Starting phenix.real_space_refine on Fri Jul 3 01:16:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kyb_23074/07_2026/7kyb_23074.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kyb_23074/07_2026/7kyb_23074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kyb_23074/07_2026/7kyb_23074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kyb_23074/07_2026/7kyb_23074.map" model { file = "/net/cci-nas-00/data/ceres_data/7kyb_23074/07_2026/7kyb_23074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kyb_23074/07_2026/7kyb_23074.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7kyb_23074/07_2026/7kyb_23074.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kyb_23074/07_2026/7kyb_23074.cif" } resolution = 3.2 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= 0.004 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 3 5.49 5 Mg 2 5.21 5 S 50 5.16 5 C 6985 2.51 5 N 1763 2.21 5 O 2006 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 145 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: 10814 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7646 Classifications: {'peptide': 957} Link IDs: {'PTRANS': 29, 'TRANS': 927} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 86 Unusual residues: {' MG': 2, 'ADP': 1, 'ALF': 1, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" 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 Time building chain proxies: 2.67, per 1000 atoms: 0.25 Number of scatterers: 10814 At special positions: 0 Unit cell: (127.204, 113.988, 132.16, 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 50 16.00 P 3 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 2006 8.00 N 1763 7.00 C 6985 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=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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 B1002 " - " ASN B 113 " " NAG C 1 " - " ASN B 240 " " NAG D 1 " - " ASN B 256 " " NAG E 1 " - " ASN B 332 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 560.5 milliseconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2478 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 7 sheets defined 52.9% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 217 through 232 removed outlier: 3.696A pdb=" N VAL A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 244 through 267 Processing helix chain 'A' and resid 543 through 577 removed outlier: 3.778A pdb=" N ARG A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 577 " --> pdb=" O VAL A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.597A pdb=" N GLU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 609 removed outlier: 3.818A pdb=" N ILE A 607 " --> pdb=" O TRP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 635 Processing helix chain 'A' and resid 694 through 705 Processing helix chain 'A' and resid 707 through 734 removed outlier: 4.202A pdb=" N GLU A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 744 removed outlier: 3.565A pdb=" N GLU A 743 " --> pdb=" O TYR A 740 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 744 " --> pdb=" O PRO A 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 744' Processing helix chain 'A' and resid 748 through 757 removed outlier: 4.031A pdb=" N VAL A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY A 757 " --> pdb=" O ARG A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 777 Processing helix chain 'A' and resid 798 through 812 removed outlier: 3.613A pdb=" N GLY A 812 " --> pdb=" O ALA A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 880 Processing helix chain 'A' and resid 891 through 907 Processing helix chain 'A' and resid 919 through 935 Processing helix chain 'A' and resid 939 through 952 removed outlier: 4.189A pdb=" N GLU A 943 " --> pdb=" O ASN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 981 Processing helix chain 'A' and resid 992 through 1003 Processing helix chain 'A' and resid 1018 through 1026 removed outlier: 4.818A pdb=" N GLU A1024 " --> pdb=" O ASP A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1045 Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1074 through 1083 removed outlier: 3.576A pdb=" N LEU A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY A1083 " --> pdb=" O LEU A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1096 removed outlier: 4.117A pdb=" N ASN A1096 " --> pdb=" O LEU A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1120 Processing helix chain 'A' and resid 1131 through 1140 removed outlier: 4.002A pdb=" N ALA A1136 " --> pdb=" O SER A1132 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1207 removed outlier: 4.266A pdb=" N ARG A1171 " --> pdb=" O ARG A1167 " (cutoff:3.500A) Proline residue: A1189 - end of helix removed outlier: 4.109A pdb=" N PHE A1198 " --> pdb=" O LYS A1194 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A1202 " --> pdb=" O PHE A1198 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE A1203 " --> pdb=" O ALA A1199 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A1207 " --> pdb=" O PHE A1203 " (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 1218 through 1228 removed outlier: 4.808A pdb=" N ASN A1226 " --> pdb=" O MET A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1241 removed outlier: 4.198A pdb=" N VAL A1234 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A1241 " --> pdb=" O LEU A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1252 Processing helix chain 'A' and resid 1253 through 1255 No H-bonds generated for 'chain 'A' and resid 1253 through 1255' Processing helix chain 'A' and resid 1256 through 1262 Processing helix chain 'A' and resid 1267 through 1287 Processing helix chain 'A' and resid 1287 through 1293 Processing helix chain 'A' and resid 1307 through 1331 Processing helix chain 'A' and resid 1336 through 1358 removed outlier: 3.890A