Starting phenix.real_space_refine on Wed Mar 4 10:24:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7drx_30829/03_2026/7drx_30829.cif Found real_map, /net/cci-nas-00/data/ceres_data/7drx_30829/03_2026/7drx_30829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7drx_30829/03_2026/7drx_30829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7drx_30829/03_2026/7drx_30829.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7drx_30829/03_2026/7drx_30829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7drx_30829/03_2026/7drx_30829.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 60 5.16 5 Be 1 3.05 5 C 8018 2.51 5 N 2046 2.21 5 O 2302 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12433 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 9351 Classifications: {'peptide': 1172} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1133} Chain breaks: 1 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 109 Unusual residues: {' MG': 1, '6PL': 2, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.78, per 1000 atoms: 0.22 Number of scatterers: 12433 At special positions: 0 Unit cell: (150.865, 109.72, 135.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 60 16.00 P 2 15.00 Mg 1 11.99 F 3 9.00 O 2302 8.00 N 2046 7.00 C 8018 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN B 240 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 602.6 milliseconds 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2870 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 11 sheets defined 40.7% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 219 through 231 removed outlier: 3.549A pdb=" N LEU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 273 removed outlier: 3.589A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 464 removed outlier: 3.523A pdb=" N ALA A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 543 through 575 removed outlier: 4.165A pdb=" N ASN A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 572 " --> pdb=" O GLY A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 removed outlier: 3.583A pdb=" N TRP A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 605 " --> pdb=" O SER A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 613 removed outlier: 3.570A pdb=" N VAL A 613 " --> pdb=" O GLN A 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 610 through 613' Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.800A pdb=" N GLU A 622 " --> pdb=" O TYR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 660 Processing helix chain 'A' and resid 708 through 723 removed outlier: 3.574A pdb=" N ALA A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 774 removed outlier: 3.537A pdb=" N ARG A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 812 Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.524A pdb=" N TYR A 878 " --> pdb=" O ASP A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 905 Processing helix chain 'A' and resid 919 through 931 removed outlier: 3.507A pdb=" N LYS A 929 " --> pdb=" O LYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 936 removed outlier: 3.717A pdb=" N SER A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 952 removed outlier: 3.781A pdb=" N ILE A 951 " --> pdb=" O VAL A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 981 Processing helix chain 'A' and resid 992 through 1003 removed outlier: 3.506A pdb=" N ALA A 996 " --> pdb=" O LYS A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1048 removed outlier: 3.729A pdb=" N ASN A1046 " --> pdb=" O LYS A1042 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1060 removed outlier: 3.503A pdb=" N LYS A1059 " --> pdb=" O GLU A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1096 Processing helix chain 'A' and resid 1106 through 1121 Processing helix chain 'A' and resid 1134 through 1141 Processing helix chain 'A' and resid 1153 through 1158 Processing helix chain 'A' and resid 1167 through 1174 removed outlier: 4.349A pdb=" N ARG A1171 " --> pdb=" O ARG A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1200 removed outlier: 3.574A pdb=" N LEU A1184 " --> pdb=" O SER A1180 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) Proline residue: A1189 - end of helix removed outlier: 4.432A pdb=" N PHE A1198 " --> pdb=" O LYS A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1205 Processing helix chain 'A' and resid 1218 through 1225 removed outlier: 3.568A pdb=" N MET A1222 " --> pdb=" O GLU A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1241 removed outlier: 4.173A pdb=" N VAL A1234 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1240 " --> pdb=" O PHE A1236 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A1241 " --> pdb=" O LEU A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1252 Processing helix chain 'A' and resid 1253 through 1255 No H-bonds generated for 'chain 'A' and resid 1253 through 1255' Processing helix chain 'A' and resid 1256 through 1261 removed outlier: 3.780A pdb=" N ILE A1260 " --> pdb=" O TYR A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1293 removed outlier: 3.642A pdb=" N ILE A1282 " --> pdb=" O