydrogen bonds : bond 0.03451 / 2.21 ( 493) hydrogen bonds : angle 4.86672 / 3.45 ( 1386) Misc. bond : bond 0.00011 / 0.01 ( 1) link_ALPHA1-4 : bond 0.00895 / 0.47 ( 1) link_ALPHA1-4 : angle 1.70182 / 0.88 ( 3) link_BETA1-4 : bond 0.00422 / 0.21 ( 3) link_BETA1-4 : angle 1.10527 / 0.69 ( 9) link_NAG-ASN : bond 0.00315 / 0.16 ( 4) link_NAG-ASN : angle 3.00295 / 3.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 PHE cc_start: 0.7361 (t80) cc_final: 0.7120 (t80) REVERT: A 784 PHE cc_start: 0.8995 (p90) cc_final: 0.8466 (t80) REVERT: A 1136 LEU cc_start: 0.9505 (pp) cc_final: 0.9199 (tp) REVERT: A 1199 VAL cc_start: 0.8713 (m) cc_final: 0.8393 (m) REVERT: A 1301 VAL cc_start: 0.8692 (p) cc_final: 0.8469 (m) REVERT: A 1303 ILE cc_start: 0.9333 (mm) cc_final: 0.9078 (mt) REVERT: A 1372 MET cc_start: 0.8749 (ttm) cc_final: 0.8537 (ttm) REVERT: A 1457 MET cc_start: 0.9022 (ppp) cc_final: 0.8765 (ppp) REVERT: B 111 MET cc_start: 0.8762 (ppp) cc_final: 0.8161 (ppp) REVERT: B 180 GLU cc_start: 0.8253 (tp30) cc_final: 0.7505 (tm-30) REVERT: B 181 LYS cc_start: 0.8781 (tmmt) cc_final: 0.8340 (tmtt) REVERT: B 182 PHE cc_start: 0.8632 (t80) cc_final: 0.8059 (t80) REVERT: B 333 ASP cc_start: 0.8252 (m-30) cc_final: 0.7989 (m-30) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.0673 time to fit residues: 20.5639 Evaluate side-chains 168 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 76 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 110 optimal weight: 0.1980 chunk 62 optimal weight: 20.0000 chunk 15 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 GLN B 155 GLN B 347 HIS B 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.106035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.081658 restraints weight = 41289.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.084490 restraints weight = 24441.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.086442 restraints weight = 16876.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.087810 restraints weight = 12883.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.088883 restraints weight = 10571.434| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10597 Z= 0.114 Angle : 0.630 10.378 14391 Z= 0.310 Chirality : 0.043 0.158 1625 Planarity : 0.003 0.037 1802 Dihedral : 5.698 107.045 1399 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % 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: -1.14 (0.24), residues: 1267 helix: 0.08 (0.22), residues: 583 sheet: -0.27 (0.42), residues: 142 loop : -1.80 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 156 TYR 0.019 0.001 TYR A 678 PHE 0.015 0.001 PHE B 130 TRP 0.022 0.001 TRP B 308 HIS 0.011 0.001 HIS B 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10586) covalent geometry : angle 0.62499 / 0.31 (14363) SS BOND : bond 0.00348 / 0.17 ( 2) SS BOND : angle 1.07845 / 0.45 ( 4) hydrogen bonds : bond 0.03365 / 2.14 ( 493) hydrogen bonds : angle 4.83957 / 3.44 ( 1386) Misc. bond : bond 0.00005 / 0.00 ( 1) link_ALPHA1-4 : bond 0.00695 / 0.37 ( 1) link_ALPHA1-4 : angle 1.53982 / 0.80 ( 3) link_BETA1-4 : bond 0.00355 / 0.18 ( 3) link_BETA1-4 : angle 1.09540 / 0.72 ( 9) link_NAG-ASN : bond 0.00260 / 0.13 ( 4) link_NAG-ASN : angle 2.68392 / 2.