Starting phenix.real_space_refine on Fri Feb 6 06:30:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q05_72087/02_2026/9q05_72087_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q05_72087/02_2026/9q05_72087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q05_72087/02_2026/9q05_72087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q05_72087/02_2026/9q05_72087.map" model { file = "/net/cci-nas-00/data/ceres_data/9q05_72087/02_2026/9q05_72087_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q05_72087/02_2026/9q05_72087_trim.cif" } resolution = 3.09 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= 0.021 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: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 6 5.49 5 S 52 5.16 5 C 7246 2.51 5 N 1953 2.21 5 O 2145 1.98 5 H 10826 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22230 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1398, 22012 Classifications: {'peptide': 1398} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1328} Chain breaks: 3 Chain: "A" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 218 Unusual residues: {'FAD': 1, 'FMN': 1, 'HEM': 2, 'NAP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7968 SG CYS A 539 30.027 62.671 104.560 1.00145.29 S Time building chain proxies: 3.89, per 1000 atoms: 0.17 Number of scatterers: 22230 At special positions: 0 Unit cell: (75.19, 103.66, 148.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 52 16.00 P 6 15.00 O 2145 8.00 N 1953 7.00 C 7246 6.00 H 10826 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 72 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 663.0 milliseconds 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2640 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 16 sheets defined 52.6% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 178 through 195 removed outlier: 3.931A pdb=" N ALA A 194 " --> pdb=" O ASN A 190 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 220 through 223 removed outlier: 4.486A pdb=" N GLU A 223 " --> pdb=" O GLU A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.625A pdb=" N TRP A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 294 " --> pdb=" O TRP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 314 through 324 Processing helix chain 'A' and resid 324 through 337 Processing helix chain 'A' and resid 340 through 352 Processing helix chain 'A' and resid 358 through 373 Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.670A pdb=" N LEU A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 405 removed outlier: 3.774A pdb=" N SER A 395 " --> pdb=" O HIS A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 431 through 447 removed outlier: 4.422A pdb=" N ILE A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 495 removed outlier: 3.649A pdb=" N VAL A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) Proline residue: A 472 - end of helix Processing helix chain 'A' and resid 497 through 516 Processing helix chain 'A' and resid 521 through 536 Processing helix chain 'A' and resid 539 through 545 removed outlier: 3.748A pdb=" N ARG A 542 " --> pdb=" O CYS A 539 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE A 543 " --> pdb=" O ILE A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 575 Processing helix chain 'A' and resid 576 through 578 No H-bonds generated for 'chain 'A' and resid 576 through 578' Processing helix chain 'A' and resid 623 through 635 removed outlier: 3.594A pdb=" N THR A 627 " --> pdb=" O ASN A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.659A pdb=" N ILE A 669 " --> pdb=" O PRO A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 686 removed outlier: 3.589A pdb=" N PHE A 682 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 683 " --> pdb=" O PRO A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 Processing helix chain 'A' and resid 733 through 742 Processing helix chain 'A' and resid 747 through 750 removed outlier: 3.797A pdb=" N THR A 750 " --> pdb=" O SER A 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 747 through 750' Processing helix chain 'A' and resid 751 through 772 Processing helix chain 'A' and resid 777 through 795 Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.934A pdb=" N GLN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 886 Processing helix chain 'A' and resid 899 through 903 removed outlier: 3.641A pdb=" N THR A 902 " --> pdb=" O ASN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 924 No H-bonds generated for 'chain 'A' and resid 922 through 924' Processing helix chain 'A' and resid 925 through 935 removed outlier: 3.690A pdb=" N GLN A 934 " --> pdb=" O GLN A 930 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 935 " --> pdb=" O TRP A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 973 Processing helix chain 'A' and resid 989 through 1005 Processing helix chain 'A' and resid 1024 through 1042 removed outlier: 3.524A pdb=" N SER A1028 " --> pdb=" O ALA A1024 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A1033 " --> pdb=" O HIS A1029 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS A1038 " --> pdb=" O LEU A1034 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A1041 " --> pdb=" O GLU A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1072 Processing helix chain 'A' and resid 1089 through 1101 