pdb=" N SER A1358 " --> pdb=" O GLY A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1373 Processing helix chain 'A' and resid 1375 through 1404 removed outlier: 3.714A pdb=" N TRP A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) Proline residue: A1392 - end of helix Processing helix chain 'A' and resid 1406 through 1418 removed outlier: 3.654A pdb=" N HIS A1417 " --> pdb=" O GLU A1413 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 99 Proline residue: B 77 - end of helix removed outlier: 3.640A pdb=" N LYS B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 111 removed outlier: 4.547A pdb=" N MET B 111 " --> pdb=" O GLN B 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 108 through 111' Processing helix chain 'B' and resid 188 through 192 removed outlier: 3.530A pdb=" N LEU B 191 " --> pdb=" O ARG B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 231 through 237 removed outlier: 4.489A pdb=" N ALA B 235 " --> pdb=" O CYS B 231 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 removed outlier: 3.520A pdb=" N LYS B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS B 271 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 372 through 399 Processing helix chain 'B' and resid 409 through 414 removed outlier: 3.987A pdb=" N LYS B 414 " --> pdb=" O SER B 410 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1011 through 1014 removed outlier: 3.588A pdb=" N VAL A1071 " --> pdb=" O LEU A1013 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR A1068 " --> pdb=" O ALA A1099 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N LEU A1101 " --> pdb=" O TYR A1068 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A1070 " --> pdb=" O LEU A1101 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N CYS A1103 " --> pdb=" O ILE A1070 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE A1072 " --> pdb=" O CYS A1103 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A1100 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE A 664 " --> pdb=" O TRP A 986 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 988 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N SER A 666 " --> pdb=" O LEU A 988 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR A1125 " --> pdb=" O VAL A1143 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE A1145 " --> pdb=" O THR A1125 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA A1127 " --> pdb=" O ILE A1145 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE A1147 " --> pdb=" O ALA A1127 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY A1129 " --> pdb=" O ILE A1147 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A1161 " --> pdb=" O GLY A1144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 687 through 689 removed outlier: 8.071A pdb=" N MET A 677 " --> pdb=" O ARG A 966 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ARG A 966 " --> pdb=" O MET A 677 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE A 679 " --> pdb=" O GLU A 964 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU A 964 " --> pdb=" O PHE A 679 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU A 957 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN A 915 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 959 " --> pdb=" O ILE A 913 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG A 848 " --> pdb=" O GLU A 841 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU A 841 " --> pdb=" O ARG A 848 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER A 850 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE A 839 " --> pdb=" O SER A 850 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE A 852 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 815 through 816 removed outlier: 3.584A pdb=" N VAL A 816 " --> pdb=" O ILE A 824 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE A 824 " --> pdb=" O VAL A 816 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1334 through 1335 Processing sheet with id=AA5, first strand: chain 'B' and resid 127 through 129 removed outlier: 5.856A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU B 179 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N THR B 324 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 120 removed outlier: 5.622A pdb=" N ASP B 343 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N GLN B 246 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 227 through 228 removed outlier: 6.090A pdb=" N ILE B 227 " --> pdb=" O ALA B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 537 hydrogen bonds defined for protein. 1563 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: 1.91 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1742 1.30 - 1.43: 3076 1.43 - 1.56: 6168 1.56 - 1.69: 6 1.69 - 1.81: 77 Bond restraints: 11069 Sorted by residual: bond pdb=" F2 ALF A1603 " pdb="AL ALF A1603 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" F4 ALF A1603 " pdb="AL ALF A1603 " ideal model delta sigma weight residual 1.686 1.783 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C31 POV A1601 " pdb=" O31 POV A1601 " ideal model delta sigma weight residual 1.327 1.421 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" F1 ALF A1603 " pdb="AL ALF A1603 " ideal model delta sigma weight residual 1.684 1.778 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" F3 ALF A1603 " pdb="AL ALF A1603 " ideal model delta sigma weight residual 1.685 1.776 -0.091 2.00e-02 2.50e+03 2.05e+01 ... (remaining 11064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.94: 14999 13.94 - 27.88: 4 27.88 - 41.82: 0 41.82 - 55.75: 0 55.75 - 69.69: 2 Bond angle restraints: 15005 Sorted by residual: angle pdb=" F1 ALF A1603 " pdb="AL ALF A1603 " pdb=" F2 ALF A1603 " ideal model delta sigma weight residual 108.68 178.37 -69.69 3.00e+00 1.11e-01 5.40e+02 angle pdb=" F3 