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 PHE cc_start: 0.7368 (t80) cc_final: 0.7137 (t80) REVERT: A 784 PHE cc_start: 0.8995 (p90) cc_final: 0.8454 (t80) REVERT: A 1136 LEU cc_start: 0.9524 (pp) cc_final: 0.9240 (tp) REVERT: A 1199 VAL cc_start: 0.8666 (m) cc_final: 0.8347 (m) REVERT: A 1231 ILE cc_start: 0.9372 (mm) cc_final: 0.9168 (mm) REVERT: A 1301 VAL cc_start: 0.8698 (p) cc_final: 0.8469 (m) REVERT: A 1303 ILE cc_start: 0.9317 (mm) cc_final: 0.9049 (mt) REVERT: A 1317 MET cc_start: 0.8031 (ttt) cc_final: 0.7764 (tmm) REVERT: A 1380 PHE cc_start: 0.8546 (t80) cc_final: 0.8085 (t80) REVERT: A 1457 MET cc_start: 0.8992 (ppp) cc_final: 0.8774 (ppp) REVERT: B 180 GLU cc_start: 0.8161 (tp30) cc_final: 0.7371 (tm-30) REVERT: B 181 LYS cc_start: 0.8762 (tmmt) cc_final: 0.8193 (tmtt) REVERT: B 182 PHE cc_start: 0.8604 (t80) cc_final: 0.7987 (t80) REVERT: B 333 ASP cc_start: 0.8240 (m-30) cc_final: 0.7979 (m-30) REVERT: B 412 ASN cc_start: 0.5257 (OUTLIER) cc_final: 0.4849 (m-40) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.0666 time to fit residues: 20.3633 Evaluate side-chains 168 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 88 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 97 optimal weight: 0.0970 chunk 85 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 GLN ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.105280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.081028 restraints weight = 41978.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.083827 restraints weight = 24802.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.085724 restraints weight = 17138.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.087150 restraints weight = 13118.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.087904 restraints weight = 10709.085| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10597 Z= 0.121 Angle : 0.621 10.630 14391 Z= 0.308 Chirality : 0.044 0.155 1625 Planarity : 0.004 0.039 1802 Dihedral : 5.503 96.886 1399 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: -1.09 (0.24), residues: 1267 helix: 0.15 (0.22), residues: 586 sheet: -0.28 (0.42), residues: 142 loop : -1.81 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 925 TYR 0.019 0.002 TYR A1299 PHE 0.019 0.001 PHE A1437 TRP 0.022 0.001 TRP B 308 HIS 0.005 0.001 HIS A1350 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (10586) covalent geometry : angle 0.61626 / 0.31 (14363) SS BOND : bond 0.00270 / 0.13 ( 2) SS BOND : angle 0.96800 / 0.41 ( 4) hydrogen bonds : bond 0.03328 / 2.10 ( 493) hydrogen bonds : angle 4.77396 / 3.41 ( 1386) Misc. bond : bond 0.00009 / 0.00 ( 1) link_ALPHA1-4 : bond 0.00649 / 0.34 ( 1) link_ALPHA1-4 : angle 1.45879 / 0.76 ( 3) link_BETA1-4 : bond 0.00257 / 0.13 ( 3) link_BETA1-4 : angle 1.11128 / 0.77 ( 9) link_NAG-ASN : bond 0.00210 / 0.11 ( 4) link_NAG-ASN : angle 2.51281 / 2.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 PHE cc_start: 0.7370 (t80) cc_final: 0.7126 (t80) REVERT: A 784 PHE cc_start: 0.8958 (p90) cc_final: 0.8416 (t80) REVERT: A 1199 VAL cc_start: 0.8637 (m) cc_final: 0.8308 (m) REVERT: A 1229 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7850 (tm-30) REVERT: A 1301 VAL cc_start: 0.8638 (p) cc_final: 0.8396 (m) REVERT: A 1303 ILE cc_start: 0.9309 (mm) cc_final: 0.9077 (mt) REVERT: B 180 GLU cc_start: 0.8195 (tp30) cc_final: 0.7401 (tm-30) REVERT: B 181 