Starting phenix.real_space_refine on Tue Jul 29 02:53:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ky6_23069/07_2025/7ky6_23069.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ky6_23069/07_2025/7ky6_23069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ky6_23069/07_2025/7ky6_23069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ky6_23069/07_2025/7ky6_23069.map" model { file = "/net/cci-nas-00/data/ceres_data/7ky6_23069/07_2025/7ky6_23069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ky6_23069/07_2025/7ky6_23069.cif" } resolution = 3.1 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 50 5.16 5 C 6933 2.51 5 N 1757 2.21 5 O 1988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 135 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10729 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} 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: 7.51, per 1000 atoms: 0.70 Number of scatterers: 10729 At special positions: 0 Unit cell: (132.16, 122.248, 129.682, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 Mg 1 11.99 O 1988 8.00 N 1757 7.00 C 6933 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=2.02 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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: 3.24 Conformation dependent library (CDL) restraints added in 1.5 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: 52 helices and 8 sheets defined 54.6% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 217 through 232 removed outlier: 3.912A pdb=" N VAL A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.598A pdb=" N ALA A 244 " --> pdb=" O PRO A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 267 Processing helix chain 'A' and resid 543 through 577 removed outlier: 3.794A pdb=" N ARG A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS A 577 " --> pdb=" O VAL A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 removed outlier: 4.266A pdb=" N SER A 584 " --> pdb=" O ARG A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 609 removed outlier: 3.860A pdb=" N ILE A 607 " --> pdb=" O TRP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 635 removed outlier: 4.596A pdb=" N ILE A 619 " --> pdb=" O ILE A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 removed outlier: 3.952A pdb=" N VAL A 661 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 705 Processing helix chain 'A' and resid 707 through 734 removed outlier: 3.513A pdb=" N SER A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 744 removed outlier: 3.545A pdb=" N GLU A 743 " --> pdb=" O TYR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 755 Processing helix chain 'A' and resid 761 through 777 Processing helix chain 'A' and resid 798 through 811 Processing helix chain 'A' and resid 873 through 880 removed outlier: 3.606A pdb=" N ARG A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 907 removed outlier: 4.071A pdb=" N LYS A 895 " --> pdb=" O ALA A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 935 Processing helix chain 'A' and resid 940 through 952 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: 3.678A pdb=" N GLU A1024 " --> pdb=" O ASP A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1045 removed outlier: 3.714A pdb=" N TYR A1044 " --> pdb=" O TYR A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1060 removed outlier: 3.819A pdb=" N LYS A1059 " --> pdb=" O PHE A1055 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A1060 " --> pdb=" O GLU A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1083 removed outlier: 4.524A pdb=" N GLY A1083 " --> pdb=" O LEU A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1096 removed outlier: 4.062A pdb=" N ASN A1096 " --> pdb=" O LEU A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1120 removed outlier: 3.741A pdb=" N SER A1120 " --> pdb=" O LEU A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1140 removed outlier: 3.722A pdb=" N SER A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1158 Processing helix chain 'A' and resid 1167 through 1209 removed outlier: 4.210A pdb=" N ARG A1171 " --> pdb=" O ARG A1167 " (cutoff:3.500A) Proline residue: A1189 - end of helix removed outlier: 3.968A pdb=" N MET A1196 " --> pdb=" O PHE A1192 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A1198 " --> pdb=" O LYS A1194 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A1202 " --> pdb=" O PHE A1198 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A1203 " --> pdb=" O ALA A1199 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A1207 " --> pdb=" O PHE A1203 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR A1208 " --> pdb=" O TRP A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1228 removed outlier: 4.863A pdb=" N ASN A1226 " --> pdb=" O MET A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1241 removed outlier: 4.429A pdb=" N VAL A1234 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 3.535A 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 1255 through 1262 removed outlier: 4.442A pdb=" N GLY A1259 " --> pdb=" O LEU A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1293 removed outlier: 4.013A pdb=" N PHE A1270 " --> pdb=" O ASN A1266 " (cutoff:3.500A) Proline residue: A1288 - end of helix Processing helix chain 'A' and resid 1307 through 1331 removed outlier: 3.504A pdb=" N VAL A1311 " --> pdb=" O HIS A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1358 Processing helix chain 'A' and resid 1367 through 1373 Processing helix chain 'A' and resid 1375 through 1404 removed outlier: 3.523A 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 1417 Processing helix chain 'B' and resid 71 through 99 Proline residue: B 77 - end of helix removed outlier: 3.860A pdb=" N