LEU A1278 " (cutoff:3.500A) Proline residue: A1288 - end of helix removed outlier: 3.662A pdb=" N VAL A1291 " --> pdb=" O PHE A1287 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A1292 " --> pdb=" O PRO A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1330 removed outlier: 3.517A pdb=" N LEU A1328 " --> pdb=" O ASN A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1347 Processing helix chain 'A' and resid 1347 through 1357 removed outlier: 3.782A pdb=" N THR A1353 " --> pdb=" O VAL A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1363 removed outlier: 6.645A pdb=" N ALA A1361 " --> pdb=" O SER A1358 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A1363 " --> pdb=" O ILE A1360 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1373 Processing helix chain 'A' and resid 1377 through 1404 removed outlier: 4.290A pdb=" N PHE A1383 " --> pdb=" O TRP A1379 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A1384 " --> pdb=" O ALA A1380 " (cutoff:3.500A) Proline residue: A1392 - end of helix removed outlier: 3.509A pdb=" N TYR A1396 " --> pdb=" O PRO A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1417 Processing helix chain 'B' and resid 71 through 98 removed outlier: 3.549A pdb=" N LEU B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) Proline residue: B 77 - end of helix removed outlier: 3.536A pdb=" N LEU B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 204 through 208 removed outlier: 3.553A pdb=" N THR B 207 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 237 removed outlier: 4.171A 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 removed outlier: 3.556A pdb=" N TRP B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 372 through 386 removed outlier: 3.571A pdb=" N ILE B 376 " --> pdb=" O PRO B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 280 Processing sheet with id=AA3, first strand: chain 'A' and resid 406 through 410 removed outlier: 6.522A pdb=" N TRP A 517 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N THR A 424 " --> pdb=" O TRP A 517 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET A 519 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASP A 418 " --> pdb=" O MET A 523 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 433 through 434 Processing sheet with id=AA5, first strand: chain 'A' and resid 663 through 666 removed outlier: 6.420A pdb=" N ILE A 664 " --> pdb=" O TRP A 986 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 988 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N SER A 666 " --> pdb=" O LEU A 988 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU A 985 " --> pdb=" O VAL A1100 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N CYS A1102 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 987 " --> pdb=" O CYS A1102 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N LEU A1101 " --> pdb=" O TYR A1068 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE A1070 " --> pdb=" O LEU A1101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 687 through 689 removed outlier: 4.894A pdb=" N VAL A 676 " --> pdb=" O ARG A 966 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA A 962 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS A 682 " --> pdb=" O GLY A 960 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY A 960 " --> pdb=" O CYS A 682 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE A 684 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LEU A 958 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 913 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY A 960 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A 911 " --> pdb=" O GLY A 960 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 962 " --> pdb=" O ARG A 909 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG A 909 " --> pdb=" O ALA A 962 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 866 " --> pdb=" O LEU A 918 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 838 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 830 " --> pdb=" O MET A 827 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LYS A 818 " --> pdb=" O GLY A 822 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE A 824 " --> pdb=" O VAL A 816 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 781 through 784 removed outlier: 3.649A pdb=" N GLU A 783 " --> pdb=" O ASP A 793 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1128 through 1129 Processing sheet with id=AA9, first strand: chain 'B' and resid 126 through 129 removed outlier: 6.203A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU B 179 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR B 324 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 119 through 120 removed outlier: 3.533A pdb=" N SER B 119 " --> pdb=" O TRP B 142 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASP B 343 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N GLN B 246 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 227 through 228 removed outlier: 6.080A pdb=" N ILE B 227 " --> pdb=" O ALA B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 