ALF A1603 " pdb="AL ALF A1603 " pdb=" F4 ALF A1603 " ideal model delta sigma weight residual 109.63 178.39 -68.76 3.00e+00 1.11e-01 5.25e+02 angle pdb=" F1 ALF A1603 " pdb="AL ALF A1603 " pdb=" F3 ALF A1603 " ideal model delta sigma weight residual 109.69 88.61 21.08 3.00e+00 1.11e-01 4.94e+01 angle pdb=" F2 ALF A1603 " pdb="AL ALF A1603 " pdb=" F4 ALF A1603 " ideal model delta sigma weight residual 110.21 90.24 19.97 3.00e+00 1.11e-01 4.43e+01 angle pdb=" F1 ALF A1603 " pdb="AL ALF A1603 " pdb=" F4 ALF A1603 " ideal model delta sigma weight residual 109.02 90.13 18.89 3.00e+00 1.11e-01 3.96e+01 ... (remaining 15000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 6237 35.11 - 70.22: 214 70.22 - 105.33: 14 105.33 - 140.45: 2 140.45 - 175.56: 1 Dihedral angle restraints: 6468 sinusoidal: 2605 harmonic: 3863 Sorted by residual: dihedral pdb=" C5' ADP A1602 " pdb=" O5' ADP A1602 " pdb=" PA ADP A1602 " pdb=" O2A ADP A1602 " ideal model delta sinusoidal sigma weight residual -60.00 115.56 -175.56 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" CA LYS B 170 " pdb=" C LYS B 170 " pdb=" N ASN B 171 " pdb=" CA ASN B 171 " ideal model delta harmonic sigma weight residual 180.00 148.60 31.40 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA PHE A1365 " pdb=" C PHE A1365 " pdb=" N PHE A1366 " pdb=" CA PHE A1366 " ideal model delta harmonic sigma weight residual -180.00 -154.95 -25.05 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 6465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1066 0.046 - 0.093: 469 0.093 - 0.139: 119 0.139 - 0.185: 13 0.185 - 0.232: 5 Chirality restraints: 1672 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 -2.63 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB VAL B 190 " pdb=" CA VAL B 190 " pdb=" CG1 VAL B 190 " pdb=" CG2 VAL B 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 332 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.29e-01 ... (remaining 1669 not shown) Planarity restraints: 1887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A1173 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C VAL A1173 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL A1173 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A1174 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1225 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C TYR A1225 " -0.040 2.00e-02 2.50e+03 pdb=" O TYR A1225 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A1226 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1174 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C LEU A1174 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU A1174 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A1175 " 0.013 2.00e-02 2.50e+03 ... (remaining 1884 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 85 2.51 - 3.11: 8306 3.11 - 3.71: 16323 3.71 - 4.30: 24528 4.30 - 4.90: 41949 Nonbonded interactions: 91191 Sorted by model distance: nonbonded pdb=" OD2 ASP A 667 " pdb=" F2 ALF A1603 " model vdw 1.917 2.990 nonbonded pdb=" OD2 ASP A 667 " pdb=" F3 ALF A1603 " model vdw 1.942 2.990 nonbonded pdb=" O1B ADP A1602 " pdb=" F2 ALF A1603 " model vdw 2.159 2.990 nonbonded pdb=" O VAL A 237 " pdb=" OG1 THR A 238 " model vdw 2.160 3.040 nonbonded pdb=" O SER B 237 " pdb=" OG SER B 237 " model vdw 2.164 3.040 ... (remaining 91186 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.660 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: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 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 : 0.012 0.099 11080 Z= 0.515 Angle : 1.243 69.693 15036 Z= 0.552 Chirality : 0.053 0.232 1672 Planarity : 0.005 0.047 1882 Dihedral : 17.443 175.557 3984 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.91 % Favored : 91.93 % Rotamer: Outliers : 8.04 % Allowed : 13.99 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.75 (0.20), residues: 1314 helix: -0.96 (0.19), residues: 616 sheet: -1.61 (0.36), residues: 158 loop : -2.89 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1167 TYR 0.024 0.003 TYR A1326 PHE 0.022 0.002 PHE A1365 TRP 0.017 0.002 TRP A 603 HIS 0.008 0.002 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.01214 / 0.51 (11069) covalent geometry : angle 1.23295 / 0.55 (15005) SS BOND : bond 0.00607 / 0.30 ( 2) SS BOND : angle 1.41971 / 0.74 ( 4) hydrogen bonds : bond 0.12621 / 8.57 ( 537) hydrogen bonds : angle 5.74176 / 3.96 ( 1563) link_ALPHA1-4 : bond 0.00569 / 0.30 ( 1) link_ALPHA1-4 : angle 4.34358 / 2.02 ( 3) link_BETA1-4 : bond 0.00947 / 0.49 ( 3) link_BETA1-4 : angle 2.88019 / 1.51 ( 9) link_NAG-ASN : bond 0.01388 / 0.66 ( 5) link_NAG-ASN : angle 4.37192 / 2.32 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 114 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 795 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8010 (mmtp) REVERT: A 849 MET cc_start: 0.8053 (ttm) cc_final: 0.7773 (ttt) REVERT: A 1006 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7985 (mt) REVERT: A 1150 GLU cc_start: 0.7254 (mm-30) cc_final: 0.7028 (tp30) REVERT: A 1190 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: A 1196 MET cc_start: 0.8255 (ttt) cc_final: 0.7862 (ttt) REVERT: A 1264 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7283 (mm-30) REVERT: B 188 ARG cc_start: 0.8112 (tpm170) cc_final: 0.7739 (ttp-170) REVERT: B 236 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8684 (t0) outliers start: 92 outliers final: 71 residues processed: 197 average time/residue: 0.0919 time to fit residues: 26.8966 Evaluate side-chains 171 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 97 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1243 ASP Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1295 ASN Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1300 