Processing helix chain 'A' and resid 1132 through 1139 Processing helix chain 'A' and resid 1148 through 1158 Processing helix chain 'A' and resid 1161 through 1176 Processing helix chain 'A' and resid 1181 through 1195 Processing helix chain 'A' and resid 1197 through 1205 Processing helix chain 'A' and resid 1211 through 1219 removed outlier: 3.609A pdb=" N LEU A1215 " --> pdb=" O THR A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1267 Processing helix chain 'A' and resid 1298 through 1301 Processing helix chain 'A' and resid 1302 through 1319 Processing helix chain 'A' and resid 1339 through 1350 Processing helix chain 'A' and resid 1368 through 1376 removed outlier: 3.682A pdb=" N ASN A1376 " --> pdb=" O LEU A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1376 through 1385 Processing helix chain 'A' and resid 1396 through 1414 Processing helix chain 'A' and resid 1418 through 1432 Processing helix chain 'A' and resid 1448 through 1459 removed outlier: 3.610A pdb=" N GLN A1452 " --> pdb=" O GLN A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1459 through 1468 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 63 removed outlier: 5.822A pdb=" N LEU A 20 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR A 131 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU A 22 " --> pdb=" O ARG A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 57 removed outlier: 3.877A pdb=" N ALA A 38 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR A 56 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR A 36 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N PHE A 74 " --> pdb=" O LYS A 96 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS A 96 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 76 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER A 94 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU A 78 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 549 through 552 removed outlier: 3.729A pdb=" N VAL A 582 " --> pdb=" O ASN A 713 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 598 through 599 Processing sheet with id=AA6, first strand: chain 'A' and resid 609 through 611 Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 673 Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 707 removed outlier: 3.552A pdb=" N ASP A 701 " --> pdb=" O ALA A 830 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 830 " --> pdb=" O ASP A 701 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 860 through 864 removed outlier: 5.730A pdb=" N ARG A 860 " --> pdb=" O GLU A 906 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU A 908 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG A 862 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU A 910 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU A 864 " --> pdb=" O LEU A 910 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL A 912 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 944 " --> pdb=" O LYS A 907 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 867 through 868 removed outlier: 3.603A pdb=" N ASN A 944 " --> pdb=" O LYS A 907 " (cutoff:3.500A) removed outlier: 9.589A pdb=" N HIS A 981 " --> pdb=" O TYR A 945 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A 947 " --> pdb=" O HIS A 981 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N GLY A 983 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY A 949 " --> pdb=" O GLY A 983 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1017 through 1018 Processing sheet with id=AB3, first strand: chain 'A' and resid 1045 through 1050 removed outlier: 3.914A pdb=" N THR A1047 " --> pdb=" O LEU A1066 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER A1061 " --> pdb=" O VAL A1246 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1225 through 1228 Processing sheet with id=AB5, first strand: chain 'A' and resid 1107 through 1108 Processing sheet with id=AB6, first strand: chain 'A' and resid 1248 through 1250 Processing sheet with id=AB7, first strand: chain 'A' and resid 1354 through 1359 removed outlier: 6.262A pdb=" N ALA A1325 " --> pdb=" O ASP A1354 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLN A1356 " --> pdb=" O ALA A1325 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU A1327 " --> pdb=" O GLN A1356 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ALA A1358 " --> pdb=" O LEU A1327 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR A1329 " --> pdb=" O ALA A1358 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU A1294 " --> pdb=" O TYR A1392 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N CYS A1394 " --> pdb=" O LEU A1294 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL A1296 " --> pdb=" O CYS A1394 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR A1391 " --> pdb=" O SER A1436 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ASP A1438 " --> pdb=" O TYR A1391 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A1393 " --> pdb=" O ASP A1438 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1605 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: 5.24 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.08: 10811 1.08 - 1.33: 2158 1.33 - 1.57: 9448 1.57 - 1.81: 96 1.81 - 2.06: 8 Bond restraints: 22521 Sorted by residual: bond pdb=" C4 FMN A1504 " pdb=" C4A FMN A1504 " ideal model delta sigma weight