LYS B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.890A pdb=" N LEU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 removed outlier: 3.610A pdb=" N ARG B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 231 through 237 removed outlier: 4.391A pdb=" N ALA B 235 " --> pdb=" O CYS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.551A pdb=" N ASN B 354 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 400 Processing helix chain 'B' and resid 405 through 408 Processing helix chain 'B' and resid 409 through 414 removed outlier: 4.317A pdb=" N LYS B 414 " --> pdb=" O SER B 410 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 648 through 649 removed outlier: 6.540A pdb=" N THR A1125 " --> pdb=" O VAL A1143 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE A1145 " --> pdb=" O THR A1125 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA A1127 " --> pdb=" O ILE A1145 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE A1147 " --> pdb=" O ALA A1127 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY A1129 " --> pdb=" O ILE A1147 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR A 663 " --> pdb=" O LEU A1126 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE A1128 " --> pdb=" O TYR A 663 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE A 665 " --> pdb=" O ILE A1128 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE A 664 " --> pdb=" O TRP A 986 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU A 988 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N SER A 666 " --> pdb=" O LEU A 988 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TYR A1068 " --> pdb=" O ALA A1099 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N LEU A1101 " --> pdb=" O TYR A1068 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A1070 " --> pdb=" O LEU A1101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 687 through 689 removed outlier: 6.387A pdb=" N VAL A 676 " --> pdb=" O ARG A 966 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG A 966 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA A 962 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N CYS A 682 " --> pdb=" O GLY A 960 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY A 960 " --> pdb=" O CYS A 682 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE A 684 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N LEU A 958 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE A 913 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 835 through 840 removed outlier: 3.756A pdb=" N GLU A 835 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A 852 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE A 839 " --> pdb=" O SER A 850 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER A 850 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE A 913 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 813 through 816 removed outlier: 3.653A pdb=" N ILE A 824 " --> pdb=" O VAL A 816 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1334 through 1335 Processing sheet with id=AA6, first strand: chain 'B' and resid 126 through 129 removed outlier: 6.622A pdb=" N VAL B 173 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE B 329 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B 175 " --> pdb=" O ILE B 327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 119 through 120 removed outlier: 5.726A pdb=" N ASP B 343 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLN B 246 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 227 through 228 removed outlier: 6.356A pdb=" N ILE B 227 " --> pdb=" O ALA B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 559 hydrogen bonds defined for protein. 1596 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: 4.39 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3381 1.34 - 1.46: 2338 1.46 - 1.58: 5193 1.58 - 1.69: 0 1.69 - 1.81: 73 Bond restraints: 10985 Sorted by residual: bond pdb=" C5 MAN C 3 " pdb=" O5 MAN C 3 " ideal model delta sigma weight residual 1.418 1.466 -0.048 2.00e-02 2.50e+03 5.68e+00 bond pdb=" N GLY B 399 " pdb=" CA GLY B 399 " ideal model delta sigma weight residual 1.449 1.482 -0.033 1.45e-02 4.76e+03 5.24e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" CB VAL A1381 " pdb=" CG2 VAL A1381 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.26e+00 bond pdb=" C1 NAG B1002 " pdb=" O5 NAG B1002 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.02e+00 ... (remaining 10980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 14344 1.58 - 3.17: 470 3.17 - 4.75: 57 4.75 - 6.33: 16 6.33 - 7.92: 8 Bond angle restraints: 14895 Sorted by residual: angle pdb=" C LYS B 170 " pdb=" CA LYS B 170 " pdb=" CB LYS B 170 " ideal model delta sigma weight residual 116.54 110.40 6.14 1.15e+00 7.56e-01 2.85e+01 angle pdb=" CA LYS B 170 " pdb=" C LYS B 170 " pdb=" N ASN B 171 " ideal model delta sigma weight residual 119.52 116.02 3.50 7.90e-01 1.60e+00 1.96e+01 angle pdb=" C LEU A1174 " pdb=" N VAL A1175 " pdb=" CA VAL A1175 " ideal model delta sigma weight residual 121.97 114.95 7.02 1.80e+00 3.09e-01 1.52e+01 angle pdb=" C MET A1196 " pdb=" N ILE A1197 " pdb=" CA ILE A1197 " ideal model delta sigma weight residual 120.77 116.00 4.77 1.31e+00 5.83e-01 1.33e+01 angle pdb=" N ILE A1197 " pdb=" CA ILE A1197 " pdb=" C ILE A1197 " ideal model delta sigma weight residual 110.23 106.59 3.64 1.04e+00 9.25e-01 1.23e+01 ... (remaining 14890 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.07: 5915 23.07 - 46.14: 570 46.14 - 69.21: 104 69.21 - 92.27: 15 92.27 - 115.34: 3 Dihedral angle restraints: 6607 sinusoidal: 2744 harmonic: 3863 Sorted by residual: dihedral pdb=" CA TYR A1292 " pdb=" C TYR A1292 " pdb=" N HIS A1293 " pdb=" CA