Starting phenix.real_space_refine on Wed May 14 03:30:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kyb_23074/05_2025/7kyb_23074.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kyb_23074/05_2025/7kyb_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_23074/05_2025/7kyb_23074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kyb_23074/05_2025/7kyb_23074.map" model { file = "/net/cci-nas-00/data/ceres_data/7kyb_23074/05_2025/7kyb_23074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kyb_23074/05_2025/7kyb_23074.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.79, per 1000 atoms: 0.63 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: 2.99 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.20 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: 3.50 Time building geometry restraints manager: 3.45 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: 6406 35.11 - 70.22: 235 70.22 - 105.33: 14 105.33 - 140.45: 5 140.45 - 175.56: 1 Dihedral angle restraints: 6661 sinusoidal: 2798 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 6658 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.400 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 17.754 175.557 4177 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.002 TRP A 603 HIS 0.008 0.002 HIS B 347 PHE 0.022 0.002 PHE A1365 TYR 0.024 0.003 TYR A1326 ARG 0.008 0.001 ARG A1167 Details of bonding type rmsd link_NAG-ASN : bond 0.01388 ( 5) link_NAG-ASN : angle 4.37192 ( 15) link_ALPHA1-4 : bond 0.00569 ( 1) link_ALPHA1-4 : angle 4.34358 ( 3) link_BETA1-4 : bond 0.00947 ( 3) link_BETA1-4 : angle 2.88019 ( 9) hydrogen bonds : bond 0.12621 ( 537) hydrogen bonds : angle 5.74176 ( 1563) SS BOND : bond 0.00607 ( 2) SS BOND : angle 1.41971 ( 4) covalent geometry : bond 0.01214 (11069) covalent geometry : angle 1.23295 (15005) *********************** 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 : 1.079 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: 0.8423 (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: 0.8304 (OUTLIER) cc_final: 0.6855 (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: 0.2146 time to fit residues: 61.8385 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 : 1.088 ------------------------------------------------------------------------------- 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 110 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 118 optimal weight: 0.2980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3848 r_free = 0.3848 target = 0.169033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.130145 restraints weight = 11337.382| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.78 r_work: 0.2896 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11080 Z= 0.147 Angle : 0.624 14.493 15036 Z= 0.316 Chirality : 0.042 0.170 1672 Planarity : 0.004 0.040 1882 Dihedral : 13.809 173.513 1811 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.22), residues: 1314 helix: -0.01 (0.20), residues: 640 sheet: -1.05 (0.37), residues: 164 loop : -2.31 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 926 HIS 0.003 0.001 HIS A1330 PHE 0.016 0.001 PHE A1285 TYR 0.022 0.002 TYR B 280 ARG 0.004 0.000 ARG A1178 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 5) link_NAG-ASN : angle 2.35784 ( 15) link_ALPHA1-4 : bond 0.01556 ( 1) link_ALPHA1-4 : angle 3.12853 ( 3) link_BETA1-4 : bond 0.00144 ( 3) link_BETA1-4 : angle 1.43663 ( 9) hydrogen bonds : bond 0.05108 ( 537) hydrogen bonds : angle 4.86803 ( 1563) SS BOND : bond 0.00386 ( 2) SS BOND : angle 1.37920 ( 4) covalent geometry : bond 0.00323 (11069) covalent geometry : angle 0.61692 (15005) *********************** 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 169 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 110 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 585 TYR cc_start: 0.8866 (m-80) cc_final: 0.8413 (m-80) REVERT: A 726 MET cc_start: 0.7663 (ttt) cc_final: 0.7057 (ttt) REVERT: A 729 GLU cc_start: 0.6981 (mt-10) cc_final: 0.5915 (mp0) REVERT: A 795 LYS cc_start: 0.8295 (mtpt) cc_final: 0.7555 (mmtp) REVERT: A 849 MET cc_start: 0.8443 (ttm) cc_final: 0.8104 (ttt) REVERT: A 1024 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.4531 (pm20) REVERT: A 1087 ARG cc_start: 0.7760 (mtm180) cc_final: 0.7151 (mtp-110) REVERT: A 1153 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7647 (mtt90) REVERT: A 1196 MET cc_start: 0.8392 (ttt) cc_final: 0.8134 (ttt) REVERT: A 1258 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8771 (m) REVERT: A 1409 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.6972 (mt-10) REVERT: B 181 LYS cc_start: 0.8745 (mttt) cc_final: 0.8449 (mttm) REVERT: B 188 ARG cc_start: 0.8440 (tpm170) cc_final: 0.7720 (ttp-170) REVERT: B 190 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8545 (m) REVERT: B 236 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8800 (t0) outliers start: 59 outliers final: 36 residues processed: 163 average time/residue: 0.2168 time to fit residues: 51.1599 Evaluate side-chains 146 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 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 122 optimal weight: 2.9990 chunk 97 optimal weight: 0.0980 chunk 93 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 125 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 GLN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1226 ASN A1417 HIS B 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.171894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.132554 restraints weight = 11488.112| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.74 r_work: 0.2970 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1601 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= 0.119 Angle : 0.565 14.175 15036 Z= 0.284 Chirality : 0.041 0.170 1672 Planarity : 0.003 0.039 1882 Dihedral : 12.405 171.514 1747 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.72 % Allowed : 19.41 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.23), residues: 1314 helix: 0.62 (0.21), residues: 634 sheet: -0.65 (0.37), residues: 166 loop : -1.97 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 926 HIS 0.002 0.001 HIS B 209 PHE 0.014 0.001 PHE A1285 TYR 0.021 0.001 TYR B 280 ARG 0.002 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 5) link_NAG-ASN : angle 2.10501 ( 15) link_ALPHA1-4 : bond 0.01624 ( 1) link_ALPHA1-4 : angle 3.49003 ( 3) link_BETA1-4 : bond 0.00258 ( 3) link_BETA1-4 : angle 1.33998 ( 9) hydrogen bonds : bond 0.04451 ( 537) hydrogen bonds : angle 4.59111 ( 1563) SS BOND : bond 0.00246 ( 2) SS BOND : angle 0.86341 ( 4) covalent geometry : bond 0.00257 (11069) covalent geometry : angle 0.55791 (15005) *********************** 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 168 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 114 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7782 (t70) cc_final: 0.7487 (t70) REVERT: A 585 TYR cc_start: 0.8852 (m-80) cc_final: 0.8528 (m-80) REVERT: A 726 MET cc_start: 0.7683 (ttt) cc_final: 0.7028 (ttt) REVERT: A 729 GLU cc_start: 0.6965 (mt-10) cc_final: 0.5951 (mp0) REVERT: A 795 LYS cc_start: 0.8303 (mtpt) cc_final: 0.7636 (mmtp) REVERT: A 849 MET cc_start: 0.8411 (ttm) cc_final: 0.8077 (ttt) REVERT: A 954 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6066 (tp30) REVERT: A 1024 GLU cc_start: 0.5712 (OUTLIER) cc_final: 0.4518 (pm20) REVERT: A 1087 ARG cc_start: 0.7797 (mtm180) cc_final: 0.7255 (mtm-85) REVERT: A 1153 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7639 (mtt90) REVERT: A 1196 MET cc_start: 0.8383 (ttt) cc_final: 0.8155 (ttt) REVERT: A 1208 TYR cc_start: 0.9092 (m-80) cc_final: 0.8577 (m-80) REVERT: A 1227 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7717 (mt) REVERT: A 1391 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7798 (tp) REVERT: A 1409 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6901 (mt-10) REVERT: B 181 LYS cc_start: 0.8684 (mttt) cc_final: 0.8379 (mttm) REVERT: B 188 ARG