469 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2041 1.32 - 1.44: 3468 1.44 - 1.56: 7112 1.56 - 1.68: 5 1.68 - 1.81: 92 Bond restraints: 12718 Sorted by residual: bond pdb=" F1 BEF A1602 " pdb="BE BEF A1602 " ideal model delta sigma weight residual 1.476 1.762 -0.286 2.00e-02 2.50e+03 2.04e+02 bond pdb=" F3 BEF A1602 " pdb="BE BEF A1602 " ideal model delta sigma weight residual 1.476 1.760 -0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" F2 BEF A1602 " pdb="BE BEF A1602 " ideal model delta sigma weight residual 1.476 1.760 -0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" N GLU A1409 " pdb=" CA GLU A1409 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.28e-02 6.10e+03 8.25e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.57e+00 ... (remaining 12713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 16804 2.63 - 5.25: 371 5.25 - 7.88: 43 7.88 - 10.50: 8 10.50 - 13.13: 3 Bond angle restraints: 17229 Sorted by residual: angle pdb=" C PHE A1063 " pdb=" N PRO A1064 " pdb=" CA PRO A1064 " ideal model delta sigma weight residual 127.00 140.13 -13.13 2.40e+00 1.74e-01 2.99e+01 angle pdb=" C PHE A1063 " pdb=" N PRO A1064 " pdb=" CD PRO A1064 " ideal model delta sigma weight residual 120.60 109.81 10.79 2.20e+00 2.07e-01 2.40e+01 angle pdb=" N LYS A 276 " pdb=" CA LYS A 276 " pdb=" C LYS A 276 " ideal model delta sigma weight residual 110.91 116.60 -5.69 1.17e+00 7.31e-01 2.37e+01 angle pdb=" N ILE B 403 " pdb=" CA ILE B 403 " pdb=" C ILE B 403 " ideal model delta sigma weight residual 111.91 107.80 4.11 8.90e-01 1.26e+00 2.14e+01 angle pdb=" CA TRP A 398 " pdb=" CB TRP A 398 " pdb=" CG TRP A 398 " ideal model delta sigma weight residual 113.60 121.89 -8.29 1.90e+00 2.77e-01 1.91e+01 ... (remaining 17224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.95: 7333 19.95 - 39.91: 236 39.91 - 59.86: 33 59.86 - 79.81: 7 79.81 - 99.76: 5 Dihedral angle restraints: 7614 sinusoidal: 3138 harmonic: 4476 Sorted by residual: dihedral pdb=" CA PHE B 398 " pdb=" C PHE B 398 " pdb=" N GLY B 399 " pdb=" CA GLY B 399 " ideal model delta harmonic sigma weight residual 180.00 148.79 31.21 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA GLN A1331 " pdb=" C GLN A1331 " pdb=" N TYR A1332 " pdb=" CA TYR A1332 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+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 -151.43 -28.57 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 7611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1669 0.090 - 0.180: 216 0.180 - 0.269: 17 0.269 - 0.359: 0 0.359 - 0.449: 1 Chirality restraints: 1903 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.06e+01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN B 240 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.85 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 1900 not shown) Planarity restraints: 2180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " 0.031 2.00e-02 2.50e+03 6.00e-02 3.60e+01 pdb=" C PHE B 398 " -0.104 2.00e-02 2.50e+03 pdb=" O PHE B 398 " 0.039 2.00e-02 2.50e+03 pdb=" N GLY B 399 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1408 " 0.030 2.00e-02 2.50e+03 5.84e-02 3.41e+01 pdb=" C VAL A1408 " -0.101 2.00e-02 2.50e+03 pdb=" O VAL A1408 " 0.037 2.00e-02 2.50e+03 pdb=" N GLU A1409 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 142 " 0.038 2.00e-02 2.50e+03 3.47e-02 3.00e+01 pdb=" CG TRP B 142 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 TRP B 142 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP B 142 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP B 142 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 142 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 142 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 142 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 142 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP B 142 " -0.000 2.00e-02 2.50e+03 ... (remaining 2177 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 279 2.69 - 3.24: 11571 3.24 - 3.79: 19482 3.79 - 4.35: 27466 4.35 - 4.90: 43885 Nonbonded interactions: 102683 Sorted by model distance: nonbonded pdb=" OD1 ASP A 667 " pdb="MG MG A1601 " model vdw 2.134 2.170 nonbonded pdb=" OD2 ASP A 667 " pdb=" F1 BEF A1602 " model vdw 2.213 2.990 nonbonded pdb=" OD2 ASP A 667 " pdb="MG MG A1601 " model vdw 2.241 2.170 nonbonded pdb=" O THR A 669 " pdb=" F1 BEF A1602 " model vdw 2.247 2.990 nonbonded pdb=" O CYS B 216 " pdb=" OG SER B 220 " model vdw 2.270 3.040 ... (remaining 102678 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.440 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.008 0.286 12724 Z= 0.375 Angle : 0.978 18.948 17242 Z= 0.524 Chirality : 0.060 0.449 1903 Planarity : 0.007 0.072 2179 Dihedral : 11.055 99.762 4738 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.07 % Allowed : 2.10 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.72 (0.16), residues: 1528 helix: -4.11 (0.10), residues: 596 sheet: -1.68 (0.34), residues: 198 loop : -2.60 (0.19), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 272 TYR 0.040 0.003 TYR A 