HIS A1293 " ideal model delta harmonic sigma weight residual -180.00 -155.09 -24.91 0 5.00e+00 4.00e-02 2.48e+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 -159.24 -20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU A1174 " pdb=" C LEU A1174 " pdb=" N VAL A1175 " pdb=" CA VAL A1175 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 6604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 993 0.036 - 0.072: 492 0.072 - 0.107: 142 0.107 - 0.143: 36 0.143 - 0.179: 4 Chirality restraints: 1667 Sorted by residual: 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 -2.22 -0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CA ILE A1197 " pdb=" N ILE A1197 " pdb=" C ILE A1197 " pdb=" CB ILE A1197 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 298 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 1664 not shown) Planarity restraints: 1883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A1175 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C VAL A1175 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL A1175 " 0.024 2.00e-02 2.50e+03 pdb=" N HIS A1176 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1172 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C LEU A1172 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU A1172 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A1173 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C PHE B 398 " 0.039 2.00e-02 2.50e+03 pdb=" O PHE B 398 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY B 399 " -0.013 2.00e-02 2.50e+03 ... (remaining 1880 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 215 2.65 - 3.22: 10190 3.22 - 3.78: 16994 3.78 - 4.34: 23903 4.34 - 4.90: 39226 Nonbonded interactions: 90528 Sorted by model distance: nonbonded pdb=" OD2 ASP A 667 " pdb="MG MG A2000 " model vdw 2.092 2.170 nonbonded pdb=" O VAL A 237 " pdb=" OG1 THR A 238 " model vdw 2.225 3.040 nonbonded pdb=" NH1 ARG A 723 " pdb=" O VAL A 744 " model vdw 2.230 3.120 nonbonded pdb=" OG SER A 798 " pdb=" OD1 ASP A 800 " model vdw 2.240 3.040 nonbonded pdb=" O LEU A1174 " pdb=" O VAL A1175 " model vdw 2.240 3.040 ... (remaining 90523 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.000 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:3.060 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.006 0.055 10996 Z= 0.267 Angle : 0.709 7.918 14926 Z= 0.398 Chirality : 0.045 0.179 1667 Planarity : 0.005 0.041 1878 Dihedral : 17.707 115.342 4123 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.93 % Favored : 92.92 % Rotamer: Outliers : 7.34 % Allowed : 18.09 % 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 (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: -2.79 (0.20), residues: 1314 helix: -1.24 (0.18), residues: 649 sheet: -1.00 (0.41), residues: 163 loop : -2.88 (0.23), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 348 HIS 0.003 0.001 HIS A1330 PHE 0.020 0.002 PHE A1285 TYR 0.022 0.002 TYR B 280 ARG 0.003 0.000 ARG A1178 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 5) link_NAG-ASN : angle 3.25420 ( 15) link_ALPHA1-4 : bond 0.00832 ( 1) link_ALPHA1-4 : angle 4.15206 ( 3) link_BETA1-4 : bond 0.00262 ( 3) link_BETA1-4 : angle 2.13259 ( 9) hydrogen bonds : bond 0.10034 ( 552) hydrogen bonds : angle 5.37385 ( 1596) SS BOND : bond 0.00527 ( 2) SS BOND : angle 1.00856 ( 4) covalent geometry : bond 0.00603 (10985) covalent geometry : angle 0.69762 (14895) *********************** 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 186 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 102 time to evaluate : 1.287 Fit side-chains revert: symmetry clash REVERT: A 548 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: A 622 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: A 679 PHE cc_start: 0.8426 (t80) cc_final: 0.8179 (t80) REVERT: A 715 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: A 718 GLU cc_start: 0.8127 (tp30) cc_final: 0.7737 (tp30) REVERT: A 726 MET cc_start: 0.8321 (ttt) cc_final: 0.8065 (ttt) REVERT: A 743 GLU cc_start: 0.7034 (mp0) cc_final: 0.6454 (pm20) REVERT: A 801 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: A 1067 ASN cc_start: 0.7248 (t0) cc_final: 0.6920 (t0) REVERT: A 1121 LEU cc_start: 0.8627 (tp) cc_final: 0.8385 (tt) REVERT: A 1145 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9085 (mm) REVERT: A 1150 GLU cc_start: 0.4397 (OUTLIER) cc_final: 0.3539 (pp20) REVERT: A 1223 MET cc_start: 0.8159 (ptp) cc_final: 0.7949 (ptp) outliers start: 84 outliers final: 64 residues processed: 179 average time/residue: 0.2138 time to fit residues: 56.3969 Evaluate side-chains 167 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 97 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1234 VAL 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 1295 ASN Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1323 CYS Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1434 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 247 LEU 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 333 ASP Chi-restraints excluded: chain B residue 343 ASP 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: 4.9990 chunk 55 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 640 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 ASN A1046 ASN A1293 HIS A1295 ASN A1331 GLN B 60 GLN B 67 ASN B 155 GLN B 176 ASN B 186 HIS B 341 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.168337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112034 restraints weight = 12833.243| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.83 r_work: 0.2856 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10996 Z= 0.215 Angle : 0.629 8.025 14926 Z= 0.326 Chirality : 0.044 0.142 