SER Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1400 GLN Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 ASN A 220 ASN A 550 ASN ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A 685 ASN A 738 GLN A 763 GLN A 797 GLN A 902 GLN A 939 ASN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 GLN A1195 ASN A1293 HIS A1295 ASN A1331 GLN A1417 HIS B 60 GLN B 97 ASN B 131 HIS B 155 GLN B 186 HIS B 246 GLN B 341 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.169237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.132415 restraints weight = 11409.577| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.69 r_work: 0.2937 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11080 Z= 0.145 Angle : 0.618 14.515 15036 Z= 0.315 Chirality : 0.042 0.154 1672 Planarity : 0.004 0.039 1882 Dihedral : 12.792 173.518 1618 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.16 % Allowed : 18.09 % Favored : 76.75 % 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: -1.54 (0.22), residues: 1314 helix: -0.00 (0.20), residues: 640 sheet: -1.04 (0.37), residues: 164 loop : -2.30 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1178 TYR 0.022 0.002 TYR B 280 PHE 0.015 0.001 PHE A1285 TRP 0.015 0.001 TRP A 926 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (11069) covalent geometry : angle 0.61157 / 0.31 (15005) SS BOND : bond 0.00344 / 0.17 ( 2) SS BOND : angle 1.35179 / 0.76 ( 4) hydrogen bonds : bond 0.05069 / 3.42 ( 537) hydrogen bonds : angle 4.86588 / 3.39 ( 1563) link_ALPHA1-4 : bond 0.00876 / 0.46 ( 1) link_ALPHA1-4 : angle 2.47140 / 1.15 ( 3) link_BETA1-4 : bond 0.00147 / 0.06 ( 3) link_BETA1-4 : angle 1.31713 / 0.69 ( 9) link_NAG-ASN : bond 0.00212 / 0.12 ( 5) link_NAG-ASN : angle 2.36330 / 1.31 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 111 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 TYR cc_start: 0.8871 (m-80) cc_final: 0.8426 (m-80) REVERT: A 726 MET cc_start: 0.7689 (ttt) cc_final: 0.7086 (ttt) REVERT: A 729 GLU cc_start: 0.7021 (mt-10) cc_final: 0.5952 (mp0) REVERT: A 795 LYS cc_start: 0.8296 (mtpt) cc_final: 0.7564 (mmtp) REVERT: A 849 MET cc_start: 0.8443 (ttm) cc_final: 0.8110 (ttt) REVERT: A 1024 GLU cc_start: 0.5900 (OUTLIER) cc_final: 0.4553 (pm20) REVERT: A 1087 ARG cc_start: 0.7773 (mtm180) cc_final: 0.7171 (mtp-110) REVERT: A 1153 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7625 (mtt90) REVERT: A 1196 MET cc_start: 0.8391 (ttt) cc_final: 0.8134 (ttt) REVERT: A 1258 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8780 (m) REVERT: A 1409 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6977 (mt-10) REVERT: B 181 LYS cc_start: 0.8757 (mttt) cc_final: 0.8463 (mttm) REVERT: B 188 ARG cc_start: 0.8440 (tpm170) cc_final: 0.7732 (ttp-170) REVERT: B 190 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8547 (m) REVERT: B 236 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8788 (t0) outliers start: 59 outliers final: 37 residues processed: 164 average time/residue: 0.1003 time to fit residues: 23.9997 Evaluate side-chains 146 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 2 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 ASN ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.166546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.130012 restraints weight = 11493.450| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.69 r_work: 0.2913 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11080 Z= 0.242 Angle : 0.649 14.498 15036 Z= 0.328 Chirality : 0.045 0.159 1672 Planarity : 0.004 0.044 1882 Dihedral : 11.955 174.377 1554 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 5.42 % Allowed : 19.32 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.22), residues: 1314 helix: 0.27 (0.20), residues: 638 sheet: -0.87 (0.38), residues: 158 loop : -2.14 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 880 TYR 0.020 0.002 TYR B 280 PHE 0.018 0.002 PHE A1365 TRP 0.014 0.001 TRP A 926 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.24 (11069) covalent geometry : angle 0.64001 / 0.33 (15005) SS BOND : bond 0.00470 / 0.23 ( 2) SS BOND : angle 1.19452 / 0.61 ( 4) hydrogen bonds : bond 0.05470 / 3.69 ( 537) hydrogen bonds : angle 4.85728 / 3.39 ( 1563) link_ALPHA1-4 : bond 0.00729 / 0.38 ( 1) link_ALPHA1-4 : angle 3.06426 / 1.44 ( 3) link_BETA1-4 : bond 0.00436 / 0.22 ( 3) link_BETA1-4 : angle 1.83308 / 0.94 ( 9) link_NAG-ASN : bond 0.00762 / 0.37 ( 5) link_NAG-ASN : angle 2.86279 / 1.53 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 107 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 726 MET cc_start: 0.7743 (ttt) cc_final: 0.7074 (ttt) REVERT: A 729 GLU cc_start: 0.7032 (mt-10) cc_final: 0.5972 (mp0) REVERT: A 795 LYS cc_start: 0.8304 (mtpt) cc_final: 0.7586 (mmtp) REVERT: A 849 MET cc_start: 0.8462 (ttm) cc_final: 0.8126 (ttt) REVERT: A 954 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6143 (tp30) REVERT: A 1087 ARG cc_start: 0.7868 (mtm180) cc_final: 0.7271 (mtm-85) REVERT: A 1153 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7680 (mtt90) REVERT: A 1196 MET cc_start: 0.8472 (ttt) cc_final: 0.8212 (ttt) REVERT: A 1227 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7971 (mp) REVERT: A 1391 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7962 (tp) REVERT: A 1409 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7022 (mt-10) REVERT: B 181 LYS cc_start: 0.8804 (mttt) cc_final: 0.8526 (mttm) REVERT: B 188 ARG cc_start: 0.8487 (tpm170) cc_final: 0.7781 (ttp-170) REVERT: B 236 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8763 (t0) outliers start: 62 outliers final: 46 residues processed: 159 average time/residue: 0.0966 time to fit residues: 22.2740 Evaluate side-chains 151 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 99 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 