618 PHE 0.047 0.004 PHE A1287 TRP 0.089 0.005 TRP B 142 HIS 0.007 0.002 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00842 (12718) covalent geometry : angle 0.95645 (17229) SS BOND : bond 0.00504 ( 2) SS BOND : angle 2.16141 ( 4) hydrogen bonds : bond 0.29366 ( 469) hydrogen bonds : angle 10.18123 ( 1335) Misc. bond : bond 0.00051 ( 1) link_BETA1-4 : bond 0.00922 ( 2) link_BETA1-4 : angle 7.04254 ( 6) link_NAG-ASN : bond 0.02304 ( 1) link_NAG-ASN : angle 11.74468 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.7342 (ttm) cc_final: 0.7125 (ttp) REVERT: A 464 ARG cc_start: 0.7758 (mtm180) cc_final: 0.6329 (ppt170) REVERT: A 1010 MET cc_start: 0.8498 (mtt) cc_final: 0.8235 (mtt) REVERT: A 1222 MET cc_start: 0.8042 (mtp) cc_final: 0.7740 (mtm) REVERT: A 1234 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8277 (p) REVERT: B 315 MET cc_start: 0.9067 (mmm) cc_final: 0.8809 (mmm) REVERT: B 403 ILE cc_start: 0.6593 (mm) cc_final: 0.6389 (mm) outliers start: 1 outliers final: 2 residues processed: 262 average time/residue: 0.6068 time to fit residues: 171.4718 Evaluate side-chains 154 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 1234 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 411 ASN A 477 ASN A 497 ASN A 504 ASN A 534 ASN A 685 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 HIS A 797 GLN A1061 HIS A1176 HIS A1195 ASN A1245 ASN A1307 HIS B 155 GLN B 171 ASN B 255 ASN B 256 ASN B 341 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.149461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118543 restraints weight = 15477.994| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.53 r_work: 0.3233 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12724 Z= 0.140 Angle : 0.672 9.420 17242 Z= 0.351 Chirality : 0.046 0.180 1903 Planarity : 0.005 0.055 2179 Dihedral : 9.607 88.175 1837 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.95 % Allowed : 9.07 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.19), residues: 1528 helix: -1.79 (0.18), residues: 604 sheet: -1.20 (0.35), residues: 196 loop : -2.19 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 731 TYR 0.023 0.002 TYR B 280 PHE 0.025 0.002 PHE A1365 TRP 0.031 0.002 TRP B 142 HIS 0.002 0.001 HIS A1176 Details of bonding type rmsd covalent geometry : bond 0.00310 (12718) covalent geometry : angle 0.66250 (17229) SS BOND : bond 0.00322 ( 2) SS BOND : angle 0.61906 ( 4) hydrogen bonds : bond 0.05007 ( 469) hydrogen bonds : angle 5.38955 ( 1335) Misc. bond : bond 0.00023 ( 1) link_BETA1-4 : bond 0.00558 ( 2) link_BETA1-4 : angle 3.78906 ( 6) link_NAG-ASN : bond 0.00814 ( 1) link_NAG-ASN : angle 6.86662 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 167 LEU cc_start: 0.7833 (mm) cc_final: 0.7604 (mt) REVERT: A 281 GLU cc_start: 0.6170 (mp0) cc_final: 0.5530 (mt-10) REVERT: A 457 ARG cc_start: 0.7750 (mmm160) cc_final: 0.7187 (mmt90) REVERT: A 464 ARG cc_start: 0.7930 (mtm180) cc_final: 0.5854 (tmm160) REVERT: A 849 MET cc_start: 0.7859 (tmt) cc_final: 0.7267 (tmt) REVERT: A 898 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7940 (tp) REVERT: A 1011 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7655 (tp30) REVERT: A 1036 LEU cc_start: 0.7492 (mp) cc_final: 0.7123 (mm) REVERT: A 1062 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6788 (pt0) REVERT: A 1222 MET cc_start: 0.8653 (mtp) cc_final: 0.8441 (mtm) REVERT: A 1234 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8308 (p) REVERT: B 403 ILE cc_start: 0.6511 (mm) cc_final: 0.6199 (mm) outliers start: 26 outliers final: 7 residues processed: 187 average time/residue: 0.6229 time to fit residues: 126.0174 Evaluate side-chains 153 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1042 LYS Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 196 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 497 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN A1330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.145579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113920 restraints weight = 15519.207| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.59 r_work: 0.3160 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 12724 Z= 0.212 Angle : 0.703 9.675 17242 Z= 0.362 Chirality : 0.048 0.187 1903 Planarity : 0.004 0.052 2179 Dihedral : 8.859 86.431 1833 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.85 % Allowed : 10.27 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.20), residues: 1528 helix: -0.78 (0.20), residues: 614 sheet: -1.11 (0.34), residues: 205 loop : -1.95 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 496 TYR 0.022 0.002 TYR B 278 PHE 0.025 0.002 PHE A1365 TRP 0.027 0.002 TRP B 142 HIS 0.005 0.001 HIS A 778 Details of bonding type rmsd covalent geometry : bond 0.00506 (12718) covalent geometry : angle 0.69074 (17229) SS BOND : bond 0.00284 ( 2) SS BOND : angle 0.88508 ( 4) hydrogen bonds : bond 0.04809 ( 469) hydrogen bonds : angle 5.03147 ( 1335) Misc. bond : bond 0.00011 ( 1) link_BETA1-4 : bond 0.00557 ( 2) link_BETA1-4 : angle 4.39374 ( 6) link_NAG-ASN : bond 0.01684 ( 1) link_NAG-ASN : angle 7.61831 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 281 GLU cc_start: 0.6134 (mp0) cc_final: 0.5872 (mp0) REVERT: A 402 LYS cc_start: 0.8306 (mttt) cc_final: 0.7740 (mtmt) REVERT: A 457 ARG cc_start: 0.7859 (mmm160) cc_final: 0.7291 (mmt90) REVERT: A 464 ARG cc_start: 0.7807 (mtm180) cc_final: 0.5761 (tmm160) REVERT: A 523 MET cc_start: 0.8320 (tpp) cc_final: 0.8002 (tpp) REVERT: A 1011 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7671 (tp30) REVERT: A 1222 MET cc_start: 0.8709 (mtp) cc_final: 0.8507 (mtm) REVERT: B 127 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7903 (mp10) REVERT: B 356 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8991 (mttm) REVERT: B 390 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7246 (tt) outliers start: 38 outliers final: 14 residues processed: 171 average time/residue: 0.5765 time to fit residues: 107.0851 Evaluate side-chains 152 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1042 LYS Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1194 LYS Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 143 optimal weight: 0.2980 chunk 149 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 92 optimal weight: 0.0870 chunk 26 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 571 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN B 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.117064 restraints weight = 15408.468| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.52 r_work: 0.3209 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12724 Z= 0.128 Angle : 0.603 7.628 17242 Z= 0.311 Chirality : 0.044 0.183 1903 Planarity : 0.004 0.045 2179 Dihedral : 7.918 86.728 1832 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.70 % Allowed : 11.17 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.21), residues: 1528 helix: -0.09 (0.21), residues: 607 sheet: -1.09 (0.34), residues: 207 loop : -1.81 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 496 TYR 0.022 0.001 TYR B 280 PHE 0.022 0.001 PHE A1365 TRP 0.018 0.002 TRP A 398 HIS 0.003 0.001 HIS A1330 Details of bonding type rmsd covalent geometry : bond 0.00293 (12718) covalent geometry : angle 0.59260 (17229) SS BOND : bond 0.00268 ( 2) SS BOND : angle 0.46404 ( 4) hydrogen bonds : bond 0.03838 ( 469) hydrogen bonds : angle 4.74287 ( 1335) Misc. bond : bond 0.00003 ( 1) link_BETA1-4 : bond 0.00414 ( 2) link_BETA1-4 : angle 3.93490 ( 6) link_NAG-ASN : bond 0.01030 ( 1) link_NAG-ASN : angle 6.71494 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.7873 (mtp) cc_final: 0.7457 (mtt) REVERT: A 402 LYS cc_start: 0.8334 (mttt) cc_final: 0.7750 (mtmt) REVERT: A 457 ARG cc_start: 0.7791 (mmm160) cc_final: 0.7308 (mmt90) REVERT: A 464 ARG cc_start: 0.7790 (mtm180) cc_final: 0.5749 (tmm160) REVERT: A 523 MET cc_start: 0.8255 (tpp) cc_final: 0.7910 (tpp) REVERT: A 1011 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7676 (tp30) REVERT: A 1222 MET cc_start: 0.8642 (mtp) cc_final: 0.8414 (mtm) REVERT: A 1266 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7732 (m110) REVERT: B 127 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: B 171 ASN cc_start: 0.8038 (t0) cc_final: 0.7823 (t0) outliers start: 36 outliers final: 20 residues processed: 172 average time/residue: 0.5696 time to fit residues: 106.9258 Evaluate side-chains 163 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1194 LYS Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 116 optimal weight: 0.0270 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 119 optimal weight: 0.3980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 ASN ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.147700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116023 restraints weight = 15536.571| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.60 r_work: 0.3189 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12724 Z= 0.141 Angle : 0.616 8.491 17242 Z= 0.315 Chirality : 0.045 0.179 1903 Planarity : 0.004 0.044 2179 Dihedral : 7.731 87.108 1832 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.77 % Allowed : 11.92 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.21), residues: 1528 helix: 0.18 (0.21), residues: 606 sheet: -1.07 (0.33), residues: 216 loop : -1.70 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1087 TYR 0.022 0.002 TYR B 280 PHE 0.022 0.002 PHE A1365 TRP 0.018 0.002 TRP A 398 HIS 0.003 0.001 HIS A1330 Details of bonding type rmsd covalent geometry : bond 0.00331 (12718) covalent geometry : angle 0.60539 (17229) SS BOND : bond 0.00213 ( 2) SS BOND : angle 0.65772 ( 4) hydrogen bonds : bond 0.03899 ( 469) hydrogen bonds : angle 4.63174 ( 1335) Misc. bond : bond 0.00008 ( 1) link_BETA1-4 : bond 0.00273 ( 2) link_BETA1-4 : angle 3.89597 ( 6) link_NAG-ASN : bond 0.01199 ( 1) link_NAG-ASN : angle 6.96957 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 402 LYS cc_start: 0.8369 (mttt) cc_final: 0.8141 (mttp) REVERT: A 460 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6063 (mtpt) REVERT: A 464 ARG cc_start: 0.7834 (mtm180) cc_final: 0.5718 (tmm160) REVERT: A 