Starting phenix.real_space_refine on Fri Sep 11 19:45:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s4t_54582/09_2026/9s4t_54582.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s4t_54582/09_2026/9s4t_54582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s4t_54582/09_2026/9s4t_54582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s4t_54582/09_2026/9s4t_54582.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s4t_54582/09_2026/9s4t_54582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s4t_54582/09_2026/9s4t_54582.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 59 5.16 5 C 7033 2.51 5 N 1751 2.21 5 O 2006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10851 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1313, 10497 Classifications: {'peptide': 1313} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 1265} Chain breaks: 4 Chain: "A" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 354 Unusual residues: {'ERG': 9, 'PO4': 2} Classifications: {'undetermined': 11, 'water': 83} Link IDs: {None: 93} Time building chain proxies: 2.32, per 1000 atoms: 0.21 Number of scatterers: 10851 At special positions: 0 Unit cell: (76.65, 109.725, 155.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 P 2 15.00 O 2006 8.00 N 1751 7.00 C 7033 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 711 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A1399 " - pdb=" SG CYS A1443 " distance=2.03 Simple disulfide: pdb=" SG CYS A1415 " - pdb=" SG CYS A1440 " 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 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 500.1 milliseconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2462 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 8 sheets defined 60.8% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 33 through 49 Processing helix chain 'A' and resid 89 through 102 removed outlier: 3.509A pdb=" N SER A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.645A pdb=" N THR A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 280 Processing helix chain 'A' and resid 299 through 315 removed outlier: 3.604A pdb=" N LYS A 304 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 347 removed outlier: 3.743A pdb=" N GLU A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 385 through 392 Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 419 through 425 removed outlier: 3.532A pdb=" N ILE A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 442 Processing helix chain 'A' and resid 443 through 458 removed outlier: 3.867A pdb=" N ALA A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 508 Processing helix chain 'A' and resid 509 through 529 removed outlier: 3.678A pdb=" N LEU A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.661A pdb=" N THR A 541 " --> pdb=" O THR A 538 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE A 542 " --> pdb=" O THR A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 543 through 558 removed outlier: 6.347A pdb=" N MET A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 558 " --> pdb=" O LEU A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' Processing helix chain 'A' and resid 563 through 570 removed outlier: 3.545A pdb=" N LEU A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 580 Processing helix chain 'A' and resid 584 through 597 removed outlier: 3.501A pdb=" N ASP A 588 " --> pdb=" O HIS A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 615 removed outlier: 3.789A pdb=" N ILE A 602 " --> pdb=" O PRO A 598 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 610 " --> pdb=" O CYS A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 649 removed outlier: 3.554A pdb=" N PHE A 626 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 635 " --> pdb=" O ASN A 631 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 669 removed outlier: 4.294A pdb=" N VAL A 657 " --> pdb=" O SER A 653 " (cutoff:3.500A) Proline residue: A 658 - end of helix removed outlier: 3.638A pdb=" N GLY A 665 " --> pdb=" O MET A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 679 Processing helix chain 'A' and resid 683 through 689 Processing helix chain 'A' and resid 690 through 705 removed outlier: 3.705A pdb=" N TYR A 694 " --> pdb=" O ASN A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 745 through 753 Processing helix chain 'A' and resid 756 through 760 Processing helix chain 'A' and resid 761 through 785 removed outlier: 3.734A pdb=" N GLY A 765 " --> pdb=" O TRP A 761 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 783 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 784 " --> pdb=" O ILE A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 908 Processing helix chain 'A' and resid 948 through 961 Processing helix chain 'A' and resid 966 through 982 Processing helix chain 'A' and resid 999 through 1013 Processing helix chain 'A' and resid 1030 through 1048 Processing helix chain 'A' and resid 1061 through 1066 removed outlier: 3.522A pdb=" N GLU A1065 " --> pdb=" O LEU A1062 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A1066 " --> pdb=" O MET A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1087 