LYS cc_start: 0.8759 (tmmt) cc_final: 0.8230 (tmtt) REVERT: B 182 PHE cc_start: 0.8643 (t80) cc_final: 0.8040 (t80) REVERT: B 333 ASP cc_start: 0.8257 (m-30) cc_final: 0.7994 (m-30) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.0662 time to fit residues: 20.0495 Evaluate side-chains 168 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 82 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 27 optimal weight: 0.0270 chunk 53 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1041 ASN A1233 GLN ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.103569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.079617 restraints weight = 41260.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.082375 restraints weight = 24254.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.084262 restraints weight = 16677.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.085366 restraints weight = 12728.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.086345 restraints weight = 10694.437| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10597 Z= 0.144 Angle : 0.649 12.216 14391 Z= 0.323 Chirality : 0.044 0.159 1625 Planarity : 0.004 0.040 1802 Dihedral : 5.413 86.243 1399 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: -1.04 (0.24), residues: 1267 helix: 0.18 (0.22), residues: 587 sheet: -0.30 (0.42), residues: 142 loop : -1.76 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 162 TYR 0.020 0.002 TYR A 678 PHE 0.013 0.001 PHE A 710 TRP 0.031 0.002 TRP B 266 HIS 0.006 0.001 HIS B 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (10586) covalent geometry : angle 0.64472 / 0.32 (14363) SS BOND : bond 0.00233 / 0.11 ( 2) SS BOND : angle 0.93396 / 0.40 ( 4) hydrogen bonds : bond 0.03427 / 2.16 ( 493) hydrogen bonds : angle 4.84221 / 3.46 ( 1386) Misc. bond : bond 0.00026 / 0.01 ( 1) link_ALPHA1-4 : bond 0.00633 / 0.33 ( 1) link_ALPHA1-4 : angle 1.31761 / 0.69 ( 3) link_BETA1-4 : bond 0.00178 / 0.09 ( 3) link_BETA1-4 : angle 1.20943 / 0.85 ( 9) link_NAG-ASN : bond 0.00153 / 0.08 ( 4) link_NAG-ASN : angle 2.45788 / 2.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 PHE cc_start: 0.7370 (t80) cc_final: 0.7131 (t80) REVERT: A 784 PHE cc_start: 0.8964 (p90) cc_final: 0.8404 (t80) REVERT: A 1199 VAL cc_start: 0.8760 (m) cc_final: 0.8450 (m) REVERT: A 1229 GLU cc_start: 0.8553 (tm-30) cc_final: 0.7992 (tm-30) REVERT: A 1301 VAL cc_start: 0.8757 (p) cc_final: 0.8513 (m) REVERT: A 1303 ILE cc_start: 0.9311 (mm) cc_final: 0.9056 (mt) REVERT: A 1317 MET cc_start: 0.8284 (ttt) cc_final: 0.8018 (tmm) REVERT: A 1457 MET cc_start: 0.9022 (ppp) cc_final: 0.8684 (ppp) REVERT: B 111 MET cc_start: 0.8800 (ppp) cc_final: 0.8357 (ppp) REVERT: B 176 ASN cc_start: 0.9022 (m-40) cc_final: 0.8796 (m-40) REVERT: B 180 GLU cc_start: 0.8245 (tp30) cc_final: 0.7441 (tm-30) REVERT: B 181 LYS cc_start: 0.8738 (tmmt) cc_final: 0.8281 (tmtt) REVERT: B 182 PHE cc_start: 0.8685 (t80) cc_final: 0.8036 (t80) REVERT: B 333 ASP cc_start: 0.8373 (m-30) cc_final: 0.8077 (m-30) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.0680 time to fit residues: 20.6330 Evaluate side-chains 166 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 100 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 103 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.104330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.080333 restraints weight = 41420.