Starting phenix.real_space_refine on Wed Jul 30 23:57:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7drx_30829/07_2025/7drx_30829.cif Found real_map, /net/cci-nas-00/data/ceres_data/7drx_30829/07_2025/7drx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7drx_30829/07_2025/7drx_30829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7drx_30829/07_2025/7drx_30829.map" model { file = "/net/cci-nas-00/data/ceres_data/7drx_30829/07_2025/7drx_30829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7drx_30829/07_2025/7drx_30829.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.47, per 1000 atoms: 0.60 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: 3.06 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.43 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: 4.41 Time building geometry restraints manager: 3.63 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.700 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.300 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.089 0.005 TRP B 142 HIS 0.007 0.002 HIS B 186 PHE 0.047 0.004 PHE A1287 TYR 0.040 0.003 TYR A 618 ARG 0.010 0.001 ARG B 272 Details of bonding type rmsd link_NAG-ASN : bond 0.02304 ( 1) link_NAG-ASN : angle 11.74468 ( 3) link_BETA1-4 : bond 0.00922 ( 2) link_BETA1-4 : angle 7.04254 ( 6) hydrogen bonds : bond 0.29366 ( 469) hydrogen bonds : angle 10.18123 ( 1335) SS BOND : bond 0.00504 ( 2) SS BOND : angle 2.16141 ( 4) covalent geometry : bond 0.00842 (12718) covalent geometry : angle 0.95645 (17229) Misc. bond : bond 0.00051 ( 1) *********************** 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 : 1.313 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: 1.3385 time to fit residues: 379.8358 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 : 1.469 ------------------------------------------------------------------------------- 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 129 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 119 optimal weight: 0.0470 chunk 46 optimal weight: 0.0050 chunk 72 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 138 optimal weight: 0.4980 overall best weight: 0.3092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 477 ASN A 497 ASN A 504 ASN A 571 ASN A 685 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 HIS A 797 GLN A1061 HIS A1176 HIS A1245 ASN A1307 HIS B 67 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN B 171 ASN B 255 ASN B 256 ASN B 341 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.150774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.119813 restraints weight = 15339.610| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.50 r_work: 0.3258 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12724 Z= 0.129 Angle : 0.649 8.909 17242 Z= 0.340 Chirality : 0.045 0.182 1903 Planarity : 0.005 0.055 2179 Dihedral : 9.292 87.068 1837 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.80 % Allowed : 8.92 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.19), residues: 1528 helix: -1.80 (0.18), residues: 604 sheet: -1.38 (0.34), residues: 206 loop : -2.17 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 142 HIS 0.002 0.001 HIS A1176 PHE 0.025 0.002 PHE A1365 TYR 0.020 0.002 TYR B 280 ARG 0.005 0.000 ARG A 848 Details of bonding type rmsd link_NAG-ASN : bond 0.00735 ( 1) link_NAG-ASN : angle 6.72782 ( 3) link_BETA1-4 : bond 0.01104 ( 2) link_BETA1-4 : angle 3.65431 ( 6) hydrogen bonds : bond 0.04844 ( 469) hydrogen bonds : angle 5.35819 ( 1335) SS BOND : bond 0.00259 ( 2) SS BOND : angle 0.58967 ( 4) covalent geometry : bond 0.00277 (12718) covalent geometry : angle 0.63981 (17229) Misc. bond : bond 0.00007 ( 1) *********************** 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 198 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: A 167 LEU cc_start: 0.7819 (mm) cc_final: 0.7597 (mt) REVERT: A 281 GLU cc_start: 0.6147 (mp0) cc_final: 0.5497 (mt-10) REVERT: A 402 LYS cc_start: 0.8252 (mttt) cc_final: 0.7790 (mtmt) REVERT: A 457 ARG cc_start: 0.7762 (mmm160) cc_final: 0.7201 (mmt90) REVERT: A 464 ARG cc_start: 0.7921 (mtm180) cc_final: 0.6142 (tmt170) REVERT: A 898 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7972 (tp) REVERT: A 1011 