residual 1.485 1.383 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C4A FMN A1504 " pdb=" N5 FMN A1504 " ideal model delta sigma weight residual 1.300 1.373 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" O5' FMN A1504 " pdb=" P FMN A1504 " ideal model delta sigma weight residual 1.676 1.609 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C10 FMN A1504 " pdb=" N1 FMN A1504 " ideal model delta sigma weight residual 1.317 1.377 -0.060 2.00e-02 2.50e+03 8.85e+00 bond pdb=" C10 FMN A1504 " pdb=" C4A FMN A1504 " ideal model delta sigma weight residual 1.443 1.386 0.057 2.00e-02 2.50e+03 8.12e+00 ... (remaining 22516 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 39871 1.53 - 3.07: 601 3.07 - 4.60: 67 4.60 - 6.14: 6 6.14 - 7.67: 5 Bond angle restraints: 40550 Sorted by residual: angle pdb=" CA GLU A 197 " pdb=" CB GLU A 197 " pdb=" CG GLU A 197 " ideal model delta sigma weight residual 114.10 119.59 -5.49 2.00e+00 2.50e-01 7.53e+00 angle pdb=" O3P FMN A1504 " pdb=" P FMN A1504 " pdb=" O5' FMN A1504 " ideal model delta sigma weight residual 102.33 110.00 -7.67 3.00e+00 1.11e-01 6.54e+00 angle pdb=" C2 FMN A1504 " pdb=" N3 FMN A1504 " pdb=" C4 FMN A1504 " ideal model delta sigma weight residual 126.69 119.28 7.41 3.00e+00 1.11e-01 6.10e+00 angle pdb=" C4A FMN A1504 " pdb=" C4 FMN A1504 " pdb=" N3 FMN A1504 " ideal model delta sigma weight residual 113.24 120.36 -7.12 3.00e+00 1.11e-01 5.63e+00 angle pdb=" CA GLU A1091 " pdb=" CB GLU A1091 " pdb=" CG GLU A1091 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.46e+00 ... (remaining 40545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9322 17.95 - 35.89: 979 35.89 - 53.84: 275 53.84 - 71.79: 62 71.79 - 89.74: 30 Dihedral angle restraints: 10668 sinusoidal: 5830 harmonic: 4838 Sorted by residual: dihedral pdb=" CAD HEM A1501 " pdb=" CBD HEM A1501 " pdb=" CGD HEM A1501 " pdb=" O2D HEM A1501 " ideal model delta sinusoidal sigma weight residual 180.00 97.55 82.45 2 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" C1A HEM A1502 " pdb=" C2A HEM A1502 " pdb=" CAA HEM A1502 " pdb=" CBA HEM A1502 " ideal model delta sinusoidal sigma weight residual 180.00 100.19 79.81 2 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP A1122 " pdb=" CB ASP A1122 " pdb=" CG ASP A1122 " pdb=" OD1 ASP A1122 " ideal model delta sinusoidal sigma weight residual -30.00 -88.41 58.41 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 10665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1109 0.026 - 0.053: 406 0.053 - 0.079: 100 0.079 - 0.106: 74 0.106 - 0.132: 34 Chirality restraints: 1723 Sorted by residual: chirality pdb=" CA ILE A 175 " pdb=" N ILE A 175 " pdb=" C ILE A 175 " pdb=" CB ILE A 175 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA VAL A 892 " pdb=" N VAL A 892 " pdb=" C VAL A 892 " pdb=" CB VAL A 892 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA VAL A 654 " pdb=" N VAL A 654 " pdb=" C VAL A 654 " pdb=" CB VAL A 654 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 1720 not shown) Planarity restraints: 3346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A1297 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A1298 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A1298 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1298 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 724 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" CG ASP A 724 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASP A 724 " 0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP A 724 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1091 " 0.006 2.00e-02 2.50e+03 1.10e-02 1.22e+00 pdb=" C GLU A1091 " -0.019 2.00e-02 2.50e+03 pdb=" O GLU A1091 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU A1092 " 0.006 2.00e-02 2.50e+03 ... (remaining 3343 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.37: 8221 2.37 - 2.93: 50394 2.93 - 3.49: 58168 3.49 - 4.04: 76686 4.04 - 4.60: 114317 Nonbonded interactions: 307786 Sorted by model distance: nonbonded pdb=" HG SER A1197 " pdb=" H ALA A1199 " model vdw 1.815 2.100 nonbonded pdb=" HD1 HIS A 520 " pdb=" HH TYR A 707 " model vdw 1.830 2.100 nonbonded pdb=" HG1 THR A1131 " pdb=" H GLN A1134 " model vdw 1.859 2.100 nonbonded pdb=" HD2 HIS A 569 " pdb=" HG1 THR A 584 " model vdw 1.868 2.100 nonbonded pdb=" H ALA A1325 " pdb=" HG1 THR A1353 " model vdw 1.869 2.100 ... (remaining 307781 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: 8.900 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: 0.140 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.240 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 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 : 0.004 0.154 11698 Z= 0.160 Angle : 0.543 7.671 15932 Z= 0.272 Chirality : 0.037 0.132 1723 Planarity : 0.003 0.041 2041 Dihedral : 17.594 89.736 4369 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.74 % Favored : 96.04 % Rotamer: Outliers : 0.83 % Allowed : 19.35 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.24), residues: 1390 helix: 2.27 (0.21), residues: 647 sheet: -1.45 (0.35), residues: 231 loop : -0.66 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 755 TYR 0.010 0.001 TYR A 690 PHE 0.011 0.001 PHE A 103 TRP 0.007 0.001 TRP A 595 HIS 0.003 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00360 (11695) covalent