62 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 6 optimal weight: 0.0970 chunk 34 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 95 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 GLN A1226 ASN B 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.170959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.132518 restraints weight = 11402.725| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.72 r_work: 0.2973 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11080 Z= 0.125 Angle : 0.563 13.699 15036 Z= 0.285 Chirality : 0.041 0.159 1672 Planarity : 0.003 0.040 1882 Dihedral : 11.314 172.454 1550 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.24 % Allowed : 20.19 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.23), residues: 1314 helix: 0.75 (0.21), residues: 630 sheet: -0.64 (0.37), residues: 163 loop : -1.89 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 723 TYR 0.021 0.001 TYR B 280 PHE 0.014 0.001 PHE A1285 TRP 0.012 0.001 TRP A 926 HIS 0.002 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (11069) covalent geometry : angle 0.55755 / 0.28 (15005) SS BOND : bond 0.00268 / 0.13 ( 2) SS BOND : angle 0.67902 / 0.35 ( 4) hydrogen bonds : bond 0.04463 / 3.01 ( 537) hydrogen bonds : angle 4.58164 / 3.20 ( 1563) link_ALPHA1-4 : bond 0.00997 / 0.52 ( 1) link_ALPHA1-4 : angle 2.23972 / 1.07 ( 3) link_BETA1-4 : bond 0.00241 / 0.12 ( 3) link_BETA1-4 : angle 1.21103 / 0.64 ( 9) link_NAG-ASN : bond 0.00361 / 0.18 ( 5) link_NAG-ASN : angle 2.20347 / 1.27 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 111 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 726 MET cc_start: 0.7698 (ttt) cc_final: 0.7058 (ttt) REVERT: A 729 GLU cc_start: 0.6979 (mt-10) cc_final: 0.5976 (mp0) REVERT: A 795 LYS cc_start: 0.8297 (mtpt) cc_final: 0.7633 (mmtp) REVERT: A 849 MET cc_start: 0.8424 (ttm) cc_final: 0.8090 (ttt) REVERT: A 954 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6063 (tp30) REVERT: A 1087 ARG cc_start: 0.7825 (mtm180) cc_final: 0.7277 (mtm-85) REVERT: A 1098 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7514 (mtt180) REVERT: A 1153 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7618 (mtt90) REVERT: A 1196 MET cc_start: 0.8406 (ttt) cc_final: 0.8148 (ttt) REVERT: A 1208 TYR cc_start: 0.9155 (m-80) cc_final: 0.8581 (m-80) REVERT: A 1227 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7713 (mt) REVERT: A 1391 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7856 (tp) REVERT: A 1409 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6945 (mt-10) REVERT: B 181 LYS cc_start: 0.8703 (mttt) cc_final: 0.8436 (mttm) REVERT: B 188 ARG cc_start: 0.8501 (tpm170) cc_final: 0.7764 (ttp-170) REVERT: B 190 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8564 (m) REVERT: B 236 ASN cc_start: 0.8975 (OUTLIER) cc_final: 0.8674 (t0) outliers start: 60 outliers final: 39 residues processed: 164 average time/residue: 0.1056 time to fit residues: 25.0785 Evaluate side-chains 151 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 104 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1098 ARG Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 77 optimal weight: 0.0070 chunk 89 optimal weight: 0.7980 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.172382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.133189 restraints weight = 11277.232| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.68 r_work: 0.2967 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11080 Z= 0.118 Angle : 0.542 12.983 15036 Z= 0.273 Chirality : 0.041 0.161 1672 Planarity : 0.003 0.039 1882 Dihedral : 10.564 170.864 1539 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.90 % Allowed : 20.72 % Favored : 74.39 % 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: -0.42 (0.23), residues: 1314 helix: 0.97 (0.21), residues: 637 sheet: -0.52 (0.38), residues: 153 loop : -1.80 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 723 TYR 0.020 0.001 TYR B 280 PHE 0.014 0.001 PHE A1285 TRP 0.012 0.001 TRP A 926 HIS 0.002 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (11069) covalent geometry : angle 0.53681 / 0.27 (15005) SS BOND : bond 0.00271 / 0.13 ( 2) SS BOND : angle 0.82162 / 0.44 ( 4) hydrogen bonds : bond 0.04240 / 2.85 ( 537) hydrogen bonds : angle 4.44649 / 3.11 ( 1563) link_ALPHA1-4 : bond 0.00908 / 0.48 ( 1) link_ALPHA1-4 : angle 2.27779 / 1.08 ( 3) link_BETA1-4 : bond 0.00274 / 0.12 ( 3) link_BETA1-4 : angle 1.21554 / 0.62 ( 9) link_NAG-ASN : bond 0.00613 / 0.31 ( 5) link_NAG-ASN : angle 2.09017 / 1.14 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 107 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 HIS cc_start: 0.4218 (OUTLIER) cc_final: 0.3039 (p-80) REVERT: A 576 ASP cc_start: 0.7695 (t70) cc_final: 0.7344 (t70) REVERT: A 741 PRO cc_start: 0.8565 (Cg_endo) cc_final: 0.8348 (Cg_exo) REVERT: A 795 LYS cc_start: 0.8327 (mtpt) cc_final: 0.7657 (mmtp) REVERT: A 849 MET cc_start: 0.8387 (ttm) cc_final: 0.8013 (ttt) REVERT: A 954 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6063 (tp30) REVERT: A 1087 ARG cc_start: 0.7852 (mtm180) cc_final: 0.7285 (mtm-85) REVERT: A 1098 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7478 (mtt180) REVERT: A 1153 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7673 (mtp85) REVERT: A 1196 MET cc_start: 0.8355 (ttt) cc_final: 0.8102 (ttt) REVERT: A 1208 TYR cc_start: 0.9113 (m-80) cc_final: 0.8641 (m-80) REVERT: A 1227 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7583 (mt) REVERT: A 1391 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7676 (tp) REVERT: A 1409 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6907 (mt-10) REVERT: B 181 LYS cc_start: 0.8690 (mttt) cc_final: 0.8404 (mttm) REVERT: B 188 ARG cc_start: 0.8480 (tpm170) cc_final: 0.7793 (ttp-170) REVERT: B 190 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8586 (m) outliers start: 56 outliers final: 39 residues processed: 155 average time/residue: 0.1042 time to fit residues: 23.3837 Evaluate side-chains 151 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 104 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1098 ARG Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 114 optimal weight: 0.3980 chunk 101 optimal weight: 0.0980 chunk 44 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1226 ASN A1417 HIS B 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.172395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.131586 restraints weight = 11477.097| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.86 r_work: 0.2969 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11080 Z= 0.177 Angle : 0.587 13.980 15036 Z= 0.294 Chirality : 0.043 0.161 1672 Planarity : 0.004 0.041 1882 Dihedral : 10.539 172.622 1534 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.81 % Allowed : 21.33 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.23), residues: 1314 helix: 0.97 (0.21), residues: 635 sheet: -0.44 (0.38), residues: 153 loop : -1.72 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 723 TYR 0.020 0.002 TYR B 280 PHE 0.017 0.001 PHE A1285 TRP 0.012 0.001 TRP A 926 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (11069) covalent geometry : angle 0.57942 / 0.29 (15005) SS BOND : bond 0.00391 / 0.19 ( 2) SS BOND : angle 0.86802 / 0.45 ( 4) hydrogen bonds : bond 0.04649 / 3.14 ( 537) hydrogen bonds : angle 4.51127 / 3.16 ( 1563) link_ALPHA1-4 : bond 0.00605 / 0.32 ( 1) link_ALPHA1-4 : angle 2.49515 / 1.18 ( 3) link_BETA1-4 : bond 0.00375 / 0.18 ( 3) link_BETA1-4 : angle 1.48052 / 0.76 ( 9) link_NAG-ASN : bond 0.00631 / 0.31 ( 5) link_NAG-ASN : angle 2.49984 / 1.33 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 109 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 HIS cc_start: 0.4189 (OUTLIER) cc_final: 0.3044 (p-80) REVERT: A 576 ASP cc_start: 0.7812 (t70) cc_final: 0.7455 (t70) REVERT: A 695 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.5852 (tm-30) REVERT: A 702 LYS cc_start: 0.8706 (tppt) cc_final: 0.8380 (ttmt) REVERT: A 795 LYS cc_start: 0.8352 (mtpt) cc_final: 0.7640 (mmtp) REVERT: A 849 MET cc_start: 0.8405 (ttm) cc_final: 0.8020 (ttt) REVERT: A 954 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6130 (tp30) REVERT: A 1087 ARG cc_start: 0.7946 (mtm180) cc_final: 0.7334 (mtm-85) REVERT: A 1098 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7487 (mtt180) REVERT: A 1153 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7678 (mtp85) REVERT: A 1196 MET cc_start: 0.8413 (ttt) cc_final: 0.8154 (ttt) REVERT: A 1227 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7724 (mt) REVERT: A 1391 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7749 (tp) REVERT: A 1409 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: B 181 LYS cc_start: 0.8731 (mttt) cc_final: 0.8479 (mttm) REVERT: B 188 ARG cc_start: 0.8502 (tpm170) cc_final: 0.7792 (ttp-170) REVERT: B 190 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8592 (m) REVERT: B 236 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8681 (t0) outliers start: 55 outliers final: 39 residues processed: 155 average time/residue: 0.0987 time to fit residues: 22.1993 Evaluate side-chains 150 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 101 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1098 ARG Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.174455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134450 restraints weight = 11413.749| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.74 r_work: 0.3011 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11080 Z= 0.126 Angle : 0.551 14.118 15036 Z= 0.276 Chirality : 0.041 0.163 1672 Planarity : 0.003 0.040 1882 Dihedral : 10.229 171.126 1533 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.55 % Allowed : 21.68 % Favored : 73.78 % 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: -0.22 (0.23), residues: 1314 helix: 1.10 (0.21), residues: 637 sheet: -0.33 (0.39), residues: 153 loop : -1.67 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 723 TYR 0.020 0.001 TYR B 280 PHE 0.013 0.001 PHE A1285 TRP 0.011 0.001 TRP A 926 HIS 0.002 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (11069) covalent geometry : angle 0.54537 / 0.28 (15005) SS BOND : bond 0.00283 / 0.14 ( 2) SS BOND : angle 0.67027 / 0.36 ( 4) hydrogen bonds : bond 0.04279 / 2.88 ( 537) hydrogen bonds : angle 4.41849 / 3.10 ( 1563) link_ALPHA1-4 : bond 0.00822 / 0.43 ( 1) link_ALPHA1-4 : angle 2.17725 / 1.04 ( 3) link_BETA1-4 : bond 0.00183 / 0.08 ( 3) link_BETA1-4 : angle 1.21868 / 0.63 ( 9) link_NAG-ASN : bond 0.00499 / 0.25 ( 5) link_NAG-ASN : angle 2.12794 / 1.16 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 106 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 HIS cc_start: 0.4085 (OUTLIER) cc_final: 0.2987 (p-80) REVERT: A 576 ASP cc_start: 0.7768 (t70) cc_final: 0.7412 (t70) REVERT: A 695 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.5843 (tm-30) REVERT: A 702 LYS cc_start: 0.8755 (tppt) cc_final: 0.8450 (ttmt) REVERT: A 747 VAL cc_start: 0.7232 (OUTLIER) cc_final: 0.6893 (t) REVERT: A 795 LYS cc_start: 0.8334 (mtpt) cc_final: 0.7640 (mmtp) REVERT: A 849 MET cc_start: 0.8367 (ttm) cc_final: 0.7984 (ttt) REVERT: A 954 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6124 (tp30) REVERT: A 976 GLU cc_start: 0.8351 (tp30) cc_final: 0.8146 (tp30) REVERT: A 1087 ARG cc_start: 0.7894 (mtm180) cc_final: 0.7312 (mtm-85) REVERT: A 1098 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7397 (mtt180) REVERT: A 1153 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7787 (mtp85) REVERT: A 1196 MET cc_start: 0.8357 (ttt) cc_final: 0.8108 (ttt) REVERT: A 1208 TYR cc_start: 0.9146 (m-80) cc_final: 0.8649 (m-80) REVERT: A 1391 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7717 (tp) REVERT: A 1409 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6961 (mt-10) REVERT: B 181 LYS cc_start: 0.8695 (mttt) cc_final: 0.8410 (mttm) REVERT: B 188 ARG cc_start: 0.8496 (tpm170) cc_final: 0.7836 (ttt180) REVERT: B 190 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8651 (m) outliers start: 52 outliers final: 37 residues processed: 151 average time/residue: 0.0926 time to fit residues: 20.2411 Evaluate side-chains 149 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 103 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1098 ARG Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 103 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.171605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.130925 restraints weight = 11500.949| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.84 r_work: 0.2957 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11080 Z= 0.194 Angle : 0.601 14.330 15036 Z= 0.302 Chirality : 0.043 0.159 1672 Planarity : 0.004 0.041 1882 Dihedral : 10.265 173.783 1529 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.55 % Allowed : 21.59 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.23), residues: 1314 helix: 1.07 (0.21), residues: 630 sheet: -0.35 (0.39), residues: 153 loop : -1.63 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 723 TYR 0.019 0.002 TYR B 280 PHE 0.017 0.001 PHE A1285 TRP 0.013 0.001 TRP A 926 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (11069) covalent geometry : angle 0.59342 / 0.30 (15005) SS BOND : bond 0.00441 / 0.22 ( 2) SS BOND : angle 0.92415 / 0.48 ( 4) hydrogen bonds : bond 0.04803 / 3.24 ( 537) hydrogen bonds : angle 4.56205 / 3.19 ( 1563) link_ALPHA1-4 : bond 0.00698 / 0.37 ( 1) link_ALPHA1-4 : angle 2.62603 / 1.24 ( 3) link_BETA1-4 : bond 0.00361 / 0.18 ( 3) link_BETA1-4 : angle 1.60985 / 0.82 ( 9) link_NAG-ASN : bond 0.00760 / 0.37 ( 5) link_NAG-ASN : angle 2.58005 / 1.37 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 106 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 HIS cc_start: 0.4183 (OUTLIER) cc_final: 0.3033 (p-80) REVERT: A 576 ASP cc_start: 0.7850 (t70) cc_final: 0.7488 (t70) REVERT: A 695 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.5834 (tm-30) REVERT: A 702 LYS cc_start: 0.8756 (tppt) cc_final: 0.8442 (ttmt) REVERT: A 849 MET cc_start: 0.8423 (ttm) cc_final: 0.8030 (ttt) REVERT: A 954 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6109 (tp30) REVERT: A 1087 ARG cc_start: 0.7979 (mtm180) cc_final: 0.7391 (mtm-85) REVERT: A 1098 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7467 (mtt180) REVERT: A 1153 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7758 (mtp85) REVERT: A 1196 MET cc_start: 0.8435 (ttt) cc_final: 0.8173 (ttt) REVERT: A 1227 LEU cc_start: 0.8079 (tp) cc_final: 0.7784 (mt) REVERT: A 1256 TYR cc_start: 0.8892 (t80) cc_final: 0.8679 (t80) REVERT: A 1391 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7762 (tp) REVERT: A 1409 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7032 (mt-10) REVERT: B 181 LYS cc_start: 0.8749 (mttt) cc_final: 0.8492 (mttm) REVERT: B 188 ARG cc_start: 0.8523 (tpm170) cc_final: 0.7806 (ttp-170) REVERT: B 190 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8487 (m) REVERT: B 236 ASN cc_start: 0.8975 (OUTLIER) cc_final: 0.8669 (t0) outliers start: 52 outliers final: 41 residues processed: 151 average time/residue: 0.1023 time to fit residues: 22.2600 Evaluate side-chains 152 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 102 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1098 ARG Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 43 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 23 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.170860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.131254 restraints weight = 11300.276| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.73 r_work: 0.3038 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11080 Z= 0.119 Angle : 0.557 15.839 15036 Z= 0.280 Chirality : 0.041 0.164 1672 Planarity : 0.003 0.039 1882 Dihedral : 9.975 172.412 1528 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.37 % Allowed : 21.77 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.23), residues: 1314 helix: 1.10 (0.21), residues: 641 sheet: -0.19 (0.39), residues: 151 loop : -1.64 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 723 TYR 0.020 0.001 TYR B 280 PHE 0.013 0.001 PHE A1285 TRP 0.011 0.001 TRP A 926 HIS 0.002 0.000 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (11069) covalent geometry : angle 0.55165 / 0.28 (15005) SS BOND : bond 0.00254 / 0.12 ( 2) SS BOND : angle 0.58658 / 0.32 ( 4) hydrogen bonds : bond 0.04223 / 2.84 ( 537) hydrogen bonds : angle 4.45879 / 3.12 ( 1563) link_ALPHA1-4 : bond 0.00901 / 0.47 ( 1) link_ALPHA1-4 : angle 2.14755 / 1.03 ( 3) link_BETA1-4 : bond 0.00230 / 0.10 ( 3) link_BETA1-4 : angle 1.19725 / 0.62 ( 9) link_NAG-ASN : bond 0.00510 / 0.26 ( 5) link_NAG-ASN : angle 2.07475 / 1.14 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 99 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 HIS cc_start: 0.4124 (OUTLIER) cc_final: 0.2969 (p-80) REVERT: A 576 ASP cc_start: 0.7730 (t70) cc_final: 0.7359 (t70) REVERT: A 685 ASN cc_start: 0.8194 (t0) cc_final: 0.7738 (t0) REVERT: A 695 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.5887 (tm-30) REVERT: A 702 LYS cc_start: 0.8757 (tppt) cc_final: 0.8467 (ttmt) REVERT: A 849 MET cc_start: 0.8390 (ttm) cc_final: 0.8012 (ttt) REVERT: A 954 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6069 (tp30) REVERT: A 1087 ARG cc_start: 0.7966 (mtm180) cc_final: 0.7374 (mtm-85) REVERT: A 