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7645 (tp30) REVERT: A 1036 LEU cc_start: 0.7438 (mp) cc_final: 0.7106 (mm) REVERT: A 1062 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6772 (pt0) REVERT: A 1195 ASN cc_start: 0.8400 (t0) cc_final: 0.8179 (t0) REVERT: A 1222 MET cc_start: 0.8636 (mtp) cc_final: 0.8423 (mtm) REVERT: B 170 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7909 (mtpp) REVERT: B 403 ILE cc_start: 0.6530 (mm) cc_final: 0.6269 (mm) outliers start: 24 outliers final: 7 residues processed: 190 average time/residue: 1.3697 time to fit residues: 282.3199 Evaluate side-chains 152 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU 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 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 80 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 410 HIS A 497 ASN A 534 ASN A 550 ASN A 571 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN A1330 HIS ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.145259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.113477 restraints weight = 15548.994| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.57 r_work: 0.3154 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 12724 Z= 0.230 Angle : 0.715 10.120 17242 Z= 0.368 Chirality : 0.049 0.188 1903 Planarity : 0.004 0.052 2179 Dihedral : 8.763 86.101 1832 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.00 % Allowed : 10.27 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.20), residues: 1528 helix: -0.78 (0.20), residues: 616 sheet: -1.11 (0.34), residues: 205 loop : -1.95 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 142 HIS 0.005 0.001 HIS A 778 PHE 0.025 0.002 PHE A1365 TYR 0.023 0.002 TYR B 278 ARG 0.004 0.001 ARG A 848 Details of bonding type rmsd link_NAG-ASN : bond 0.01731 ( 1) link_NAG-ASN : angle 7.76915 ( 3) link_BETA1-4 : bond 0.00036 ( 2) link_BETA1-4 : angle 4.43119 ( 6) hydrogen bonds : bond 0.04912 ( 469) hydrogen bonds : angle 5.02648 ( 1335) SS BOND : bond 0.00263 ( 2) SS BOND : angle 0.96405 ( 4) covalent geometry : bond 0.00550 (12718) covalent geometry : angle 0.70291 (17229) Misc. bond : bond 0.00008 ( 1) *********************** 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 184 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 1.385 Fit side-chains revert: symmetry clash REVERT: A 202 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7981 (p) REVERT: A 281 GLU cc_start: 0.6110 (mp0) cc_final: 0.5761 (mp0) REVERT: A 402 LYS cc_start: 0.8318 (mttt) cc_final: 0.7744 (mtmt) REVERT: A 457 ARG cc_start: 0.7802 (mmm160) cc_final: 0.7252 (mmt90) REVERT: A 464 ARG cc_start: 0.7815 (mtm180) cc_final: 0.5778 (tmm160) REVERT: A 523 MET cc_start: 0.8325 (tpp) cc_final: 0.8014 (tpp) REVERT: A 953 ARG cc_start: 0.6740 (OUTLIER) cc_final: 0.6370 (mmt180) REVERT: A 1011 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7692 (tp30) REVERT: A 1195 ASN cc_start: 0.8438 (t0) cc_final: 0.8224 (t0) REVERT: B 333 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7674 (m-30) REVERT: B 356 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8986 (mttm) REVERT: B 390 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7286 (tt) outliers start: 40 outliers final: 14 residues processed: 166 average time/residue: 1.3174 time to fit residues: 238.7222 Evaluate side-chains 152 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 458 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 782 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 953 ARG 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 1416 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 99 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 126 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.0270 chunk 62 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN A1245 ASN B 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.147382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.115858 restraints weight = 15326.325| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.53 r_work: 0.3190 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12724 Z= 0.146 Angle : 0.626 8.188 17242 Z= 0.322 Chirality : 0.045 0.178 1903 Planarity : 0.004 0.045 2179 