No H-bonds generated for 'chain 'A' and resid 1085 through 1087' Processing helix chain 'A' and resid 1088 through 1098 Processing helix chain 'A' and resid 1108 through 1118 Processing helix chain 'A' and resid 1128 through 1135 removed outlier: 3.689A pdb=" N VAL A1132 " --> pdb=" O ASP A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1157 removed outlier: 3.621A pdb=" N GLN A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) Proline residue: A1154 - end of helix removed outlier: 3.681A pdb=" N ASN A1157 " --> pdb=" O LEU A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1189 Processing helix chain 'A' and resid 1190 through 1212 removed outlier: 4.219A pdb=" N LEU A1194 " --> pdb=" O SER A1190 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A1212 " --> pdb=" O ILE A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1232 removed outlier: 3.690A pdb=" N GLN A1223 " --> pdb=" O LEU A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1257 removed outlier: 3.664A pdb=" N LEU A1239 " --> pdb=" O ILE A1235 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A1244 " --> pdb=" O LEU A1240 " (cutoff:3.500A) Proline residue: A1245 - end of helix removed outlier: 3.541A pdb=" N ARG A1257 " --> pdb=" O LEU A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1297 removed outlier: 4.117A pdb=" N GLU A1277 " --> pdb=" O GLN A1273 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE A1278 " --> pdb=" O ILE A1274 " (cutoff:3.500A) Proline residue: A1279 - end of helix removed outlier: 3.999A pdb=" N TYR A1294 " --> pdb=" O VAL A1290 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A1297 " --> pdb=" O TYR A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 3.726A pdb=" N ALA A1302 " --> pdb=" O PHE A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1336 removed outlier: 3.849A pdb=" N GLY A1327 " --> pdb=" O TYR A1323 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE A1336 " --> pdb=" O PHE A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1357 removed outlier: 3.777A pdb=" N ALA A1343 " --> pdb=" O VAL A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1370 No H-bonds generated for 'chain 'A' and resid 1368 through 1370' Processing helix chain 'A' and resid 1371 through 1378 removed outlier: 3.523A pdb=" N TYR A1375 " --> pdb=" O TRP A1371 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A1376 " --> pdb=" O ILE A1372 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A1378 " --> pdb=" O MET A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1392 removed outlier: 4.251A pdb=" N TYR A1382 " --> pdb=" O SER A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1419 Processing helix chain 'A' and resid 1419 through 1427 Processing helix chain 'A' and resid 1447 through 1455 removed outlier: 3.918A pdb=" N PHE A1451 " --> pdb=" O HIS A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1462 removed outlier: 3.879A pdb=" N ARG A1461 " --> pdb=" O LYS A1458 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG A1462 " --> pdb=" O TYR A1459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1458 through 1462' Processing helix chain 'A' and resid 1463 through 1489 removed outlier: 3.512A pdb=" N ILE A1473 " --> pdb=" O PHE A1469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 165 removed outlier: 5.675A pdb=" N LYS A 163 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLY A 124 " --> pdb=" O LYS A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 228 through 231 removed outlier: 6.616A pdb=" N VAL A 229 " --> pdb=" O CYS A 320 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ASP A 322 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN A 231 " --> pdb=" O ASP A 322 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 178 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL A 369 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE A 380 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 371 " --> pdb=" O ILE A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 708 through 710 Processing sheet with id=AA5, first strand: chain 'A' and resid 714 through 715 Processing sheet with id=AA6, first strand: chain 'A' and resid 871 through 883 removed outlier: 5.901A pdb=" N ARG A 873 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE A 868 " --> pdb=" O ARG A 873 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE A 875 " --> pdb=" O VAL A 866 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N VAL A 866 " --> pdb=" O ILE A 875 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ASN A 877 " --> pdb=" O TYR A 864 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR A 864 " --> pdb=" O ASN A 877 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 879 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLY A 881 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ARG A 860 " --> pdb=" O GLY A 881 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL A 883 " --> pdb=" O HIS A 858 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N HIS A 858 " --> pdb=" O VAL A 883 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TRP A 859 " --> pdb=" O SER A 920 