521 VAL cc_start: 0.8408 (t) cc_final: 0.8158 (p) REVERT: A 523 MET cc_start: 0.8233 (tpp) cc_final: 0.7947 (tpp) REVERT: A 731 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6983 (pmm-80) REVERT: A 994 GLU cc_start: 0.8414 (pm20) cc_final: 0.8179 (mp0) REVERT: A 1011 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7629 (tp30) REVERT: A 1062 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7319 (mp0) REVERT: A 1222 MET cc_start: 0.8679 (mtp) cc_final: 0.8440 (mtm) REVERT: A 1266 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7797 (m110) REVERT: B 127 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: B 333 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7682 (m-30) REVERT: B 356 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8975 (mttm) REVERT: B 390 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7322 (tt) outliers start: 37 outliers final: 17 residues processed: 165 average time/residue: 0.5956 time to fit residues: 106.7901 Evaluate side-chains 163 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 731 ARG Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1194 LYS Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 49 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 138 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1195 ASN A1245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116084 restraints weight = 15441.201| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.52 r_work: 0.3192 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12724 Z= 0.147 Angle : 0.617 7.990 17242 Z= 0.315 Chirality : 0.045 0.178 1903 Planarity : 0.004 0.046 2179 Dihedral : 7.695 89.154 1832 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.92 % Allowed : 12.14 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.21), residues: 1528 helix: 0.22 (0.21), residues: 617 sheet: -0.97 (0.33), residues: 214 loop : -1.70 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1087 TYR 0.022 0.002 TYR B 280 PHE 0.022 0.002 PHE A1365 TRP 0.018 0.002 TRP A 398 HIS 0.004 0.001 HIS A1330 Details of bonding type rmsd covalent geometry : bond 0.00345 (12718) covalent geometry : angle 0.60566 (17229) SS BOND : bond 0.00266 ( 2) SS BOND : angle 0.60973 ( 4) hydrogen bonds : bond 0.03873 ( 469) hydrogen bonds : angle 4.57589 ( 1335) Misc. bond : bond 0.00016 ( 1) link_BETA1-4 : bond 0.00350 ( 2) link_BETA1-4 : angle 3.83649 ( 6) link_NAG-ASN : bond 0.01225 ( 1) link_NAG-ASN : angle 7.03313 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7549 (mtt) REVERT: A 402 LYS cc_start: 0.8373 (mttt) cc_final: 0.8145 (mttp) REVERT: A 460 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6036 (mtpt) REVERT: A 464 ARG cc_start: 0.7831 (mtm180) cc_final: 0.5726 (tmm160) REVERT: A 521 VAL cc_start: 0.8368 (t) cc_final: 0.8124 (p) REVERT: A 523 MET cc_start: 0.8229 (tpp) cc_final: 0.7956 (tpp) REVERT: A 994 GLU cc_start: 0.8398 (pm20) cc_final: 0.8187 (mp0) REVERT: A 1011 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: A 1036 LEU cc_start: 0.7409 (mp) cc_final: 0.7015 (mm) REVERT: A 1223 MET cc_start: 0.8421 (mtp) cc_final: 0.7779 (ttm) REVERT: A 1266 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7792 (m110) REVERT: B 127 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7844 (mp10) REVERT: B 333 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7594 (m-30) REVERT: B 356 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8992 (mttm) REVERT: B 390 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7339 (tt) outliers start: 39 outliers final: 21 residues processed: 172 average time/residue: 0.6127 time to fit residues: 114.0158 Evaluate side-chains 174 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 783 GLU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1194 LYS Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 134 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 0.0010 chunk 120 optimal weight: 0.7980 chunk 147 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 127 optimal weight: 0.0070 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1195 ASN A1245 ASN A1295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.149255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.117756 restraints weight = 15323.541| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.54 r_work: 0.3220 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12724 Z= 0.119 Angle : 0.589 7.531 17242 Z= 0.301 Chirality : 0.044 0.183 1903 Planarity : 0.003 0.047 2179 Dihedral : 7.471 89.643 1832 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.92 % Allowed : 12.82 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.21), residues: 1528 helix: 0.35 (0.21), residues: 625 sheet: -0.82 (0.34), residues: 206 loop : -1.69 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1087 TYR 0.022 0.001 TYR B 280 PHE 0.021 0.001 PHE A1365 TRP 0.014 0.001 TRP A 398 HIS 0.002 0.001 HIS A1330 Details of bonding type rmsd covalent geometry : bond 0.00271 (12718) covalent geometry : angle 0.57808 (17229) SS BOND : bond 0.00199 ( 2) SS BOND : angle 0.46112 ( 4) hydrogen bonds : bond 0.03605 ( 469) hydrogen bonds : angle 4.48827 ( 1335) Misc. bond : bond 0.00011 ( 1) link_BETA1-4 : bond 0.00354 ( 2) link_BETA1-4 : angle 3.60254 ( 6) link_NAG-ASN : bond 0.01013 ( 1) link_NAG-ASN : angle 6.71542 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7549 (mtt) REVERT: A 402 LYS cc_start: 0.8359 (mttt) cc_final: 0.8154 (mttp) REVERT: A 460 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6037 (mtpt) REVERT: A 464 ARG cc_start: 0.7806 (mtm180) cc_final: 0.5710 (tmm160) REVERT: A 521 VAL cc_start: 0.8340 (t) cc_final: 0.8112 (p) REVERT: A 523 MET cc_start: 0.8190 (tpp) cc_final: 0.7918 (tpp) REVERT: A 994 GLU cc_start: 0.8388 (pm20) cc_final: 0.8103 (mp0) REVERT: A 1011 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7605 (tp30) REVERT: A 1036 LEU cc_start: 0.7250 (mp) cc_final: 0.6865 (mm) REVERT: A 1223 MET cc_start: 0.8346 (mtp) cc_final: 0.7738 (ttm) REVERT: B 127 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7832 (mp10) REVERT: B 170 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7866 (mtpp) REVERT: B 333 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: B 356 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8957 (mttm) outliers start: 39 outliers final: 18 residues processed: 174 average time/residue: 0.5600 time to fit residues: 106.0206 Evaluate side-chains 164 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1194 LYS Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 19 optimal weight: 2.9990 chunk 127 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.146764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.115036 restraints weight = 15305.963| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.53 r_work: 0.3176 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12724 Z= 0.168 Angle : 0.640 8.454 17242 Z= 0.327 Chirality : 0.046 0.185 1903 Planarity : 0.004 0.049 2179 Dihedral : 7.706 87.817 1832 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.55 % Allowed : 13.42 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.21), residues: 1528 helix: 0.35 (0.21), residues: 620 sheet: -0.76 (0.34), residues: 214 loop : -1.61 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1087 TYR 0.022 0.002 TYR B 280 PHE 0.023 0.002 PHE A1365 TRP 0.018 0.002 TRP A 398 HIS 0.005 0.001 HIS A1330 Details of bonding type rmsd covalent geometry : bond 0.00398 (12718) covalent geometry : angle 0.62912 (17229) SS BOND : bond 0.00239 ( 2) SS BOND : angle 0.74762 ( 4) hydrogen bonds : bond 0.03957 ( 469) hydrogen bonds : angle 4.54536 ( 1335) Misc. bond : bond 0.00020 ( 1) link_BETA1-4 : bond 0.00451 ( 2) link_BETA1-4 : angle 3.90863 ( 6) link_NAG-ASN : bond 0.01328 ( 1) link_NAG-ASN : angle 7.29420 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7489 (mtp) REVERT: A 402 LYS cc_start: 0.8367 (mttt) cc_final: 0.8127 (mttp) REVERT: A 460 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6035 (mtpt) REVERT: A 464 ARG cc_start: 0.7924 (mtm180) cc_final: 0.5754 (tmm160) REVERT: A 521 VAL cc_start: 0.8370 (t) cc_final: 0.8139 (p) REVERT: A 523 MET cc_start: 0.8148 (tpp) cc_final: 0.7887 (tpp) REVERT: A 954 GLU cc_start: 0.5531 (tp30) cc_final: 0.4413 (tm-30) REVERT: A 1011 GLU cc_start: 0.7935 (mp0) cc_final: 0.7629 (tp30) REVERT: A 1036 LEU cc_start: 0.7485 (mp) cc_final: 0.7100 (mm) REVERT: A 1223 MET cc_start: 0.8427 (mtp) cc_final: 0.7781 (ttm) REVERT: B 127 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7864 (mp10) REVERT: B 333 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: B 356 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.9013 (mttm) outliers start: 34 outliers final: 22 residues processed: 164 average time/residue: 0.5734 time to fit residues: 102.2369 Evaluate side-chains 170 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1194 LYS Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.147577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.115870 restraints weight = 15404.477| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.57 r_work: 0.3190 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12724 Z= 0.144 Angle : 0.620 7.861 17242 Z= 0.317 Chirality : 0.045 0.179 1903 Planarity : 0.003 0.049 2179 Dihedral : 7.647 84.737 1832 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.55 % Allowed : 13.79 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.21), residues: 1528 helix: 0.36 (0.21), residues: 627 sheet: -0.68 (0.34), residues: 214 loop : -1.59 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1087 TYR 0.022 0.001 TYR B 280 PHE 0.023 0.001 PHE A1365 TRP 0.016 0.002 TRP B 348 HIS 0.004 0.001 HIS A1330 Details of bonding type rmsd covalent geometry : bond 0.00338 (12718) covalent geometry : angle 0.60937 (17229) SS BOND : bond 0.00252 ( 2) SS BOND : angle 0.56116 ( 4) hydrogen bonds : bond 0.03804 ( 469) hydrogen bonds : angle 4.51294 ( 1335) Misc. bond : bond 0.00031 ( 1) link_BETA1-4 : bond 0.00336 ( 2) link_BETA1-4 : angle 3.78882 ( 6) link_NAG-ASN : bond 0.01181 ( 1) link_NAG-ASN : angle 7.02227 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7525 (mtp) REVERT: A 276 LYS cc_start: 0.7828 (mmtt) cc_final: 