Dihedral : 8.055 89.402 1832 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.92 % Allowed : 10.79 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.21), residues: 1528 helix: -0.18 (0.21), residues: 609 sheet: -1.15 (0.33), residues: 215 loop : -1.80 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 398 HIS 0.004 0.001 HIS A1330 PHE 0.023 0.002 PHE A1365 TYR 0.022 0.002 TYR B 280 ARG 0.004 0.000 ARG A 496 Details of bonding type rmsd link_NAG-ASN : bond 0.01234 ( 1) link_NAG-ASN : angle 7.01613 ( 3) link_BETA1-4 : bond 0.00500 ( 2) link_BETA1-4 : angle 4.03882 ( 6) hydrogen bonds : bond 0.04005 ( 469) hydrogen bonds : angle 4.78331 ( 1335) SS BOND : bond 0.00271 ( 2) SS BOND : angle 0.58136 ( 4) covalent geometry : bond 0.00338 (12718) covalent geometry : angle 0.61453 (17229) Misc. bond : bond 0.00007 ( 1) *********************** 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 188 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 1.422 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.7879 (mtp) cc_final: 0.7437 (mtt) REVERT: A 202 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7922 (p) REVERT: A 402 LYS cc_start: 0.8329 (mttt) cc_final: 0.7757 (mtmt) REVERT: A 457 ARG cc_start: 0.7811 (mmm160) cc_final: 0.7400 (mmt90) REVERT: A 464 ARG cc_start: 0.7819 (mtm180) cc_final: 0.5718 (tmm160) REVERT: A 523 MET cc_start: 0.8325 (tpp) cc_final: 0.8068 (tpp) REVERT: A 953 ARG cc_start: 0.6573 (OUTLIER) cc_final: 0.6325 (mmt180) REVERT: A 1011 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7700 (tp30) REVERT: A 1195 ASN cc_start: 0.8369 (t0) cc_final: 0.8156 (t160) REVERT: A 1266 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7767 (m110) REVERT: B 127 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: B 390 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7295 (tt) outliers start: 39 outliers final: 16 residues processed: 171 average time/residue: 1.2461 time to fit residues: 232.7027 Evaluate side-chains 160 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 421 LEU 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 953 ARG Chi-restraints excluded: chain A residue 989 THR 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 1234 VAL Chi-restraints excluded: chain A residue 1266 ASN 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 207 THR Chi-restraints excluded: chain B residue 390 LEU 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 67 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.144865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113375 restraints weight = 15456.931| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.55 r_work: 0.3147 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12724 Z= 0.211 Angle : 0.685 9.543 17242 Z= 0.350 Chirality : 0.048 0.189 1903 Planarity : 0.004 0.045 2179 Dihedral : 8.160 89.138 1832 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.15 % Allowed : 11.39 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.21), residues: 1528 helix: -0.06 (0.21), residues: 612 sheet: -1.09 (0.33), residues: 215 loop : -1.78 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 398 HIS 0.006 0.001 HIS A1330 PHE 0.024 0.002 PHE A1365 TYR 0.022 0.002 TYR B 280 ARG 0.005 0.000 ARG A1087 Details of bonding type rmsd link_NAG-ASN : bond 0.01712 ( 1) link_NAG-ASN : angle 7.69997 ( 3) link_BETA1-4 : bond 0.00383 ( 2) link_BETA1-4 : angle 4.34188 ( 6) hydrogen bonds : bond 0.04403 ( 469) hydrogen bonds : angle 4.77663 ( 1335) SS BOND : bond 0.00257 ( 2) SS BOND : angle 0.90844 ( 4) covalent geometry : bond 0.00507 (12718) covalent geometry : angle 0.67300 (17229) Misc. bond : bond 0.00014 ( 1) *********************** 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 186 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 1.409 Fit side-chains revert: symmetry clash REVERT: A 202 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7958 (p) REVERT: A 402 LYS cc_start: 0.8354 (mttt) cc_final: 0.7765 (mtmt) REVERT: A 457 ARG cc_start: 0.7756 (mmm160) cc_final: 0.7381 (mmt90) REVERT: A 460 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6141 (mtpt) REVERT: A 464 ARG cc_start: 0.7839 (mtm180) cc_final: 0.5663 (tmm160) REVERT: A 523 MET cc_start: 0.8255 (tpp) cc_final: 0.7982 (tpp) REVERT: A 765 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.7148 (mmp-170) REVERT: A 953 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6507 (mmt180) REVERT: A 1011 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7640 (tp30) REVERT: A 1062 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7318 (mp0) REVERT: B 169 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8216 (mtt) REVERT: B 333 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7633 (m-30) REVERT: B 356 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.9013 (mttm) REVERT: B 390 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7380 (tt) outliers start: 42 outliers final: 23 residues processed: 168 average time/residue: 1.2625 time to fit residues: 231.2865 Evaluate side-chains 167 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 262 ASP 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 765 ARG 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 953 ARG 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 1266 ASN Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1408 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 169 MET Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 264 ILE 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 61 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3682 r_free = 0.3682 target = 0.141905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110238 restraints weight = 15663.179| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.55 r_work: 0.3105 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 12724 Z= 0.313 Angle : 0.792 11.863 17242 Z= 0.403 Chirality : 0.053 0.217 1903 Planarity : 0.005 0.048 2179 Dihedral : 8.602 84.196 1832 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.67 % Allowed : 11.84 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.21), residues: 1528 helix: -0.23 (0.20), residues: 617 sheet: -0.96 (0.34), residues: 215 loop : -1.86 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 398 HIS 0.009 0.002 HIS A1330 PHE 0.029 0.003 PHE B 86 TYR 0.023 0.002 TYR A1326 ARG 0.005 0.001 ARG A1183 Details of bonding type rmsd link_NAG-ASN : bond 0.02365 ( 1) link_NAG-ASN : angle 8.43645 ( 3) link_BETA1-4 : bond 0.00353 ( 2) link_BETA1-4 : angle 5.16202 ( 6) hydrogen bonds : bond 0.05045 ( 469) hydrogen bonds : angle 4.98104 ( 1335) SS BOND : bond 0.00377 ( 2) SS BOND : angle 1.14317 ( 4) covalent geometry : bond 0.00755 (12718) covalent geometry : angle 0.77845 (17229) Misc. bond : bond 0.00033 ( 1) *********************** 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 193 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 1.561 Fit side-chains revert: symmetry clash REVERT: A 202 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7912 (p) REVERT: A 402 LYS cc_start: 0.8358 (mttt) cc_final: 0.7743 (mtmt) REVERT: A 457 ARG cc_start: 0.7888 (mmm160) cc_final: 0.7551 (mmt90) REVERT: A 460 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6096 (mtpt) REVERT: A 464 ARG cc_start: 0.7828 (mtm180) cc_final: 0.5659 (tmm160) REVERT: A 523 MET cc_start: 0.8263 (tpp) cc_final: 0.7926 (tpp) REVERT: A 765 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7061 (mmp-170) REVERT: A 953 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6671 (mmt180) REVERT: A 1011 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: A 1062 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7310 (mp0) REVERT: B 169 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8153 (mtt) REVERT: B 333 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: B 356 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9048 (mttm) REVERT: B 390 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7420 (tt) outliers start: 49 outliers final: 25 residues processed: 172 average time/residue: 1.2675 time to fit residues: 240.0597 Evaluate side-chains 172 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 485 MET 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 765 ARG 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 953 ARG Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1040 TYR Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1408 