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.083103 restraints weight = 24504.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.085029 restraints weight = 16924.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.086268 restraints weight = 12927.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.087300 restraints weight = 10708.322| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10597 Z= 0.130 Angle : 0.661 11.054 14391 Z= 0.326 Chirality : 0.045 0.163 1625 Planarity : 0.004 0.038 1802 Dihedral : 5.300 78.061 1399 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: -1.02 (0.24), residues: 1267 helix: 0.21 (0.22), residues: 583 sheet: -0.30 (0.42), residues: 144 loop : -1.76 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1130 TYR 0.038 0.002 TYR B 378 PHE 0.027 0.002 PHE A1426 TRP 0.026 0.002 TRP A1308 HIS 0.016 0.001 HIS B 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (10586) covalent geometry : angle 0.65681 / 0.33 (14363) SS BOND : bond 0.00257 / 0.12 ( 2) SS BOND : angle 0.93032 / 0.40 ( 4) hydrogen bonds : bond 0.03372 / 2.15 ( 493) hydrogen bonds : angle 4.83993 / 3.46 ( 1386) Misc. bond : bond 0.00019 / 0.01 ( 1) link_ALPHA1-4 : bond 0.00711 / 0.37 ( 1) link_ALPHA1-4 : angle 1.20833 / 0.65 ( 3) link_BETA1-4 : bond 0.00231 / 0.12 ( 3) link_BETA1-4 : angle 1.20083 / 0.85 ( 9) link_NAG-ASN : bond 0.00149 / 0.07 ( 4) link_NAG-ASN : angle 2.37259 / 2.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 PHE cc_start: 0.7397 (t80) cc_final: 0.7162 (t80) REVERT: A 784 PHE cc_start: 0.8958 (p90) cc_final: 0.8405 (t80) REVERT: A 1129 MET cc_start: 0.9124 (tpt) cc_final: 0.8924 (tpp) REVERT: A 1136 LEU cc_start: 0.9514 (pp) cc_final: 0.9203 (tp) REVERT: A 1158 LYS cc_start: 0.9121 (pptt) cc_final: 0.8805 (pptt) REVERT: A 1199 VAL cc_start: 0.8746 (m) cc_final: 0.8437 (m) REVERT: A 1229 GLU cc_start: 0.8581 (tm-30) cc_final: 0.7995 (tm-30) REVERT: A 1301 VAL cc_start: 0.8635 (p) cc_final: 0.8381 (m) REVERT: A 1303 ILE cc_start: 0.9311 (mm) cc_final: 0.9102 (mt) REVERT: A 1317 MET cc_start: 0.8209 (ttt) cc_final: 0.7951 (tmm) REVERT: A 1457 MET cc_start: 0.9031 (ppp) cc_final: 0.8690 (ppp) REVERT: B 111 MET cc_start: 0.8812 (ppp) cc_final: 0.8364 (ppp) REVERT: B 176 ASN cc_start: 0.9009 (m-40) cc_final: 0.8763 (m-40) REVERT: B 180 GLU cc_start: 0.8239 (tp30) cc_final: 0.7399 (tm-30) REVERT: B 181 LYS cc_start: 0.8837 (tmmt) cc_final: 0.8290 (tmmt) REVERT: B 182 PHE cc_start: 0.8675 (t80) cc_final: 0.7966 (t80) REVERT: B 326 LEU cc_start: 0.9412 (tp) cc_final: 0.9145 (tp) REVERT: B 333 ASP cc_start: 0.8366 (m-30) cc_final: 0.8060 (m-30) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.0670 time to fit residues: 20.8103 Evaluate side-chains 168 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 91 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.100808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.077254 restraints weight = 42782.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.079901 restraints weight = 25122.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.081798 restraints weight = 17318.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.083096 restraints weight = 13149.