1667 Planarity : 0.004 0.037 1878 Dihedral : 11.000 94.156 1757 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.59 % Allowed : 21.68 % Favored : 72.73 % 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: -1.64 (0.22), residues: 1314 helix: -0.25 (0.20), residues: 649 sheet: -0.65 (0.41), residues: 172 loop : -2.34 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 603 HIS 0.012 0.001 HIS A 899 PHE 0.019 0.002 PHE A1285 TYR 0.023 0.002 TYR B 280 ARG 0.005 0.000 ARG A 848 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 5) link_NAG-ASN : angle 2.72112 ( 15) link_ALPHA1-4 : bond 0.01381 ( 1) link_ALPHA1-4 : angle 4.40785 ( 3) link_BETA1-4 : bond 0.00269 ( 3) link_BETA1-4 : angle 1.73584 ( 9) hydrogen bonds : bond 0.05298 ( 552) hydrogen bonds : angle 4.87525 ( 1596) SS BOND : bond 0.00574 ( 2) SS BOND : angle 1.02998 ( 4) covalent geometry : bond 0.00509 (10985) covalent geometry : angle 0.61878 (14895) *********************** 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 165 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 101 time to evaluate : 1.233 Fit side-chains revert: symmetry clash REVERT: A 548 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: A 622 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: A 718 GLU cc_start: 0.8345 (tp30) cc_final: 0.7931 (tp30) REVERT: A 726 MET cc_start: 0.8288 (ttt) cc_final: 0.8009 (ttt) REVERT: A 801 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: A 876 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7323 (mt) REVERT: A 964 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7178 (tp30) REVERT: A 1121 LEU cc_start: 0.8364 (tp) cc_final: 0.8100 (tt) REVERT: A 1391 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8112 (tm) outliers start: 64 outliers final: 44 residues processed: 155 average time/residue: 0.2213 time to fit residues: 50.2607 Evaluate side-chains 143 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 93 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1003 CYS Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1140 SER Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1193 TYR 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 1344 LEU Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1434 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 377 VAL 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 46 optimal weight: 40.0000 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 80 optimal weight: 0.0170 chunk 73 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1267 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 = 0.4017 r_free = 0.4017 target = 0.172485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121184 restraints weight = 12903.963| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 4.02 r_work: 0.2986 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10996 Z= 0.121 Angle : 0.550 7.868 14926 Z= 0.283 Chirality : 0.041 0.186 1667 Planarity : 0.004 0.037 1878 Dihedral : 9.317 87.268 1701 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.90 % Allowed : 23.25 % Favored : 71.85 % 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: -0.86 (0.23), residues: 1314 helix: 0.39 (0.20), residues: 655 sheet: -0.37 (0.40), residues: 174 loop : -1.95 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 348 HIS 0.011 0.001 HIS A 899 PHE 0.018 0.001 PHE A 679 TYR 0.022 0.001 TYR B 280 ARG 0.005 0.000 ARG B 199 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 5) link_NAG-ASN : angle 2.20921 ( 15) link_ALPHA1-4 : bond 0.01757 ( 1) link_ALPHA1-4 : angle 3.97218 ( 3) link_BETA1-4 : bond 0.00298 ( 3) link_BETA1-4 : angle 1.38864 ( 9) hydrogen bonds : bond 0.04364 ( 552) hydrogen bonds : angle 4.65165 ( 1596) SS BOND : bond 0.00289 ( 2) SS BOND : angle 0.46684 ( 4) covalent geometry : bond 0.00260 (10985) covalent geometry : angle 0.54188 (14895) *********************** 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 164 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 108 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 548 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: A 622 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: A 726 MET cc_start: 0.8372 (ttt) cc_final: 0.8101 (ttt) REVERT: A 801 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: A 848 ARG cc_start: 0.7279 (mtm180) cc_final: 0.7065 (mtm180) REVERT: A 964 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7063 (tp30) REVERT: A 985 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8581 (mt) REVERT: A 1101 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8740 (tt) REVERT: A 1121 LEU cc_start: 0.8409 (tp) cc_final: 0.7944 (tt) REVERT: A 1150 GLU cc_start: 0.4301 (OUTLIER) cc_final: 0.3460 (pp20) REVERT: A 1190 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7485 (mm-30) REVERT: A 1296 MET cc_start: 0.8930 (mmm) cc_final: 0.8687 (mmt) REVERT: B 171 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7390 (t0) REVERT: B 269 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8467 (t0) outliers start: 56 outliers final: 29 residues processed: 158 average time/residue: 0.2106 time to fit residues: 48.7189 Evaluate side-chains 134 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 95 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1003 CYS Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1193 TYR 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 1348 VAL Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1434 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 343 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 35 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 50 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 20.