cc_start: 0.8481 (tpm170) cc_final: 0.7750 (ttp-170) REVERT: B 190 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8591 (m) REVERT: B 236 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8690 (t0) outliers start: 54 outliers final: 34 residues processed: 161 average time/residue: 0.2200 time to fit residues: 51.2453 Evaluate side-chains 145 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 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 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 1391 LEU 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 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 298 ASN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 chunk 88 optimal weight: 0.0030 chunk 42 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 ASN ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3844 r_free = 0.3844 target = 0.168814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.131437 restraints weight = 11351.225| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.71 r_work: 0.2901 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11080 Z= 0.196 Angle : 0.605 13.902 15036 Z= 0.304 Chirality : 0.043 0.166 1672 Planarity : 0.004 0.043 1882 Dihedral : 12.098 171.546 1737 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.81 % Allowed : 20.10 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.23), residues: 1314 helix: 0.68 (0.21), residues: 639 sheet: -0.64 (0.37), residues: 163 loop : -1.90 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 926 HIS 0.003 0.001 HIS B 209 PHE 0.016 0.001 PHE A1285 TYR 0.020 0.002 TYR B 280 ARG 0.002 0.000 ARG A 940 Details of bonding type rmsd link_NAG-ASN : bond 0.00686 ( 5) link_NAG-ASN : angle 2.60713 ( 15) link_ALPHA1-4 : bond 0.01295 ( 1) link_ALPHA1-4 : angle 3.79566 ( 3) link_BETA1-4 : bond 0.00278 ( 3) link_BETA1-4 : angle 1.64855 ( 9) hydrogen bonds : bond 0.04923 ( 537) hydrogen bonds : angle 4.62799 ( 1563) SS BOND : bond 0.00398 ( 2) SS BOND : angle 0.99911 ( 4) covalent geometry : bond 0.00465 (11069) covalent geometry : angle 0.59646 (15005) *********************** 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 161 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 106 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 ASP cc_start: 0.7823 (t70) cc_final: 0.7479 (t70) REVERT: A 726 MET cc_start: 0.7664 (ttt) cc_final: 0.7032 (ttt) REVERT: A 729 GLU cc_start: 0.6965 (mt-10) cc_final: 0.5948 (mp0) REVERT: A 795 LYS cc_start: 0.8283 (mtpt) cc_final: 0.7624 (mmtp) REVERT: A 849 MET cc_start: 0.8448 (ttm) cc_final: 0.8079 (ttt) REVERT: A 954 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6079 (tp30) REVERT: A 1087 ARG cc_start: 0.7893 (mtm180) cc_final: 0.7308 (mtm-85) REVERT: A 1098 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7521 (mtt180) REVERT: A 1153 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7643 (mtt90) REVERT: A 1196 MET cc_start: 0.8437 (ttt) cc_final: 0.8184 (ttt) REVERT: A 1227 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7746 (mp) REVERT: A 1391 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7783 (tp) REVERT: A 1409 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6983 (mt-10) REVERT: B 181 LYS cc_start: 0.8752 (mttt) cc_final: 0.8490 (mttm) REVERT: B 188 ARG cc_start: 0.8471 (tpm170) cc_final: 0.7781 (ttp-170) REVERT: B 190 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8503 (m) REVERT: B 236 ASN cc_start: 0.9007 (OUTLIER) cc_final: 0.8697 (t0) outliers start: 55 outliers final: 43 residues processed: 153 average time/residue: 0.2539 time to fit residues: 56.1420 Evaluate side-chains 151 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 100 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 643 LEU 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 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 1098 ARG Chi-restraints excluded: chain A residue 1133 ASN 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 1409 GLU Chi-restraints excluded: chain B residue 