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 169 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 264 ILE 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 151 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 46 optimal weight: 0.0010 chunk 16 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.147121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.115633 restraints weight = 15457.299| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.56 r_work: 0.3184 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12724 Z= 0.131 Angle : 0.625 10.439 17242 Z= 0.319 Chirality : 0.045 0.176 1903 Planarity : 0.004 0.046 2179 Dihedral : 7.982 85.745 1832 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.32 % Allowed : 13.79 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.21), residues: 1528 helix: 0.15 (0.21), residues: 622 sheet: -0.90 (0.35), residues: 207 loop : -1.76 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 348 HIS 0.003 0.001 HIS A1330 PHE 0.021 0.001 PHE A1365 TYR 0.023 0.001 TYR A1040 ARG 0.004 0.000 ARG A 496 Details of bonding type rmsd link_NAG-ASN : bond 0.01271 ( 1) link_NAG-ASN : angle 7.10456 ( 3) link_BETA1-4 : bond 0.00489 ( 2) link_BETA1-4 : angle 3.85058 ( 6) hydrogen bonds : bond 0.03807 ( 469) hydrogen bonds : angle 4.66070 ( 1335) SS BOND : bond 0.00304 ( 2) SS BOND : angle 0.43205 ( 4) covalent geometry : bond 0.00302 (12718) covalent geometry : angle 0.61390 (17229) Misc. bond : bond 0.00024 ( 1) *********************** 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 186 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 1.501 Fit side-chains revert: symmetry clash REVERT: A 402 LYS cc_start: 0.8349 (mttt) cc_final: 0.7772 (mtmt) REVERT: A 457 ARG cc_start: 0.7849 (mmm160) cc_final: 0.7518 (mmt90) REVERT: A 464 ARG cc_start: 0.7944 (mtm180) cc_final: 0.5668 (tmm160) REVERT: A 496 ARG cc_start: 0.7716 (mtt90) cc_final: 0.7257 (mmm160) REVERT: A 523 MET cc_start: 0.8252 (tpp) cc_final: 0.7935 (tpp) REVERT: A 953 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6711 (mmt180) REVERT: A 1011 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7622 (tp30) REVERT: A 1195 ASN cc_start: 0.8217 (t0) cc_final: 0.7992 (t0) REVERT: B 356 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8968 (mttm) REVERT: B 402 LYS cc_start: 0.6404 (mptt) cc_final: 0.6118 (mmmm) outliers start: 31 outliers final: 16 residues processed: 171 average time/residue: 1.2720 time to fit residues: 237.3825 Evaluate side-chains 164 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 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 953 ARG Chi-restraints excluded: chain A residue 1011 GLU 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 170 LYS 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 0 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A1245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112204 restraints weight = 15528.721| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.57 r_work: 0.3133 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 12724 Z= 0.229 Angle : 0.709 10.208 17242 Z= 0.361 Chirality : 0.049 0.202 1903 Planarity : 0.004 0.049 2179 Dihedral : 8.258 83.471 1832 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.40 % Allowed : 14.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1528 helix: 0.06 (0.21), residues: 621 sheet: -0.86 (0.35), residues: 215 loop : -1.73 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 398 HIS 0.007 0.001 HIS A1330 PHE 0.023 0.002 PHE A1365 TYR 0.022 0.002 TYR B 280 ARG 0.005 0.001 ARG A 496 Details of bonding type rmsd link_NAG-ASN : bond 0.01744 ( 1) link_NAG-ASN : angle 7.94968 ( 3) link_BETA1-4 : bond 0.00387 ( 2) link_BETA1-4 : angle 4.45000 ( 6) hydrogen bonds : bond 0.04431 ( 469) hydrogen bonds : angle 4.74860 ( 1335) SS BOND : bond 0.00274 ( 2) SS BOND : angle 0.88758 ( 4) covalent geometry : bond 0.00551 (12718) covalent geometry : angle 0.69613 (17229) Misc. bond : bond 0.00050 ( 1) *********************** 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 177 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 1.443 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7741 (mtp) REVERT: A 202 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.7781 (p) REVERT: A 402 LYS cc_start: 0.8355 (mttt) cc_final: 0.7752 (mtmt) REVERT: A 460 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6052 (mtpt) REVERT: A 464 ARG cc_start: 0.7951 (mtm180) cc_final: 0.5677 (tmm160) REVERT: A 496 ARG cc_start: 0.7722 (mtt90) cc_final: 0.7265 (mmm160) REVERT: A 523 MET cc_start: 0.8291 (tpp) cc_final: 0.7948 (tpp) REVERT: A 765 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6970 (mmp-170) REVERT: A 994 GLU cc_start: 0.8459 (pm20) cc_final: 0.8209 (mp0) REVERT: A 1011 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7651 (tp30) REVERT: B 333 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7633 (m-30) REVERT: B 356 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.9035 (mttm) REVERT: B 390 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7470 (tt) outliers start: 32 outliers final: 16 residues processed: 160 average time/residue: 1.4058 time to fit residues: 245.2630 Evaluate side-chains 166 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 229 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 765 ARG 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 876 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1011 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 85 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 22 optimal weight: 0.0470 chunk 29 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.146281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.114641 restraints weight = 15341.760| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.52 r_work: 0.3175 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12724 Z= 0.143 Angle : 0.640 9.628 17242 Z= 0.326 Chirality : 0.045 0.192 1903 Planarity : 0.004 0.050 2179 Dihedral : 8.062 83.679 1832 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.10 % Allowed : 14.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.21), residues: 1528 helix: 0.16 (0.21), residues: 630 sheet: -0.81 (0.35), residues: 213 loop : -1.68 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 348 HIS 0.003 0.001 HIS A1330 PHE 0.021 0.002 PHE A1365 TYR 0.023 0.002 TYR B 280 ARG 0.004 0.000 ARG A 496 Details of bonding type rmsd link_NAG-ASN : bond 0.01226 ( 1) link_NAG-ASN : angle 7.18701 ( 3) link_BETA1-4 : bond 0.00388 ( 2) link_BETA1-4 : angle 3.90439 ( 6) hydrogen bonds : bond 0.03894 ( 469) hydrogen bonds : angle 4.62897 ( 1335) SS BOND : bond 0.00272 ( 2) SS BOND : angle 0.53117 ( 4) covalent geometry : bond 0.00333 (12718) covalent geometry : angle 0.62885 (17229) Misc. bond : bond 0.00028 ( 1) *********************** 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 175 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 1.387 Fit side-chains revert: symmetry clash REVERT: A 402 LYS cc_start: 0.8351 (mttt) cc_final: 0.7766 (mtmt) REVERT: A 464 ARG cc_start: 0.7909 (mtm180) cc_final: 0.5657 (tmm160) REVERT: A 496 ARG cc_start: 0.7686 (mtt90) cc_final: 0.7240 (mmm160) REVERT: A 523 MET cc_start: 0.8268 (tpp) cc_final: 0.7916 (tpp) REVERT: A 765 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6940 (mmp-170) REVERT: A 994 GLU cc_start: 0.8414 (pm20) cc_final: 0.8201 (mp0) REVERT: A 1011 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7648 (tp30) REVERT: A 1223 MET cc_start: 0.8407 (mtp) cc_final: 0.7793 (ttm) REVERT: B 333 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7637 (m-30) REVERT: B 356 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8975 (mttm) REVERT: B 402 LYS cc_start: 0.6295 (mptt) cc_final: 0.5909 (mmmm) outliers start: 28 outliers final: 19 residues processed: 161 average time/residue: 1.3649 time to fit residues: 240.1684 Evaluate side-chains 169 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 713 ARG Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 765 ARG 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 989 THR Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1075 ASP 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 170 LYS 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 47 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 75 optimal weight: 0.2980 chunk 56 optimal weight: 0.4980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3739 r_free = 0.3739 target = 0.146606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.115000 restraints weight = 15309.555| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.57 r_work: 0.3177 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12724 Z= 0.144 Angle : 0.636 9.370 17242 Z= 0.324 Chirality : 0.045 0.196 1903 Planarity : 0.004 0.051 2179 Dihedral : 7.958 84.368 1832 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.10 % Allowed : 14.