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N SER A 920 " --> pdb=" O TRP A 859 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASN A 861 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU A 918 " --> pdb=" O ASN A 861 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 935 through 937 removed outlier: 6.388A pdb=" N VAL A1020 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR A1054 " --> pdb=" O VAL A1020 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU A1022 " --> pdb=" O THR A1054 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 888 " --> pdb=" O ARG A1068 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N LEU A1070 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA A 890 " --> pdb=" O LEU A1070 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LEU A1072 " --> pdb=" O ALA A 890 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET A 892 " --> pdb=" O LEU A1072 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A1080 " --> pdb=" O PHE A1071 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLN A1073 " --> pdb=" O THR A1078 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N THR A1078 " --> pdb=" O GLN A1073 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1405 through 1407 546 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3332 1.34 - 1.46: 2128 1.46 - 1.58: 5515 1.58 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 11066 Sorted by residual: bond pdb=" CA ASP A 104 " pdb=" CB ASP A 104 " ideal model delta sigma weight residual 1.525 1.538 -0.013 8.30e-03 1.45e+04 2.40e+00 bond pdb=" CB GLN A1424 " pdb=" CG GLN A1424 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CB GLN A 852 " pdb=" CG GLN A 852 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CA GLU A 87 " pdb=" C GLU A 87 " ideal model delta sigma weight residual 1.523 1.536 -0.013 1.34e-02 5.57e+03 9.22e-01 bond pdb=" CA ASP A 32 " pdb=" CB ASP A 32 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 8.48e-01 ... (remaining 11061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 14951 2.28 - 4.56: 94 4.56 - 6.84: 18 6.84 - 9.12: 2 9.12 - 11.40: 2 Bond angle restraints: 15067 Sorted by residual: angle pdb=" C22 ERG A1607 " pdb=" C23 ERG A1607 " pdb=" C24 ERG A1607 " ideal model delta sigma weight residual 125.68 137.08 -11.40 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C20 ERG A1605 " pdb=" C22 ERG A1605 " pdb=" C23 ERG A1605 " ideal model delta sigma weight residual 125.47 134.88 -9.41 3.00e+00 1.11e-01 9.84e+00 angle pdb=" CB GLN A1424 " pdb=" CG GLN A1424 " pdb=" CD GLN A1424 " ideal model delta sigma weight residual 112.60 117.77 -5.17 1.70e+00 3.46e-01 9.26e+00 angle pdb=" C20 ERG A1607 " pdb=" C22 ERG A1607 " pdb=" C23 ERG A1607 " ideal model delta sigma weight residual 125.47 134.54 -9.07 3.00e+00 1.11e-01 9.14e+00 angle pdb=" C SER A 103 " pdb=" N ASP A 104 " pdb=" CA ASP A 104 " ideal model delta sigma weight residual 124.21 127.78 -3.57 1.21e+00 6.83e-01 8.69e+00 ... (remaining 15062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 6021 17.71 - 35.41: 663 35.41 - 53.12: 191 53.12 - 70.82: 36 70.82 - 88.53: 11 Dihedral angle restraints: 6922 sinusoidal: 3082 harmonic: 3840 Sorted by residual: dihedral pdb=" CA ASP A 367 " pdb=" CB ASP A 367 " pdb=" CG ASP A 367 " pdb=" OD1 ASP A 367 " ideal model delta sinusoidal sigma weight residual -30.00 -86.82 56.82 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CB GLU A1341 " pdb=" CG GLU A1341 " pdb=" CD GLU A1341 " pdb=" OE1 GLU A1341 " ideal model delta sinusoidal sigma weight residual 0.00 88.06 -88.06 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU A 399 " pdb=" CG GLU A 399 " pdb=" CD GLU A 399 " pdb=" OE1 GLU A 399 " ideal model delta sinusoidal sigma weight residual 0.00 -87.87 87.87 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 6919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1281 0.042 - 0.084: 301 0.084 - 0.126: 80 0.126 - 0.168: 2 0.168 - 0.210: 3 Chirality restraints: 1667 Sorted by residual: chirality pdb=" C20 ERG A1603 " pdb=" C17 ERG A1603 " pdb=" C21 ERG A1603 " pdb=" C22 ERG A1603 " both_signs ideal model delta sigma weight residual False 2.58 2.37 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C24 ERG A1607 " pdb=" C23 ERG A1607 " pdb=" C25 ERG A1607 " pdb=" C28 ERG A1607 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" C20 ERG A1606 " pdb=" C17 ERG A1606 " pdb=" C21 ERG A1606 " pdb=" C22 ERG A1606 " both_signs ideal model delta sigma weight residual False 2.58 2.40 0.18 2.00e-01 2.50e+01 7.92e-01 ... (remaining 1664 not shown) Planarity restraints: 1856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1148 " 0.010 2.00e-02 2.50e+03 1.16e-02 3.38e+00 pdb=" CG TRP A1148 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A1148 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A1148 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1148 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1148 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1148 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1148 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1148 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A1148 