59 THR 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 108 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 1 optimal weight: 0.0040 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 72 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1226 ASN B 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.174584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.136571 restraints weight = 11331.136| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.73 r_work: 0.3011 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11080 Z= 0.115 Angle : 0.552 12.893 15036 Z= 0.277 Chirality : 0.041 0.191 1672 Planarity : 0.003 0.039 1882 Dihedral : 11.653 169.119 1737 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.81 % Allowed : 20.37 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.23), residues: 1314 helix: 0.94 (0.21), residues: 638 sheet: -0.51 (0.38), residues: 153 loop : -1.80 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 926 HIS 0.002 0.000 HIS B 209 PHE 0.013 0.001 PHE A1285 TYR 0.020 0.001 TYR B 280 ARG 0.002 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00666 ( 5) link_NAG-ASN : angle 2.06143 ( 15) link_ALPHA1-4 : bond 0.01505 ( 1) link_ALPHA1-4 : angle 3.47246 ( 3) link_BETA1-4 : bond 0.00238 ( 3) link_BETA1-4 : angle 1.31151 ( 9) hydrogen bonds : bond 0.04306 ( 537) hydrogen bonds : angle 4.46413 ( 1563) SS BOND : bond 0.00276 ( 2) SS BOND : angle 0.71088 ( 4) covalent geometry : bond 0.00247 (11069) covalent geometry : angle 0.54496 (15005) *********************** 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: 55 poor density : 108 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 HIS cc_start: 0.4185 (OUTLIER) cc_final: 0.3040 (p-80) REVERT: A 576 ASP cc_start: 0.7736 (t70) cc_final: 0.7387 (t70) REVERT: A 695 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5836 (tm-30) REVERT: A 795 LYS cc_start: 0.8328 (mtpt) cc_final: 0.7650 (mmtp) REVERT: A 849 MET cc_start: 0.8390 (ttm) cc_final: 0.8008 (ttt) REVERT: A 954 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6065 (tp30) REVERT: A 1087 ARG cc_start: 0.7879 (mtm180) cc_final: 0.7313 (mtm-85) REVERT: A 1098 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7445 (mtt180) REVERT: A 1153 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7669 (mtp85) REVERT: A 1196 MET cc_start: 0.8396 (ttt) cc_final: 0.8155 (ttt) REVERT: A 1208 TYR cc_start: 0.9128 (m-80) cc_final: 0.8565 (m-80) REVERT: A 1227 LEU cc_start: 0.7869 (tp) cc_final: 0.7558 (mt) REVERT: A 1391 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7674 (tp) REVERT: A 1409 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6925 (mt-10) REVERT: B 181 LYS cc_start: 0.8698 (mttt) cc_final: 0.8417 (mttm) REVERT: B 188 ARG cc_start: 0.8478 (tpm170) cc_final: 0.7791 (ttp-170) REVERT: B 190 VAL cc_start: 0.9045 (OUTLIER) cc_final: 0.8588 (m) outliers start: 55 outliers final: 41 residues processed: 156 average time/residue: 0.2363 time to fit residues: 52.4256 Evaluate side-chains 152 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 103 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 100 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3881 r_free = 0.3881 target = 0.172746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.131628 restraints weight = 11419.221| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.81 r_work: 0.2955 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11080 Z= 0.165 Angle : 0.586 14.047 15036 Z= 0.293 Chirality : 0.043 0.186 1672 Planarity : 0.004 0.041 1882 Dihedral : 11.468 169.815 1733 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.81 % Allowed : 20.