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.21), residues: 1528 helix: 0.23 (0.21), residues: 632 sheet: -0.75 (0.35), residues: 213 loop : -1.63 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 348 HIS 0.003 0.001 HIS A1330 PHE 0.021 0.002 PHE A1365 TYR 0.023 0.002 TYR B 280 ARG 0.004 0.000 ARG A 496 Details of bonding type rmsd link_NAG-ASN : bond 0.01162 ( 1) link_NAG-ASN : angle 7.06298 ( 3) link_BETA1-4 : bond 0.00398 ( 2) link_BETA1-4 : angle 3.80020 ( 6) hydrogen bonds : bond 0.03833 ( 469) hydrogen bonds : angle 4.55897 ( 1335) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.57421 ( 4) covalent geometry : bond 0.00338 (12718) covalent geometry : angle 0.62507 (17229) Misc. bond : bond 0.00023 ( 1) ********************** 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 175 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7551 (mtt) REVERT: A 202 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7754 (t) REVERT: A 402 LYS cc_start: 0.8356 (mttt) cc_final: 0.7770 (mtmt) REVERT: A 464 ARG cc_start: 0.7910 (mtm180) cc_final: 0.5647 (tmm160) REVERT: A 496 ARG cc_start: 0.7673 (mtt90) cc_final: 0.7255 (mmm160) REVERT: A 523 MET cc_start: 0.8274 (tpp) cc_final: 0.7964 (tpp) REVERT: A 765 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6930 (mmp-170) REVERT: A 945 GLU cc_start: 0.6284 (mp0) cc_final: 0.5824 (pm20) REVERT: A 1011 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7637 (tp30) REVERT: A 1223 MET cc_start: 0.8377 (mtp) cc_final: 0.7791 (ttm) REVERT: B 333 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7641 (m-30) REVERT: B 356 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8983 (mttm) REVERT: B 402 LYS cc_start: 0.6253 (mptt) cc_final: 0.5820 (mmmm) outliers start: 28 outliers final: 16 residues processed: 161 average time/residue: 1.3019 time to fit residues: 229.5302 Evaluate side-chains 168 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 765 ARG 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 1011 GLU Chi-restraints excluded: chain A residue 1075 ASP 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 170 LYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 391 ILE 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 7 optimal weight: 0.0010 chunk 134 optimal weight: 0.8980 chunk 71 optimal weight: 0.0870 chunk 129 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 chunk 139 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3754 r_free = 0.3754 target = 0.147894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116342 restraints weight = 15309.320| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.52 r_work: 0.3202 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12724 Z= 0.126 Angle : 0.617 9.176 17242 Z= 0.313 Chirality : 0.044 0.188 1903 Planarity : 0.003 0.048 2179 Dihedral : 7.785 86.460 1832 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.02 % Allowed : 14.24 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.21), residues: 1528 helix: 0.37 (0.21), residues: 625 sheet: -0.65 (0.35), residues: 206 loop : -1.60 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 348 HIS 0.003 0.001 HIS A1330 PHE 0.020 0.001 PHE A1365 TYR 0.025 0.001 TYR A1040 ARG 0.004 0.000 ARG A 496 Details of bonding type rmsd link_NAG-ASN : bond 0.01009 ( 1) link_NAG-ASN : angle 6.78999 ( 3) link_BETA1-4 : bond 0.00427 ( 2) link_BETA1-4 : angle 3.63986 ( 6) hydrogen bonds : bond 0.03634 ( 469) hydrogen bonds : angle 4.48033 ( 1335) SS BOND : bond 0.00228 ( 2) SS BOND : angle 0.39673 ( 4) covalent geometry : bond 0.00291 (12718) covalent geometry : angle 0.60646 (17229) Misc. bond : bond 0.00021 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9976.22 seconds wall clock time: 171 minutes 6.23 seconds (10266.23 seconds total)