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 674 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO A 675 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 675 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 675 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 584 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO A 585 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 585 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 585 " -0.022 5.00e-02 4.00e+02 ... (remaining 1853 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2350 2.78 - 3.31: 9522 3.31 - 3.84: 17074 3.84 - 4.37: 19864 4.37 - 4.90: 35521 Nonbonded interactions: 84331 Sorted by model distance: nonbonded pdb=" O SER A 51 " pdb=" OG SER A 51 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR A1414 " pdb=" OE2 GLU A1417 " model vdw 2.274 3.040 nonbonded pdb=" OG SER A 581 " pdb=" O HOH A1701 " model vdw 2.333 3.040 nonbonded pdb=" OG SER A 592 " pdb=" O HOH A1702 " model vdw 2.344 3.040 nonbonded pdb=" O ARG A1262 " pdb=" O HOH A1703 " model vdw 2.345 3.040 ... (remaining 84326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 10.070 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: 0.330 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.320 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 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 : 0.002 0.039 11070 Z= 0.115 Angle : 0.513 11.402 15073 Z= 0.260 Chirality : 0.039 0.210 1667 Planarity : 0.003 0.043 1856 Dihedral : 15.941 88.527 4451 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 2.64 % Allowed : 22.11 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.23), residues: 1303 helix: 1.65 (0.19), residues: 731 sheet: 0.78 (0.46), residues: 100 loop : -1.06 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.012 0.001 TYR A 627 PHE 0.012 0.001 PHE A 551 TRP 0.031 0.001 TRP A1148 HIS 0.004 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (11066) covalent geometry : angle 0.51322 / 0.26 (15067) SS BOND : bond 0.00123 / 0.06 ( 3) SS BOND : angle 0.53785 / 0.26 ( 6) hydrogen bonds : bond 0.17060 / 11.53 ( 546) hydrogen bonds : angle 5.14494 / 3.63 ( 1584) Misc. bond : bond 0.00113 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 215 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7332 (mtm) REVERT: A 385 LYS cc_start: 0.8629 (mttt) cc_final: 0.8293 (mtpp) REVERT: A 399 GLU cc_start: 0.8339 (tp30) cc_final: 0.7979 (tp30) REVERT: A 850 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.5977 (tm) REVERT: A 1074 ARG cc_start: 0.7950 (ttm170) cc_final: 0.7721 (ttt180) REVERT: A 1369 ARG cc_start: 0.8239 (mmt180) cc_final: 0.7963 (tmt170) outliers start: 30 outliers final: 24 residues processed: 120 average time/residue: 0.5346 time to fit residues: 69.6157 Evaluate side-chains 118 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 431 GLN Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1047 HIS Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1412 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 ASN A 519 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.136721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109783 restraints weight = 14527.641| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.20 r_work: 0.3122 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11070 Z= 0.190 Angle : 0.609 11.588 15073 Z= 0.311 Chirality : 0.043 0.233 1667 Planarity : 0.004 0.050 1856 Dihedral : 8.569 69.699 2085 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 3.79 % Allowed : 20.26 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.23), residues: 1303 helix: 1.56 (0.19), residues: 738 sheet: 0.71 (0.44), residues: 101 loop : -1.24 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 954 TYR 0.014 0.002 TYR A1484 PHE 0.017 0.002 PHE A 642 TRP 0.016 0.001 TRP A1148 HIS 0.005 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (11066) covalent geometry : angle 0.60876 / 0.31 (15067) SS BOND : bond 0.00271 / 0.13 ( 3) SS BOND : angle 0.80989 / 0.40 ( 6) hydrogen bonds : bond 0.07530 / 5.00 ( 546) hydrogen bonds : angle 4.20545 / 3.00 ( 1584) Misc. bond : bond 0.00204 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 94 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 227 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: A 385 LYS cc_start: 0.8533 (mttt) cc_final: 0.8229 (mtpp) REVERT: A 399 GLU cc_start: 0.8393 (tp30) cc_final: 0.8027 (tp30) REVERT: A 687 TRP cc_start: 0.7676 (t60) cc_final: 0.7214 (t-100) REVERT: A 1074 ARG cc_start: 0.8252 (ttm170) cc_final: 0.7881 (ttt180) REVERT: A 1167 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8311 (tt0) REVERT: A 1195 TRP cc_start: 0.7242 (t60) cc_final: 0.5984 (m-10) REVERT: A 1283 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8008 (mp) REVERT: A 1369 ARG cc_start: 0.8372 (mmt180) cc_final: 0.8014 (tmt170) outliers start: 43 outliers final: 23 residues processed: 129 average time/residue: 0.5289 time to fit residues: 74.1674 Evaluate side-chains 117 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 431 GLN Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain A residue 1428 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 9 optimal weight: 0.0000 chunk 82 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 431 GLN A 722 ASN A 852 GLN A1465 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.141773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115009 restraints weight = 14664.545| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.20 r_work: 0.3212 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11070 Z= 0.109 Angle : 0.503 11.258 15073 Z= 0.254 Chirality : 0.039 0.213 1667 Planarity : 0.003 0.045 1856 Dihedral : 7.824 69.822 2056 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 2.56 % Allowed : 20.97 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.23), residues: 1303 helix: 1.82 (0.19), residues: 742 sheet: 0.89 (0.44), residues: 101 loop : -1.20 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.012 0.001 TYR A 627 PHE 0.014 0.001 PHE A1236 TRP 0.011 0.001 TRP A 117 HIS 0.004 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (11066) covalent geometry : angle 0.50281 / 0.25 (15067) SS BOND : bond 0.00184 / 0.09 ( 3) SS BOND : angle 0.62332 / 0.28 ( 6) hydrogen bonds : bond 0.05205 / 3.43 ( 546) hydrogen bonds : angle 3.96133 / 2.83 ( 1584) Misc. bond : bond 0.00142 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7247 (ttm-80) cc_final: 0.6746 (mtm-85) REVERT: A 215 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7656 (mtm) REVERT: A 227 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7350 (mm-30) REVERT: A 263 ILE cc_start: 0.7275 (OUTLIER) cc_final: 0.6921 (mt) REVERT: A 303 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7334 (mtp180) REVERT: A 385 LYS cc_start: 0.8496 (mttt) cc_final: 0.8199 (mtpp) REVERT: A 399 GLU cc_start: 0.8378 (tp30) cc_final: 0.7973 (tp30) REVERT: A 687 TRP cc_start: 0.7645 (t60) cc_final: 0.7211 (t-100) REVERT: A 880 ASP cc_start: 0.8426 (p0) cc_final: 0.8215 (p0) REVERT: A 1074 ARG cc_start: 0.8275 (ttm170) cc_final: 0.7921 (ttt180) REVERT: A 1167 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: A 1369 ARG cc_start: 0.8348 (mmt180) cc_final: 0.7801 (tpp-160) outliers start: 29 outliers final: 19 residues processed: 114 average time/residue: 0.5966 time to fit residues: 73.1954 Evaluate side-chains 114 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1214 LYS Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1428 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 18 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 722 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.140091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.113329 restraints weight = 14715.888| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.20 r_work: 0.3192 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11070 Z= 0.125 Angle : 0.519 11.453 15073 Z= 0.261 Chirality : 0.040 0.219 1667 Planarity : 0.004 0.044 1856 Dihedral : 7.679 70.499 2051 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.24 % Rotamer: Outliers : 3.61 % Allowed : 20.09 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.23), residues: 1303 helix: 1.84 (0.19), residues: 742 sheet: 0.96 (0.45), residues: 101 loop : -1.25 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 954 TYR 0.012 0.001 TYR A 627 PHE 0.013 0.001 PHE A1236 TRP 0.011 0.001 TRP A 117 HIS 0.004 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (11066) covalent geometry : angle 0.51900 / 0.26 (15067) SS BOND : bond 0.00206 / 0.10 ( 3) SS BOND : angle 0.70218 / 0.31 ( 6) hydrogen bonds : bond 0.05668 / 3.74 ( 546) hydrogen bonds : angle 3.88731 / 2.79 ( 1584) Misc. bond : bond 0.00163 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 89 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7265 (ttm-80) cc_final: 0.6718 (mtm-85) REVERT: A 215 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7718 (mtm) REVERT: A 263 ILE cc_start: 0.7327 (OUTLIER) cc_final: 0.6968 (mt) REVERT: A 385 LYS cc_start: 0.8546 (mttt) cc_final: 0.8257 (mtpp) REVERT: A 399 GLU cc_start: 0.8368 (tp30) cc_final: 0.7978 (tp30) REVERT: A 687 TRP cc_start: 0.7664 (t60) cc_final: 0.7236 (t-100) REVERT: A 880 ASP cc_start: 0.8401 (p0) cc_final: 0.8175 (p0) REVERT: A 1074 ARG cc_start: 0.8301 (ttm170) cc_final: 0.7945 (ttt180) REVERT: A 1167 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: A 1369 ARG cc_start: 0.8390 (mmt180) cc_final: 0.7830 (tpp-160) outliers start: 41 outliers final: 27 residues processed: 120 average time/residue: 0.5366 time to fit residues: 69.9348 Evaluate side-chains 117 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1047 HIS Chi-restraints excluded: chain A residue 1059 SER Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1214 LYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1346 MET Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain A residue 1428 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.114739 restraints weight = 14578.462| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.19 r_work: 0.3208 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11070 Z= 0.109 Angle : 0.497 11.379 15073 Z= 0.250 Chirality : 0.039 