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 660 GLN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.169735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.101743 restraints weight = 12799.328| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.22 r_work: 0.2997 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10996 Z= 0.181 Angle : 0.579 8.729 14926 Z= 0.298 Chirality : 0.042 0.141 1667 Planarity : 0.004 0.037 1878 Dihedral : 8.786 78.124 1684 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 5.51 % Allowed : 22.99 % Favored : 71.50 % 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: -0.67 (0.23), residues: 1314 helix: 0.51 (0.20), residues: 655 sheet: -0.20 (0.40), residues: 174 loop : -1.82 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 603 HIS 0.010 0.001 HIS A 899 PHE 0.018 0.001 PHE A1285 TYR 0.022 0.001 TYR B 280 ARG 0.004 0.000 ARG B 199 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 5) link_NAG-ASN : angle 2.45680 ( 15) link_ALPHA1-4 : bond 0.01788 ( 1) link_ALPHA1-4 : angle 4.68376 ( 3) link_BETA1-4 : bond 0.00110 ( 3) link_BETA1-4 : angle 1.63250 ( 9) hydrogen bonds : bond 0.04786 ( 552) hydrogen bonds : angle 4.68807 ( 1596) SS BOND : bond 0.00477 ( 2) SS BOND : angle 0.84732 ( 4) covalent geometry : bond 0.00426 (10985) covalent geometry : angle 0.56891 (14895) *********************** 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 160 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 97 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: A 548 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: A 622 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: A 678 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7435 (mm-30) REVERT: A 726 MET cc_start: 0.8406 (ttt) cc_final: 0.8142 (ttt) REVERT: A 771 MET cc_start: 0.7609 (mmp) cc_final: 0.7355 (mmp) REVERT: A 801 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: A 1101 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8726 (tt) REVERT: A 1150 GLU cc_start: 0.4296 (OUTLIER) cc_final: 0.3536 (pp20) REVERT: A 1190 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7679 (mm-30) REVERT: B 171 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7513 (t0) REVERT: B 181 LYS cc_start: 0.8976 (mttt) cc_final: 0.8391 (mttp) outliers start: 63 outliers final: 43 residues processed: 151 average time/residue: 0.2216 time to fit residues: 48.9707 Evaluate side-chains 141 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 91 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1003 CYS Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1278 LEU 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 1360 ILE Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1434 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 343 ASP 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 113 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.171697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.121225 restraints weight = 12799.631| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 4.12 r_work: 0.2967 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10996 Z= 0.130 Angle : 0.549 9.330 14926 Z= 0.280 Chirality : 0.041 0.138 1667 Planarity : 0.004 0.040 1878 Dihedral : 8.228 69.082 1679 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.68 % Allowed : 23.08 % Favored : 71.24 % 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 (0.24), residues: 1314 helix: 0.78 (0.21), residues: 648 sheet: -0.06 (0.41), residues: 174 loop : -1.69 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1352 HIS 0.003 0.001 HIS B 363 PHE 0.014 0.001 PHE A1285 TYR 0.022 0.001 TYR B 280 ARG 0.004 0.000 ARG B 199 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 5) link_NAG-ASN : angle 2.21889 ( 15) link_ALPHA1-4 : bond 0.01978 ( 1) link_ALPHA1-4 : angle 4.61663 ( 3) link_BETA1-4 : bond 0.00297 ( 3) link_BETA1-4 : angle 1.45656 ( 9) hydrogen bonds : bond 0.04329 ( 552) hydrogen bonds : angle 4.57292 ( 1596) SS BOND : bond 0.00327 ( 2) SS BOND : angle 0.47739 ( 4) covalent geometry : bond 0.00291 (10985) covalent geometry : angle 0.53940 (14895) *********************** 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 166 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 101 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 548 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6928 (mp0) REVERT: A 622 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: A 726 MET cc_start: 0.8415 (ttt) cc_final: 0.8126 (ttt) REVERT: A 743 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6939 (mp0) REVERT: A 801 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: A 849 MET cc_start: 0.6058 (ttp) cc_final: 0.5602 (ttm) REVERT: A 991 ASP cc_start: 0.7641 (m-30) cc_final: 0.7336 (m-30) REVERT: A 1034 ASP cc_start: 0.8510 (t0) cc_final: 0.8215 (t0) REVERT: A 1101 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8682 (tt) REVERT: A 1150 GLU cc_start: 0.4241 (OUTLIER) cc_final: 0.3463 (pp20) REVERT: A 1190 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7500 (mm-30) REVERT: B 171 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7487 (t0) REVERT: B 238 MET cc_start: 0.9120 (ttt) cc_final: 0.8890 (ttt) REVERT: B 269 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8477 (t0) outliers start: 65 outliers final: 46 residues processed: 160 average time/residue: 0.2197 time to fit residues: 51.6248 Evaluate side-chains 151 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 97 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1003 CYS Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1278 LEU 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 1360 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1434 