0.6728 (mppt) REVERT: A 395 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8433 (ttmm) REVERT: A 402 LYS cc_start: 0.8374 (mttt) cc_final: 0.8146 (mttp) REVERT: A 460 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6036 (mtpt) REVERT: A 464 ARG cc_start: 0.7904 (mtm180) cc_final: 0.5642 (tmm160) REVERT: A 521 VAL cc_start: 0.8343 (t) cc_final: 0.8119 (p) REVERT: A 523 MET cc_start: 0.8148 (tpp) cc_final: 0.7883 (tpp) REVERT: A 954 GLU cc_start: 0.5606 (tp30) cc_final: 0.4439 (tm-30) REVERT: A 1011 GLU cc_start: 0.7918 (mp0) cc_final: 0.7635 (tp30) REVERT: A 1036 LEU cc_start: 0.7354 (mp) cc_final: 0.6972 (mm) REVERT: A 1223 MET cc_start: 0.8401 (mtp) cc_final: 0.7769 (ttm) REVERT: B 127 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7864 (mp10) REVERT: B 333 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: B 356 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8991 (mttm) REVERT: B 390 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7441 (tt) outliers start: 34 outliers final: 18 residues processed: 164 average time/residue: 0.5954 time to fit residues: 105.9072 Evaluate side-chains 168 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 136 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 151 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.116179 restraints weight = 15407.520| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.57 r_work: 0.3194 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12724 Z= 0.138 Angle : 0.622 7.732 17242 Z= 0.318 Chirality : 0.045 0.192 1903 Planarity : 0.003 0.049 2179 Dihedral : 7.628 82.892 1832 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.95 % Allowed : 14.47 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.21), residues: 1528 helix: 0.41 (0.21), residues: 626 sheet: -0.62 (0.34), residues: 214 loop : -1.56 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1087 TYR 0.023 0.001 TYR A1040 PHE 0.022 0.001 PHE A1365 TRP 0.015 0.002 TRP A 468 HIS 0.003 0.001 HIS A1330 Details of bonding type rmsd covalent geometry : bond 0.00322 (12718) covalent geometry : angle 0.61119 (17229) SS BOND : bond 0.00225 ( 2) SS BOND : angle 0.54261 ( 4) hydrogen bonds : bond 0.03733 ( 469) hydrogen bonds : angle 4.45632 ( 1335) Misc. bond : bond 0.00024 ( 1) link_BETA1-4 : bond 0.00377 ( 2) link_BETA1-4 : angle 3.68323 ( 6) link_NAG-ASN : bond 0.01073 ( 1) link_NAG-ASN : angle 6.99945 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7448 (mtp) REVERT: A 402 LYS cc_start: 0.8384 (mttt) cc_final: 0.8165 (mttp) REVERT: A 460 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6027 (mtpt) REVERT: A 464 ARG cc_start: 0.7902 (mtm180) cc_final: 0.5640 (tmm160) REVERT: A 484 ASN cc_start: 0.8250 (m-40) cc_final: 0.7937 (m-40) REVERT: A 521 VAL cc_start: 0.8322 (t) cc_final: 0.8103 (p) REVERT: A 523 MET cc_start: 0.8124 (tpp) cc_final: 0.7858 (tpp) REVERT: A 945 GLU cc_start: 0.6196 (mp0) cc_final: 0.5890 (pm20) REVERT: A 1011 GLU cc_start: 0.7908 (mp0) cc_final: 0.7643 (tp30) REVERT: A 1036 LEU cc_start: 0.7374 (mp) cc_final: 0.6994 (mm) REVERT: A 1223 MET cc_start: 0.8401 (mtp) cc_final: 0.7777 (ttm) REVERT: B 127 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: B 333 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7639 (m-30) REVERT: B 356 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8992 (mttm) outliers start: 26 outliers final: 17 residues processed: 159 average time/residue: 0.5858 time to fit residues: 101.3538 Evaluate side-chains 167 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 130 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 0.0370 chunk 118 optimal weight: 0.0170 chunk 150 optimal weight: 2.9990 chunk 99 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1195 ASN A1245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.149764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118379 restraints weight = 15281.457| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.48 r_work: 0.3230 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12724 Z= 0.109 Angle : 0.590 7.709 17242 Z= 0.301 Chirality : 0.044 0.189 1903 Planarity : 0.003 0.049 2179 Dihedral : 7.474 82.801 1832 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.72 % Allowed : 14.62 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.22), residues: 1528 helix: 0.52 (0.21), residues: 623 sheet: -0.48 (0.35), residues: 206 loop : -1.57 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1087 TYR 0.025 0.001 TYR A1040 PHE 0.020 0.001 PHE A1365 TRP 0.020 0.001 TRP B 348 HIS 0.002 0.000 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00241 (12718) covalent geometry : angle 0.57983 (17229) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.36302 ( 4) hydrogen bonds : bond 0.03497 ( 469) hydrogen bonds : angle 4.36181 ( 1335) Misc. bond : bond 0.00001 ( 1) link_BETA1-4 : bond 0.00582 ( 2) link_BETA1-4 : angle 3.51764 ( 6) link_NAG-ASN : bond 0.00750 ( 1) link_NAG-ASN : angle 6.48732 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4578.92 seconds wall clock time: 78 minutes 39.47 seconds (4719.47 seconds total)