0.215 1667 Planarity : 0.003 0.043 1856 Dihedral : 7.556 70.388 2049 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.30 % Favored : 96.55 % Rotamer: Outliers : 3.52 % Allowed : 20.53 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.23), residues: 1303 helix: 1.99 (0.19), residues: 737 sheet: 1.01 (0.45), residues: 101 loop : -1.27 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 44 TYR 0.012 0.001 TYR A 627 PHE 0.013 0.001 PHE A1236 TRP 0.010 0.001 TRP A 117 HIS 0.003 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (11066) covalent geometry : angle 0.49691 / 0.25 (15067) SS BOND : bond 0.00175 / 0.08 ( 3) SS BOND : angle 0.60831 / 0.27 ( 6) hydrogen bonds : bond 0.05095 / 3.36 ( 546) hydrogen bonds : angle 3.82674 / 2.74 ( 1584) Misc. bond : bond 0.00146 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 87 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7279 (ttm-80) cc_final: 0.6703 (mtm-85) REVERT: A 215 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7699 (mtm) REVERT: A 227 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7401 (mm-30) REVERT: A 263 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.6969 (mt) REVERT: A 303 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.7384 (mtp180) REVERT: A 385 LYS cc_start: 0.8542 (mttt) cc_final: 0.8254 (mtpp) REVERT: A 399 GLU cc_start: 0.8351 (tp30) cc_final: 0.7949 (tp30) REVERT: A 687 TRP cc_start: 0.7674 (t60) cc_final: 0.7237 (t-100) REVERT: A 880 ASP cc_start: 0.8370 (p0) cc_final: 0.8152 (p0) REVERT: A 1074 ARG cc_start: 0.8296 (ttm170) cc_final: 0.7952 (ttt180) REVERT: A 1167 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: A 1369 ARG cc_start: 0.8382 (mmt180) cc_final: 0.7823 (tpp-160) outliers start: 40 outliers final: 26 residues processed: 119 average time/residue: 0.5500 time to fit residues: 71.1466 Evaluate side-chains 116 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1047 HIS Chi-restraints excluded: chain A residue 1059 SER Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1214 LYS Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1428 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 61 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 117 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 53 optimal weight: 0.0030 chunk 81 optimal weight: 1.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.114787 restraints weight = 14666.258| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.20 r_work: 0.3212 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11070 Z= 0.111 Angle : 0.499 11.399 15073 Z= 0.251 Chirality : 0.039 0.182 1667 Planarity : 0.003 0.042 1856 Dihedral : 7.615 70.546 2049 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.53 % Favored : 96.39 % Rotamer: Outliers : 4.14 % Allowed : 19.82 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.23), residues: 1303 helix: 2.00 (0.19), residues: 738 sheet: 1.03 (0.45), residues: 101 loop : -1.30 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 296 TYR 0.012 0.001 TYR A 627 PHE 0.013 0.001 PHE A1236 TRP 0.012 0.001 TRP A1148 HIS 0.003 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (11066) covalent geometry : angle 0.49938 / 0.25 (15067) SS BOND : bond 0.00173 / 0.08 ( 3) SS BOND : angle 0.60065 / 0.26 ( 6) hydrogen bonds : bond 0.05073 / 3.34 ( 546) hydrogen bonds : angle 3.78166 / 2.71 ( 1584) Misc. bond : bond 0.00148 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 84 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7282 (ttm-80) cc_final: 0.6750 (mtm-85) REVERT: A 215 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7693 (mtm) REVERT: A 227 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7409 (mm-30) REVERT: A 303 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.7419 (mtp180) REVERT: A 385 LYS cc_start: 0.8550 (mttt) cc_final: 0.8268 (mtpp) REVERT: A 399 GLU cc_start: 0.8332 (tp30) cc_final: 0.7832 (tp30) REVERT: A 687 TRP cc_start: 0.7676 (t60) cc_final: 0.7246 (t-100) REVERT: A 880 ASP cc_start: 0.8359 (p0) cc_final: 0.8135 (p0) REVERT: A 1074 ARG cc_start: 0.8289 (ttm170) cc_final: 0.7942 (ttt180) REVERT: A 1167 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: A 1369 ARG cc_start: 0.8387 (mmt180) cc_final: 0.7822 (tpp-160) outliers start: 47 outliers final: 29 residues processed: 121 average time/residue: 0.5546 time to fit residues: 72.6265 Evaluate side-chains 117 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 84 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 899 LYS Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1047 HIS Chi-restraints excluded: chain A residue 1059 SER Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1214 LYS Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1428 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 24 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 30 optimal weight: 0.0270 chunk 9 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.115578 restraints weight = 14559.022| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.21 r_work: 0.3204 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11070 Z= 0.101 Angle : 0.482 11.361 15073 Z= 