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU 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 171 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 343 ASP 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 111 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 123 optimal weight: 0.0770 chunk 129 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.171260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120651 restraints weight = 12823.498| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 4.18 r_work: 0.2952 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10996 Z= 0.159 Angle : 0.564 9.519 14926 Z= 0.287 Chirality : 0.042 0.157 1667 Planarity : 0.004 0.038 1878 Dihedral : 7.795 59.636 1675 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 6.12 % Allowed : 22.99 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.34 (0.24), residues: 1314 helix: 0.77 (0.21), residues: 655 sheet: 0.01 (0.41), residues: 174 loop : -1.67 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1352 HIS 0.003 0.001 HIS A1176 PHE 0.017 0.001 PHE A1285 TYR 0.022 0.001 TYR B 280 ARG 0.005 0.000 ARG B 199 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 5) link_NAG-ASN : angle 2.36409 ( 15) link_ALPHA1-4 : bond 0.02182 ( 1) link_ALPHA1-4 : angle 5.50721 ( 3) link_BETA1-4 : bond 0.00130 ( 3) link_BETA1-4 : angle 1.60482 ( 9) hydrogen bonds : bond 0.04526 ( 552) hydrogen bonds : angle 4.56432 ( 1596) SS BOND : bond 0.00402 ( 2) SS BOND : angle 0.67621 ( 4) covalent geometry : bond 0.00368 (10985) covalent geometry : angle 0.55289 (14895) *********************** 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 168 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 98 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: A 622 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: A 678 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7328 (mm-30) REVERT: A 718 GLU cc_start: 0.8464 (tp30) cc_final: 0.7999 (tp30) REVERT: A 726 MET cc_start: 0.8444 (ttt) cc_final: 0.8175 (ttt) REVERT: A 743 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6965 (mp0) REVERT: A 771 MET cc_start: 0.7546 (mmp) cc_final: 0.7337 (mmm) REVERT: A 801 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: A 849 MET cc_start: 0.6112 (ttp) cc_final: 0.5611 (ttm) REVERT: A 991 ASP cc_start: 0.7606 (m-30) cc_final: 0.7276 (m-30) REVERT: A 1101 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8686 (tt) REVERT: A 1150 GLU cc_start: 0.4226 (OUTLIER) cc_final: 0.3459 (pp20) REVERT: A 1190 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7526 (mm-30) REVERT: B 169 MET cc_start: 0.8594 (mmt) cc_final: 0.8146 (mmt) REVERT: B 171 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7624 (t0) REVERT: B 269 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8547 (t0) outliers start: 70 outliers final: 52 residues processed: 161 average time/residue: 0.2186 time to fit residues: 52.0410 Evaluate side-chains 154 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 94 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1003 CYS Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1278 LEU 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 1360 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1400 GLN Chi-restraints excluded: chain A residue 1434 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 343 ASP 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 35 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 37 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.170719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117244 restraints weight = 13008.976| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 4.01 r_work: 0.2921 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10996 Z= 0.175 Angle : 0.574 10.908 14926 Z= 0.292 Chirality : 0.042 0.137 1667 Planarity : 0.004 0.038 1878 Dihedral : 7.525 58.122 1675 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 6.03 % Allowed : 23.60 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.33 (0.23), residues: 1314 helix: 0.78 (0.20), residues: 653 sheet: 0.07 (0.41), residues: 174 loop : -1.70 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 266 HIS 0.003 0.001 HIS A1176 PHE 0.016 0.001 PHE A1285 TYR 0.022 0.001 TYR B 280 ARG 0.006 0.000 ARG B 199 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 5) link_NAG-ASN : angle 2.42949 ( 15) link_ALPHA1-4 : bond 0.02074 ( 1) link_ALPHA1-4 : angle 6.81681 ( 3) link_BETA1-4 : bond 0.00200 ( 3) link_BETA1-4 : angle 1.72221 ( 9) hydrogen bonds : bond 0.04658 ( 552) hydrogen bonds : angle 4.58927 ( 1596) SS BOND : bond 0.00437 ( 2) SS BOND : angle 0.71232 ( 4) covalent geometry : bond 0.00409 (10985) covalent geometry : angle 0.55934 (14895) *********************** 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 165 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 96 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: A 622 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: A 678 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7364 (mm-30) REVERT: A 726 MET cc_start: 0.8474 (ttt) cc_final: 0.8201 (ttt) REVERT: A 743 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6949 (mp0) REVERT: A 801 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: A 849 MET cc_start: 0.6147 (ttp) cc_final: 0.5658 (ttm) REVERT: A 1101 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8673 (tt) REVERT: A 1150 GLU cc_start: 0.4240 (OUTLIER) cc_final: 0.3469 (pp20) REVERT: A 1190 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7613 (mm-30) REVERT: B 171 ASN cc_start: 0.8121 (OUTLIER) cc_final: 0.7828 (t0) REVERT: B 269 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8555 (t0) outliers