1153 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7763 (mtp85) REVERT: A 1196 MET cc_start: 0.8360 (ttt) cc_final: 0.8099 (ttt) REVERT: A 1208 TYR cc_start: 0.9126 (m-80) cc_final: 0.8647 (m-80) REVERT: A 1227 LEU cc_start: 0.7834 (tp) cc_final: 0.7443 (mp) REVERT: A 1323 CYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7311 (m) REVERT: A 1391 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7727 (tp) REVERT: A 1409 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6976 (mt-10) REVERT: B 181 LYS cc_start: 0.8696 (mttt) cc_final: 0.8423 (mttm) REVERT: B 188 ARG cc_start: 0.8520 (tpm170) cc_final: 0.7880 (ttt180) REVERT: B 190 VAL cc_start: 0.9076 (OUTLIER) cc_final: 0.8647 (m) outliers start: 50 outliers final: 37 residues processed: 143 average time/residue: 0.1100 time to fit residues: 22.3554 Evaluate side-chains 142 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 97 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 18 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 75 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 3 optimal weight: 0.0040 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN B 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.173532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134000 restraints weight = 11296.505| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.69 r_work: 0.3018 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11080 Z= 0.118 Angle : 0.562 15.903 15036 Z= 0.283 Chirality : 0.041 0.201 1672 Planarity : 0.003 0.039 1882 Dihedral : 9.787 170.751 1528 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.02 % Allowed : 22.03 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.23), residues: 1314 helix: 1.18 (0.21), residues: 641 sheet: -0.12 (0.40), residues: 151 loop : -1.64 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 723 TYR 0.020 0.001 TYR B 280 PHE 0.013 0.001 PHE A1285 TRP 0.011 0.001 TRP A 926 HIS 0.002 0.001 HIS A 769 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (11069) covalent geometry : angle 0.55731 / 0.28 (15005) SS BOND : bond 0.00245 / 0.12 ( 2) SS BOND : angle 0.61397 / 0.35 ( 4) hydrogen bonds : bond 0.04093 / 2.75 ( 537) hydrogen bonds : angle 4.41642 / 3.10 ( 1563) link_ALPHA1-4 : bond 0.00841 / 0.44 ( 1) link_ALPHA1-4 : angle 2.14562 / 1.03 ( 3) link_BETA1-4 : bond 0.00230 / 0.10 ( 3) link_BETA1-4 : angle 1.20449 / 0.63 ( 9) link_NAG-ASN : bond 0.00506 / 0.25 ( 5) link_NAG-ASN : angle 2.05212 / 1.14 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 103 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 HIS cc_start: 0.4116 (OUTLIER) cc_final: 0.2974 (p-80) REVERT: A 576 ASP cc_start: 0.7667 (t70) cc_final: 0.7307 (t70) REVERT: A 685 ASN cc_start: 0.8089 (t0) cc_final: 0.7709 (t0) REVERT: A 695 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.5862 (tm-30) REVERT: A 702 LYS cc_start: 0.8748 (tppt) cc_final: 0.8466 (ttmt) REVERT: A 849 MET cc_start: 0.8336 (ttm) cc_final: 0.7946 (ttt) REVERT: A 943 GLU cc_start: 0.8077 (mp0) cc_final: 0.7818 (mp0) REVERT: A 954 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6034 (tp30) REVERT: A 1087 ARG cc_start: 0.7917 (mtm180) cc_final: 0.7317 (mtm-85) REVERT: A 1153 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7516 (mtp85) REVERT: A 1196 MET cc_start: 0.8287 (ttt) cc_final: 0.8052 (ttt) REVERT: A 1208 TYR cc_start: 0.9101 (m-80) cc_final: 0.8642 (m-80) REVERT: A 1323 CYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7282 (m) REVERT: A 1391 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7677 (tp) REVERT: A 1409 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6883 (mt-10) REVERT: B 181 LYS cc_start: 0.8672 (mttt) cc_final: 0.8385 (mttm) REVERT: B 188 ARG cc_start: 0.8506 (tpm170) cc_final: 0.7840 (ttt180) REVERT: B 190 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8644 (m) outliers start: 46 outliers final: 36 residues processed: 144 average time/residue: 0.1073 time to fit residues: 22.2502 Evaluate side-chains 142 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 98 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1153 ARG Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1274 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1406 THR Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 108 optimal weight: 0.8980 chunk 3 optimal weight: 0.0040 chunk 40 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.173251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.133144 restraints weight = 11406.547| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.81 r_work: 0.2953 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 11080 Z= 0.166 Angle : 0.850 59.196 15036 Z= 0.477 Chirality : 0.043 0.340 1672 Planarity : 0.003 0.039 1882 Dihedral : 9.672 170.719 1526 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.93 % Allowed : 21.94 % Favored : 74.13 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.23), residues: 1314 helix: 1.18 (0.21), residues: 641 sheet: -0.11 (0.40), residues: 151 loop : -1.65 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 723 TYR 0.020 0.001 TYR B 280 PHE 0.013 0.001 PHE A1285 TRP 0.011 0.001 TRP A 926 HIS 0.002 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (11069) covalent geometry : angle 0.84705 / 0.48 (15005) SS BOND : bond 0.00252 / 0.12 ( 2) SS BOND : angle 0.56066 / 0.31 ( 4) hydrogen bonds : bond 0.04169 / 2.81 ( 537) hydrogen bonds : angle 4.45914 / 3.14 ( 1563) link_ALPHA1-4 : bond 0.00861 / 0.45 ( 1) link_ALPHA1-4 : angle 2.26745 / 1.09 ( 3) link_BETA1-4 : bond 0.00152 / 0.07 ( 3) link_BETA1-4 : angle 1.28423 / 0.67 ( 9) link_NAG-ASN : bond 0.00512 / 0.26 ( 5) link_NAG-ASN : angle 2.07484 / 1.15 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2995.65 seconds wall clock time: 52 minutes 1.36 seconds (3121.36 seconds total)