0.242 Chirality : 0.039 0.195 1667 Planarity : 0.003 0.041 1856 Dihedral : 7.560 69.536 2049 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.15 % Favored : 96.78 % Rotamer: Outliers : 3.00 % Allowed : 20.97 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.23), residues: 1303 helix: 2.11 (0.19), residues: 736 sheet: 1.05 (0.45), residues: 101 loop : -1.25 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 296 TYR 0.012 0.001 TYR A 627 PHE 0.013 0.001 PHE A1236 TRP 0.015 0.001 TRP A1148 HIS 0.003 0.000 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (11066) covalent geometry : angle 0.48216 / 0.24 (15067) SS BOND : bond 0.00145 / 0.07 ( 3) SS BOND : angle 0.54872 / 0.24 ( 6) hydrogen bonds : bond 0.04586 / 3.01 ( 546) hydrogen bonds : angle 3.71356 / 2.67 ( 1584) Misc. bond : bond 0.00130 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7222 (ttm-80) cc_final: 0.6682 (mtm-85) REVERT: A 215 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7622 (mtm) REVERT: A 227 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7395 (mm-30) REVERT: A 303 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7323 (mtp180) REVERT: A 385 LYS cc_start: 0.8498 (mttt) cc_final: 0.8133 (mtpp) REVERT: A 399 GLU cc_start: 0.8298 (tp30) cc_final: 0.7789 (tp30) REVERT: A 687 TRP cc_start: 0.7647 (t60) cc_final: 0.7213 (t-100) REVERT: A 880 ASP cc_start: 0.8303 (p0) cc_final: 0.8061 (p0) REVERT: A 1074 ARG cc_start: 0.8292 (ttm170) cc_final: 0.7919 (ttt180) REVERT: A 1167 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: A 1369 ARG cc_start: 0.8337 (mmt180) cc_final: 0.7770 (tpp-160) outliers start: 34 outliers final: 24 residues processed: 113 average time/residue: 0.5713 time to fit residues: 69.6965 Evaluate side-chains 114 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 303 ARG Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 899 LYS Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1047 HIS Chi-restraints excluded: chain A residue 1059 SER Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1214 LYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1428 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 44 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 103 optimal weight: 0.2980 chunk 90 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112014 restraints weight = 14608.777| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.20 r_work: 0.3152 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11070 Z= 0.135 Angle : 0.530 11.471 15073 Z= 0.267 Chirality : 0.040 0.214 1667 Planarity : 0.003 0.042 1856 Dihedral : 7.693 69.803 2048 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.09 % Rotamer: Outliers : 3.08 % Allowed : 21.23 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.23), residues: 1303 helix: 1.92 (0.19), residues: 739 sheet: 1.03 (0.44), residues: 101 loop : -1.32 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 296 TYR 0.013 0.001 TYR A1484 PHE 0.014 0.001 PHE A 551 TRP 0.019 0.001 TRP A1148 HIS 0.004 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (11066) covalent geometry : angle 0.52981 / 0.27 (15067) SS BOND : bond 0.00232 / 0.11 ( 3) SS BOND : angle 0.75637 / 0.34 ( 6) hydrogen bonds : bond 0.05916 / 3.92 ( 546) hydrogen bonds : angle 3.80784 / 2.74 ( 1584) Misc. bond : bond 0.00170 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7268 (ttm-80) cc_final: 0.6664 (mtm-85) REVERT: A 227 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7372 (mm-30) REVERT: A 385 LYS cc_start: 0.8516 (mttt) cc_final: 0.8213 (mtpp) REVERT: A 399 GLU cc_start: 0.8315 (tp30) cc_final: 0.7801 (tp30) REVERT: A 687 TRP cc_start: 0.7644 (t60) cc_final: 0.7182 (t-100) REVERT: A 880 ASP cc_start: 0.8382 (p0) cc_final: 0.8152 (p0) REVERT: A 1074 ARG cc_start: 0.8302 (ttm170) cc_final: 0.7934 (ttt180) REVERT: A 1167 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: A 1369 ARG cc_start: 0.8380 (mmt180) cc_final: 0.7913 (tpp-160) outliers start: 35 outliers final: 28 residues processed: 114 average time/residue: 0.5471 time to fit residues: 67.6350 Evaluate side-chains 113 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1059 SER Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1142 VAL Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1214 LYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1428 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 118 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 chunk 98 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.142702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115871 restraints weight = 14425.599| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.20 r_work: 0.3206 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11070 Z= 0.099 Angle : 0.481 11.256 15073 Z= 0.242 Chirality : 0.038 0.201 1667 Planarity : 0.003 0.041 1856 Dihedral : 7.604 69.855 2048 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.01 % Rotamer: Outliers : 2.73 % Allowed : 21.50 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.23), residues: 1303 helix: 2.13 (0.20), residues: 736 sheet: 0.98 (0.44), residues: 101 loop : -1.24 