start: 69 outliers final: 54 residues processed: 159 average time/residue: 0.2346 time to fit residues: 54.9190 Evaluate side-chains 157 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 95 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1003 CYS Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1278 LEU 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 1360 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1400 GLN Chi-restraints excluded: chain A residue 1434 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 343 ASP 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 80 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 3 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 128 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 38 optimal weight: 0.0670 chunk 130 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1139 GLN B 155 GLN B 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.174002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.122072 restraints weight = 12712.978| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.94 r_work: 0.3006 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10996 Z= 0.115 Angle : 0.542 11.873 14926 Z= 0.274 Chirality : 0.040 0.144 1667 Planarity : 0.004 0.039 1878 Dihedral : 7.179 58.503 1675 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.59 % Allowed : 23.86 % Favored : 70.54 % 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: -0.11 (0.24), residues: 1314 helix: 1.00 (0.21), residues: 649 sheet: 0.11 (0.41), residues: 169 loop : -1.59 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1352 HIS 0.003 0.001 HIS B 363 PHE 0.015 0.001 PHE A 599 TYR 0.023 0.001 TYR B 136 ARG 0.009 0.000 ARG A 966 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 5) link_NAG-ASN : angle 2.07833 ( 15) link_ALPHA1-4 : bond 0.01885 ( 1) link_ALPHA1-4 : angle 5.94967 ( 3) link_BETA1-4 : bond 0.00331 ( 3) link_BETA1-4 : angle 1.43817 ( 9) hydrogen bonds : bond 0.04041 ( 552) hydrogen bonds : angle 4.43301 ( 1596) SS BOND : bond 0.00247 ( 2) SS BOND : angle 0.31893 ( 4) covalent geometry : bond 0.00251 (10985) covalent geometry : angle 0.53091 (14895) *********************** 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 164 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 100 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6489 (mp0) REVERT: A 556 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7467 (t0) REVERT: A 622 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: A 678 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7285 (mm-30) REVERT: A 743 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7022 (mp0) REVERT: A 801 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: A 849 MET cc_start: 0.6227 (ttp) cc_final: 0.5811 (ttm) REVERT: A 991 ASP cc_start: 0.7544 (m-30) cc_final: 0.7203 (m-30) REVERT: A 1034 ASP cc_start: 0.8542 (t0) cc_final: 0.8160 (t0) REVERT: A 1101 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8723 (tt) REVERT: A 1190 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7462 (mm-30) REVERT: A 1391 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8012 (tp) REVERT: A 1434 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.5517 (ptp90) REVERT: B 269 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8491 (t0) outliers start: 64 outliers final: 45 residues processed: 155 average time/residue: 0.2116 time to fit residues: 48.0200 Evaluate side-chains 151 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 97 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1003 CYS Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1133 ASN 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 1278 LEU 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 1360 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1434 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 343 ASP 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 108 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.171814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.105410 restraints weight = 13054.486| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.43 r_work: 0.3012 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10996 Z= 0.159 Angle : 0.572 11.233 14926 Z= 0.290 Chirality : 0.042 0.141 1667 Planarity : 0.004 0.038 1878 Dihedral : 7.149 59.940 1673 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.24 % Allowed : 24.39 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.15 (0.23), residues: 1314 helix: 0.98 (0.21), residues: 646 sheet: 0.14 (0.40), residues: 169 loop : -1.64 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 266 HIS 0.004 0.001 HIS A 769 PHE 0.017 0.001 PHE A1285 TYR 0.022 0.001 TYR B 280 ARG 0.007 0.000 ARG A 966 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 5) link_NAG-ASN : angle 2.34249 ( 15) link_ALPHA1-4 : bond 0.01719 ( 1) link_ALPHA1-4 : angle 6.24460 ( 3) link_BETA1-4 : bond 0.00130 ( 3) link_BETA1-4 : angle 1.66877 ( 9) hydrogen bonds : bond 0.04432 ( 552) hydrogen bonds : angle 4.50393 ( 1596) SS BOND : bond 0.00399 ( 2) SS BOND : angle 0.67409 ( 4) covalent geometry : bond 0.00371 (10985) covalent geometry : angle 0.55895 (14895) *********************** 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 154 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 94 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: A 556 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7490 (t0) REVERT: A 622 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: A 678 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7384 (mm-30) REVERT: A 726 MET cc_start: 0.8350 (ttt) cc_final: 0.8097 (mtp) REVERT: A 743 GLU cc_start: 0.7519 (mt-10) cc_final: 