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.23), residues: 1314 helix: 0.98 (0.21), residues: 635 sheet: -0.43 (0.38), residues: 153 loop : -1.74 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 926 HIS 0.003 0.001 HIS B 209 PHE 0.016 0.001 PHE A1285 TYR 0.020 0.002 TYR B 280 ARG 0.009 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 5) link_NAG-ASN : angle 2.48002 ( 15) link_ALPHA1-4 : bond 0.01361 ( 1) link_ALPHA1-4 : angle 3.74981 ( 3) link_BETA1-4 : bond 0.00205 ( 3) link_BETA1-4 : angle 1.55083 ( 9) hydrogen bonds : bond 0.04596 ( 537) hydrogen bonds : angle 4.49361 ( 1563) SS BOND : bond 0.00375 ( 2) SS BOND : angle 0.88423 ( 4) covalent geometry : bond 0.00383 (11069) covalent geometry : angle 0.57709 (15005) *********************** 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 166 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 111 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 HIS cc_start: 0.4175 (OUTLIER) cc_final: 0.3035 (p-80) REVERT: A 576 ASP cc_start: 0.7784 (t70) cc_final: 0.7430 (t70) REVERT: A 695 GLU cc_start: 0.6413 (OUTLIER) cc_final: 0.5849 (tm-30) REVERT: A 795 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7658 (mmtp) REVERT: A 849 MET cc_start: 0.8417 (ttm) cc_final: 0.8019 (ttt) REVERT: A 954 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6094 (tp30) REVERT: A 976 GLU cc_start: 0.8377 (tp30) cc_final: 0.8132 (tp30) REVERT: A 1087 ARG cc_start: 0.7913 (mtm180) cc_final: 0.7323 (mtm-85) REVERT: A 1098 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7446 (mtt180) REVERT: A 1153 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7693 (mtp85) REVERT: A 1196 MET cc_start: 0.8409 (ttt) cc_final: 0.8159 (ttt) REVERT: A 1227 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7617 (mp) REVERT: A 1391 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7729 (tp) REVERT: A 1409 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7001 (mt-10) REVERT: B 181 LYS cc_start: 0.8731 (mttt) cc_final: 0.8469 (mttm) REVERT: B 188 ARG cc_start: 0.8502 (tpm170) cc_final: 0.7790 (ttp-170) REVERT: B 190 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8598 (m) outliers start: 55 outliers final: 40 residues processed: 159 average time/residue: 0.2276 time to fit residues: 52.2956 Evaluate side-chains 154 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 105 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 30 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1226 ASN B 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.172733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.131822 restraints weight = 11495.737| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.96 r_work: 0.2991 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.004 0.035 11080 Z= 0.165 Angle : 0.586 14.193 15036 Z= 0.293 Chirality : 0.043 0.167 1672 Planarity : 0.004 0.040 1882 Dihedral : 11.228 170.056 1729 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.24 % Allowed : 20.72 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.23), residues: 1314 helix: 1.00 (0.21), residues: 636 sheet: -0.35 (0.39), residues: 153 loop : -1.69 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 926 HIS 0.003 0.001 HIS B 209 PHE 0.015 0.001 PHE A1285 TYR 0.020 0.001 TYR B 280 ARG 0.007 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 5) link_NAG-ASN : angle 2.45573 ( 15) link_ALPHA1-4 : bond 0.01389 ( 1) link_ALPHA1-4 : angle 3.72879 ( 3) link_BETA1-4 : bond 0.00157 ( 3) link_BETA1-4 : angle 1.52679 ( 9) hydrogen bonds : bond 0.04617 ( 537) hydrogen bonds : angle 4.49471 ( 1563) SS BOND : bond 0.00385 ( 2) SS BOND : angle 0.82007 ( 4) covalent geometry : bond 0.00385 (11069) covalent geometry : angle 0.57803 (15005) *********************** 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 171 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 111 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 HIS cc_start: 0.4120 (OUTLIER) cc_final: 0.3009 (p-80) REVERT: A 576 ASP cc_start: 0.7809 (t70) cc_final: 0.7456 (t70) REVERT: A 695 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.5842 (tm-30) REVERT: A 702 LYS cc_start: 0.8655 (tppt) cc_final: 0.8343 (ttmt) REVERT: A 747 VAL cc_start: 0.7264 (OUTLIER) cc_final: 0.6902 (t) REVERT: A 795 LYS cc_start: 0.8341 (mtpt) cc_final: 0.7730 (mttm) REVERT: A 849 MET cc_start: 0.8417 (ttm) cc_final: 