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 296 TYR 0.012 0.001 TYR A 627 PHE 0.014 0.001 PHE A1236 TRP 0.019 0.001 TRP A1148 HIS 0.003 0.000 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (11066) covalent geometry : angle 0.48135 / 0.24 (15067) SS BOND : bond 0.00128 / 0.06 ( 3) SS BOND : angle 0.50629 / 0.23 ( 6) hydrogen bonds : bond 0.04464 / 2.94 ( 546) hydrogen bonds : angle 3.70349 / 2.66 ( 1584) Misc. bond : bond 0.00133 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.329 Fit side-chains REVERT: A 44 ARG cc_start: 0.7223 (ttm-80) cc_final: 0.6680 (mtm-85) REVERT: A 92 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: A 215 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7608 (mtm) REVERT: A 385 LYS cc_start: 0.8515 (mttt) cc_final: 0.8156 (mtpp) REVERT: A 399 GLU cc_start: 0.8278 (tp30) cc_final: 0.7764 (tp30) REVERT: A 687 TRP cc_start: 0.7615 (t60) cc_final: 0.7169 (t-100) REVERT: A 880 ASP cc_start: 0.8305 (p0) cc_final: 0.8102 (p0) REVERT: A 1074 ARG cc_start: 0.8283 (ttm170) cc_final: 0.7921 (ttt180) REVERT: A 1167 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8312 (tt0) REVERT: A 1369 ARG cc_start: 0.8332 (mmt180) cc_final: 0.7873 (tpp-160) outliers start: 31 outliers final: 25 residues processed: 110 average time/residue: 0.5531 time to fit residues: 66.0827 Evaluate side-chains 113 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1047 HIS Chi-restraints excluded: chain A residue 1059 SER Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1214 LYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1428 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 867 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.141187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114285 restraints weight = 14494.758| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.20 r_work: 0.3209 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11070 Z= 0.113 Angle : 0.497 11.384 15073 Z= 0.250 Chirality : 0.039 0.213 1667 Planarity : 0.003 0.041 1856 Dihedral : 7.632 69.824 2048 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 2.73 % Allowed : 21.50 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.23), residues: 1303 helix: 2.02 (0.19), residues: 742 sheet: 0.97 (0.44), residues: 101 loop : -1.24 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 296 TYR 0.012 0.001 TYR A 627 PHE 0.012 0.001 PHE A1236 TRP 0.030 0.001 TRP A1148 HIS 0.003 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (11066) covalent geometry : angle 0.49696 / 0.25 (15067) SS BOND : bond 0.00175 / 0.08 ( 3) SS BOND : angle 0.60574 / 0.27 ( 6) hydrogen bonds : bond 0.05030 / 3.32 ( 546) hydrogen bonds : angle 3.70286 / 2.67 ( 1584) Misc. bond : bond 0.00146 / 0.08 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.360 Fit side-chains REVERT: A 44 ARG cc_start: 0.7283 (ttm-80) cc_final: 0.6745 (mtm-85) REVERT: A 92 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: A 385 LYS cc_start: 0.8579 (mttt) cc_final: 0.8235 (mtpp) REVERT: A 399 GLU cc_start: 0.8290 (tp30) cc_final: 0.7782 (tp30) REVERT: A 687 TRP cc_start: 0.7658 (t60) cc_final: 0.7217 (t-100) REVERT: A 880 ASP cc_start: 0.8368 (p0) cc_final: 0.8159 (p0) REVERT: A 918 GLU cc_start: 0.7579 (tt0) cc_final: 0.7062 (tt0) REVERT: A 1074 ARG cc_start: 0.8309 (ttm170) cc_final: 0.7957 (ttt180) REVERT: A 1167 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: A 1369 ARG cc_start: 0.8398 (mmt180) cc_final: 0.7932 (tpp-160) outliers start: 31 outliers final: 26 residues processed: 109 average time/residue: 0.5591 time to fit residues: 66.0070 Evaluate side-chains 111 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1059 SER Chi-restraints excluded: chain A residue 1167 GLU Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1214 LYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1428 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 92 optimal weight: 0.0970 chunk 117 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 867 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.112116 restraints weight = 14620.414| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.21 r_work: 0.3150 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11070 Z= 0.133 Angle : 0.527 11.459 15073 Z= 0.266 Chirality : 0.040 0.217 1667 Planarity : 0.004 0.042 1856 Dihedral : 7.747 69.734 2048 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 2.82 % Allowed : 21.23 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.23), residues: 1303 helix: 1.91 (0.19), residues: 743 sheet: 0.98 (0.44), residues: 101 loop : -1.28 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 296 TYR 0.013 0.001 TYR A1484 PHE 0.014 0.001 PHE A 551 TRP 0.033 0.001 TRP A1148 HIS 0.004 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (11066) covalent geometry : angle 0.52733 / 0.27 (15067) SS BOND : bond 0.00231 / 0.11 ( 3) SS BOND : angle 0.74106 / 0.34 ( 6) hydrogen bonds : bond 0.05824 / 3.85 ( 546) hydrogen bonds : angle 3.78021 / 2.72 ( 1584) Misc. bond : bond 0.00163 / 0.09 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3666.87 seconds wall clock time: 63 minutes 15.73 seconds (3795.73 seconds total)