0.6984 (mp0) REVERT: A 771 MET cc_start: 0.7144 (mmm) cc_final: 0.6683 (mmt) REVERT: A 801 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: A 811 VAL cc_start: 0.8001 (OUTLIER) cc_final: 0.7780 (p) REVERT: A 849 MET cc_start: 0.6417 (ttp) cc_final: 0.5947 (ttm) REVERT: A 1101 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8737 (tt) REVERT: A 1150 GLU cc_start: 0.4263 (OUTLIER) cc_final: 0.3501 (pp20) REVERT: A 1190 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7691 (mm-30) REVERT: B 269 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8579 (t0) outliers start: 60 outliers final: 44 residues processed: 149 average time/residue: 0.2526 time to fit residues: 56.4381 Evaluate side-chains 147 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 94 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1278 LEU 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 1360 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1400 GLN Chi-restraints excluded: chain A residue 1434 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 343 ASP 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 107 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 30 optimal weight: 20.0000 chunk 96 optimal weight: 0.3980 chunk 41 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 899 HIS B 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.170929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.102231 restraints weight = 12900.578| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.92 r_work: 0.3029 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10996 Z= 0.180 Angle : 0.585 11.277 14926 Z= 0.298 Chirality : 0.042 0.136 1667 Planarity : 0.004 0.038 1878 Dihedral : 7.183 59.812 1672 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 5.07 % Allowed : 24.83 % Favored : 70.10 % 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: -0.22 (0.23), residues: 1314 helix: 0.91 (0.20), residues: 652 sheet: 0.02 (0.40), residues: 175 loop : -1.66 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 266 HIS 0.003 0.001 HIS A 769 PHE 0.017 0.001 PHE A1285 TYR 0.022 0.002 TYR B 280 ARG 0.006 0.000 ARG A 966 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 5) link_NAG-ASN : angle 2.42143 ( 15) link_ALPHA1-4 : bond 0.01495 ( 1) link_ALPHA1-4 : angle 6.32011 ( 3) link_BETA1-4 : bond 0.00138 ( 3) link_BETA1-4 : angle 1.81917 ( 9) hydrogen bonds : bond 0.04658 ( 552) hydrogen bonds : angle 4.55907 ( 1596) SS BOND : bond 0.00484 ( 2) SS BOND : angle 0.79213 ( 4) covalent geometry : bond 0.00423 (10985) covalent geometry : angle 0.57179 (14895) ********************** 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 153 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 95 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: A 556 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7531 (t0) REVERT: A 622 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: A 678 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7386 (mm-30) REVERT: A 726 MET cc_start: 0.8356 (ttt) cc_final: 0.8111 (mtp) REVERT: A 743 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7008 (mp0) REVERT: A 771 MET cc_start: 0.7040 (mmm) cc_final: 0.6670 (mmt) REVERT: A 801 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: A 811 VAL cc_start: 0.8015 (OUTLIER) cc_final: 0.7781 (p) REVERT: A 849 MET cc_start: 0.6451 (ttp) cc_final: 0.5977 (ttm) REVERT: A 991 ASP cc_start: 0.7611 (m-30) cc_final: 0.7270 (m-30) REVERT: A 1101 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8722 (tt) REVERT: A 1190 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7666 (mm-30) REVERT: A 1434 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.5492 (ptp90) REVERT: B 269 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8559 (t0) outliers start: 58 outliers final: 45 residues processed: 150 average time/residue: 0.2249 time to fit residues: 49.0160 Evaluate side-chains 145 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 91 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1278 LEU 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 1360 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1400 GLN Chi-restraints excluded: chain A residue 1434 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 343 ASP 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 127 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.173762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123808 restraints weight = 12723.532| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 4.13 r_work: 0.3008 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10996 Z= 0.121 Angle : 0.547 11.113 14926 Z= 0.279 Chirality : 0.041 0.140 1667 Planarity : 0.004 0.039 1878 Dihedral : 6.976 59.962 1672 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.90 % Allowed : 25.09 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.05 (0.23), residues: 1314 helix: 1.11 (0.21), residues: 647 sheet: 0.04 (0.39), residues: 175 loop : -1.60 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1352 HIS 0.002 0.001 HIS B 363 PHE 0.015 0.001 PHE A 599 TYR 0.023 0.001 TYR B 136 ARG 0.006 0.000 ARG A 966 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 5) link_NAG-ASN : angle 2.20095 ( 15) link_ALPHA1-4 : bond 0.01728 ( 1) link_ALPHA1-4 : angle 5.67796 ( 3) link_BETA1-4 : bond 0.00283 ( 3) link_BETA1-4 : angle 1.54460 ( 9) hydrogen bonds : bond 0.04062 ( 552) hydrogen bonds : angle 4.41891 ( 1596) SS BOND : bond 0.00279 ( 2) SS BOND : angle 0.44364 ( 4) covalent geometry : bond 0.00269 (10985) covalent geometry : angle 0.53575 (14895) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7174.30 seconds wall clock time: 124 minutes 5.97 seconds (7445.97 seconds total)