0.8029 (ttt) REVERT: A 954 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6125 (tp30) REVERT: A 1087 ARG cc_start: 0.7924 (mtm180) cc_final: 0.7340 (mtm-85) REVERT: A 1098 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7433 (mtt180) REVERT: A 1153 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7730 (mtp85) REVERT: A 1196 MET cc_start: 0.8418 (ttt) cc_final: 0.8167 (ttt) REVERT: A 1227 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7666 (mt) REVERT: A 1391 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7754 (tp) REVERT: A 1409 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7046 (mt-10) REVERT: B 181 LYS cc_start: 0.8728 (mttt) cc_final: 0.8463 (mttm) REVERT: B 188 ARG cc_start: 0.8526 (tpm170) cc_final: 0.7807 (ttp-170) REVERT: B 190 VAL cc_start: 0.9112 (OUTLIER) cc_final: 0.8602 (m) REVERT: B 236 ASN cc_start: 0.8983 (OUTLIER) cc_final: 0.8689 (t0) outliers start: 60 outliers final: 43 residues processed: 162 average time/residue: 0.2294 time to fit residues: 53.4711 Evaluate side-chains 159 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 105 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 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 989 THR Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1098 ARG Chi-restraints excluded: chain A residue 1133 ASN 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.5974 > 50: distance: 39 - 45: 18.012 distance: 40 - 74: 14.609 distance: 45 - 46: 6.234 distance: 45 - 51: 16.123 distance: 46 - 47: 13.095 distance: 46 - 49: 17.934 distance: 47 - 48: 10.046 distance: 47 - 52: 13.389 distance: 48 - 81: 12.882 distance: 49 - 50: 28.622 distance: 50 - 51: 24.612 distance: 52 - 53: 4.045 distance: 53 - 54: 7.917 distance: 53 - 56: 9.977 distance: 54 - 55: 17.423 distance: 54 - 63: 19.703 distance: 55 - 93: 11.030 distance: 56 - 57: 21.979 distance: 57 - 58: 10.144 distance: 58 - 59: 8.155 distance: 59 - 60: 4.061 distance: 60 - 61: 8.211 distance: 60 - 62: 10.610 distance: 63 - 64: 7.686 distance: 64 - 65: 3.025 distance: 64 - 67: 8.525 distance: 65 - 66: 5.161 distance: 65 - 74: 10.212 distance: 66 - 101: 31.156 distance: 67 - 68: 5.293 distance: 68 - 69: 6.034 distance: 68 - 70: 5.332 distance: 69 - 71: 10.007 distance: 70 - 72: 4.889 distance: 71 - 73: 4.895 distance: 72 - 73: 8.242 distance: 74 - 75: 9.277 distance: 75 - 76: 5.634 distance: 75 - 78: 12.179 distance: 76 - 77: 5.841 distance: 76 - 81: 11.006 distance: 77 - 107: 7.059 distance: 78 - 79: 12.737 distance: 78 - 80: 19.580 distance: 81 - 82: 17.197 distance: 82 - 83: 9.615 distance: 82 - 85: 16.388 distance: 83 - 84: 4.671 distance: 83 - 93: 7.834 distance: 84 - 118: 15.568 distance: 85 - 86: 3.757 distance: 86 - 87: 8.950 distance: 86 - 88: 8.125 distance: 87 - 89: 4.447 distance: 88 - 90: 15.526 distance: 89 - 91: 15.826 distance: 90 - 91: 4.358 distance: 91 - 92: 12.909 distance: 93 - 94: 7.951 distance: 94 - 95: 9.485 distance: 94 - 97: 12.984 distance: 95 - 96: 8.997 distance: 95 - 101: 17.083 distance: 96 - 127: 14.332 distance: 97 - 98: 5.142 distance: 98 - 99: 4.063 distance: 98 - 100: 16.470 distance: 101 - 102: 8.052 distance: 102 - 103: 11.054 distance: 102 - 105: 19.562 distance: 103 - 104: 10.632 distance: 103 - 107: 7.943 distance: 104 - 136: 12.779 distance: 105 - 106: 10.593 distance: 107 - 108: 7.685 distance: 108 - 109: 9.952 distance: 109 - 110: 5.562 distance: 109 - 118: 4.034 distance: 110 - 147: 19.525 distance: 111 - 112: 3.715 distance: 112 - 114: 4.200 distance: 113 - 115: 6.874 distance: 114 - 116: 5.214 distance: 116 - 117: 4.381 distance: 118 - 119: 8.277 distance: 119 - 120: 22.017 distance: 119 - 122: 4.385 distance: 120 - 127: 5.129 distance: 121 - 156: 27.812 distance: 122 - 123: 14.847 distance: 123 - 124: 19.680 distance: 124 - 125: 15.497 distance: 124 - 126: 49.381 distance: 127 - 128: 39.733 distance: 128 - 129: 9.821 distance: 129 - 136: 32.744 distance: 131 - 132: 27.666 distance: 132 - 133: 20.917 distance: 133 - 134: 8.254 distance: 134 - 135: 17.577