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.083911 restraints weight = 10784.078| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10597 Z= 0.196 Angle : 0.709 10.735 14391 Z= 0.358 Chirality : 0.046 0.174 1625 Planarity : 0.004 0.045 1802 Dihedral : 5.469 68.030 1399 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: -1.12 (0.24), residues: 1267 helix: 0.08 (0.22), residues: 591 sheet: -0.30 (0.42), residues: 142 loop : -1.78 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 162 TYR 0.030 0.002 TYR B 278 PHE 0.026 0.002 PHE B 86 TRP 0.029 0.003 TRP A1308 HIS 0.005 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (10586) covalent geometry : angle 0.70421 / 0.36 (14363) SS BOND : bond 0.00175 / 0.09 ( 2) SS BOND : angle 0.91471 / 0.42 ( 4) hydrogen bonds : bond 0.03767 / 2.33 ( 493) hydrogen bonds : angle 5.02025 / 3.58 ( 1386) Misc. bond : bond 0.00046 / 0.02 ( 1) link_ALPHA1-4 : bond 0.00492 / 0.26 ( 1) link_ALPHA1-4 : angle 1.15185 / 0.63 ( 3) link_BETA1-4 : bond 0.00197 / 0.10 ( 3) link_BETA1-4 : angle 1.41151 / 0.99 ( 9) link_NAG-ASN : bond 0.00203 / 0.10 ( 4) link_NAG-ASN : angle 2.62678 / 2.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 PHE cc_start: 0.7356 (t80) cc_final: 0.7134 (t80) REVERT: A 784 PHE cc_start: 0.8946 (p90) cc_final: 0.8386 (t80) REVERT: A 1129 MET cc_start: 0.9161 (tpt) cc_final: 0.8944 (tpp) REVERT: A 1229 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8272 (tm-30) REVERT: A 1236 TYR cc_start: 0.8217 (t80) cc_final: 0.7628 (t80) REVERT: A 1317 MET cc_start: 0.8244 (ttt) cc_final: 0.7980 (tmm) REVERT: A 1457 MET cc_start: 0.9069 (ppp) cc_final: 0.8643 (ppp) REVERT: B 180 GLU cc_start: 0.8330 (tp30) cc_final: 0.8123 (tp30) REVERT: B 182 PHE cc_start: 0.8764 (t80) cc_final: 0.8069 (t80) REVERT: B 333 ASP cc_start: 0.8436 (m-30) cc_final: 0.8143 (m-30) REVERT: B 360 TYR cc_start: 0.9041 (t80) cc_final: 0.8811 (t80) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.0695 time to fit residues: 20.1177 Evaluate side-chains 154 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 55 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 7 optimal weight: 0.1980 chunk 90 optimal weight: 0.0010 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.103865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.079970 restraints weight = 41118.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.082738 restraints weight = 24210.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.084632 restraints weight = 16672.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.085955 restraints weight = 12759.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.086646 restraints weight = 10480.828| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10597 Z= 0.123 Angle : 0.686 11.371 14391 Z= 0.338 Chirality : 0.045 0.159 1625 Planarity : 0.004 0.041 1802 Dihedral : 5.225 60.458 1399 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: -1.05 (0.25), residues: 1267 helix: 0.14 (0.22), residues: 582 sheet: -0.36 (0.42), residues: 149 loop : -1.70 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1414 TYR 0.028 0.002 TYR A1299 PHE 0.014 0.001 PHE A1408 TRP 0.036 0.002 TRP A1308 HIS 0.004 0.001 HIS B 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10586) covalent geometry : angle 0.68260 / 0.34 (14363) SS BOND : bond 0.00284 / 0.14 ( 2) SS BOND : angle 0.93501 / 0.41 ( 4) hydrogen bonds : bond 0.03480 / 2.22 ( 493) hydrogen bonds : angle 4.87100 / 3.46 ( 1386) Misc. bond : bond 0.00004 / 0.00 ( 1) link_ALPHA1-4 : bond 0.00765 / 0.40 ( 1) link_ALPHA1-4 : angle 1.10893 / 0.63 ( 3) link_BETA1-4 : bond 0.00349 / 0.17 ( 3) link_BETA1-4 : angle 1.13579 / 0.76 ( 9) link_NAG-ASN : bond 0.00224 / 0.11 ( 4) link_NAG-ASN : angle 2.39097 / 2.42 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 PHE cc_start: 0.7356 (t80) cc_final: 0.7121 (t80) REVERT: A 706 ILE cc_start: 0.8450 (mm) cc_final: 0.8216 (tp) REVERT: A 784 PHE cc_start: 0.8934 (p90) cc_final: 0.8383 (t80) REVERT: A 1129 MET cc_start: 0.9145 (tpt) cc_final: 0.8911 (tpp) REVERT: A 1158 LYS cc_start: 0.9047 (pptt) cc_final: 0.8705 (pptt) REVERT: A 1199 VAL cc_start: 0.8727 (m) cc_final: 0.8410 (m) REVERT: A 1200 MET cc_start: 0.9094 (mmp) cc_final: 0.8891 (mmm) REVERT: A 1229 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8060 (tm-30) REVERT: A 1301 VAL cc_start: 0.8665 (p) cc_final: 0.8407 (m) REVERT: A 1303 ILE cc_start: 0.9306 (mm) cc_final: 0.9091 (mt) REVERT: A 1317 MET cc_start: 0.8124 (ttt) cc_final: 0.7870 (tmm) REVERT: A 1457 MET cc_start: 0.9043 (ppp) cc_final: 0.8603 (ppp) REVERT: B 111 MET cc_start: 0.8794 (ppp) cc_final: 0.8428 (ppp) REVERT: B 180 GLU cc_start: 0.8360 (tp30) cc_final: 0.8124 (tp30) REVERT: B 182 PHE cc_start: 0.8706 (t80) cc_final: 0.7922 (t80) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.0683 time to fit residues: 20.5857 Evaluate side-chains 169 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 55 optimal weight: 6.9990 chunk 96 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.103310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.079330 restraints weight = 42396.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.082068 restraints weight = 24998.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.083966 restraints weight = 17327.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.085185 restraints weight = 13233.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.086203 restraints weight = 11027.758| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10597 Z= 0.131 Angle : 0.681 11.198 14391 Z= 0.336 Chirality : 0.045 0.190 1625 Planarity : 0.004 0.040 1802 Dihedral : 5.112 62.066 1399 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: -1.06 (0.25), residues: 1267 helix: 0.10 (0.22), residues: 583 sheet: -0.41 (0.41), residues: 149 loop : -1.66 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 62 TYR 0.020 0.001 TYR A 678 PHE 0.012 0.001 PHE A1313 TRP 0.041 0.002 TRP A1308 HIS 0.005 0.001 HIS B 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (10586) covalent geometry : angle 0.67621 / 0.33 (14363) SS BOND : bond 0.00162 / 0.08 ( 2) SS BOND : angle 0.82932 / 0.36 ( 4) hydrogen bonds : bond 0.03463 / 2.20 ( 493) hydrogen bonds : angle 4.84589 / 3.44 ( 1386) Misc. bond : bond 0.00013 / 0.01 ( 1) link_ALPHA1-4 : bond 0.00636 / 0.33 ( 1) link_ALPHA1-4 : angle 1.10642 / 0.60 ( 3) link_BETA1-4 : bond 0.00219 / 0.11 ( 3) link_BETA1-4 : angle 1.29934 / 0.93 ( 9) link_NAG-ASN : bond 0.00121 / 0.06 ( 4) link_NAG-ASN : angle 2.62205 / 2.65 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1709.75 seconds wall clock time: 30 minutes 20.92 seconds (1820.92 seconds total)