geometry : angle 0.54254 (15930) SS BOND : bond 0.00037 ( 1) SS BOND : angle 0.62732 ( 2) hydrogen bonds : bond 0.15173 ( 552) hydrogen bonds : angle 6.34083 ( 1605) Misc. bond : bond 0.10860 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8062 (mm-30) REVERT: A 345 GLN cc_start: 0.9190 (tp40) cc_final: 0.8874 (tp-100) REVERT: A 618 MET cc_start: 0.7330 (tmm) cc_final: 0.6950 (tmm) REVERT: A 723 ARG cc_start: 0.9006 (mtp-110) cc_final: 0.8437 (mtp180) outliers start: 10 outliers final: 10 residues processed: 88 average time/residue: 0.2455 time to fit residues: 30.9669 Evaluate side-chains 88 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 966 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 90 HIS ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 ASN A 927 GLN A 934 GLN ** A1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.069179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.051715 restraints weight = 107462.795| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.97 r_work: 0.2736 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.163 11698 Z= 0.286 Angle : 0.612 5.576 15932 Z= 0.309 Chirality : 0.039 0.140 1723 Planarity : 0.004 0.036 2041 Dihedral : 9.372 89.498 1676 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.68 % Favored : 94.10 % Rotamer: Outliers : 2.82 % Allowed : 18.69 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.46 (0.23), residues: 1390 helix: 1.88 (0.20), residues: 655 sheet: -1.58 (0.33), residues: 231 loop : -0.80 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 551 TYR 0.020 0.002 TYR A1064 PHE 0.012 0.002 PHE A 712 TRP 0.009 0.001 TRP A 283 HIS 0.008 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00659 (11695) covalent geometry : angle 0.61174 (15930) SS BOND : bond 0.00197 ( 1) SS BOND : angle 0.70317 ( 2) hydrogen bonds : bond 0.04067 ( 552) hydrogen bonds : angle 4.96134 ( 1605) Misc. bond : bond 0.11672 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 70 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8302 (pm20) REVERT: A 723 ARG cc_start: 0.9078 (mtp-110) cc_final: 0.8532 (mtt-85) outliers start: 34 outliers final: 16 residues processed: 101 average time/residue: 0.2483 time to fit residues: 35.8657 Evaluate side-chains 85 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 1064 TYR Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1373 MET Chi-restraints excluded: chain A residue 1394 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 138 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.069971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.052502 restraints weight = 105872.913| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.96 r_work: 0.2758 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 11698 Z= 0.132 Angle : 0.490 5.007 15932 Z= 0.243 Chirality : 0.037 0.146 1723 Planarity : 0.003 0.041 2041 Dihedral : 8.437 81.878 1665 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.32 % Favored : 95.47 % Rotamer: Outliers : 1.41 % Allowed : 19.60 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.81 (0.23), residues: 1390 helix: 2.21 (0.20), residues: 661 sheet: -1.43 (0.33), residues: 229 loop : -0.72 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1312 TYR 0.013 0.001 TYR A1064 PHE 0.010 0.001 PHE A 103 TRP 0.008 0.001 TRP A 283 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00319 (11695) covalent geometry : angle 0.48991 (15930) SS BOND : bond 0.00070 ( 1) SS BOND : angle 0.56993 ( 2) hydrogen bonds : bond 0.03730 ( 552) hydrogen bonds : angle 4.57596 ( 1605) Misc. bond : bond 0.08802 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8256 (pm20) REVERT: A 232 MET cc_start: 0.8637 (tmm) cc_final: 0.8346 (tmm) REVERT: A 723 ARG cc_start: 0.9088 (mtp-110) cc_final: 0.8549 (mtt-85) outliers start: 17 outliers final: 14 residues processed: 86 average time/residue: 0.2535 time to fit residues: 31.5558 Evaluate side-chains 85 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 1178 GLU Chi-restraints excluded: chain A residue 1373 MET Chi-restraints excluded: chain A residue 1376 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 106 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.070078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.052596 restraints weight = 105257.662| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.97 r_work: 0.2763 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 11698 Z= 0.123 Angle : 0.471 4.985 15932 Z= 0.232 Chirality : 0.037 0.141 1723 Planarity : 0.003 0.037 2041 Dihedral : 7.845 76.633 1665 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.68 % Favored : 95.11 % Rotamer: Outliers : 1.99 % Allowed : 19.35 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.99 (0.24), residues: 1390 helix: 2.41 (0.20), residues: 661 sheet: -1.42 (0.33), residues: 235 loop : -0.67 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 542 TYR 0.013 0.001 TYR A1064 PHE 0.014 0.001 PHE A 103 TRP 0.007 0.001 TRP A 283 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00302 (11695) covalent geometry : angle 0.47113 (15930) SS BOND : bond 0.00121 ( 1) SS BOND : angle 0.56279 ( 2) hydrogen bonds : bond 0.03246 ( 552) hydrogen bonds : angle 4.26114 ( 1605) Misc. bond : bond 0.08234 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8189 (pm20) REVERT: A 232 MET cc_start: 0.8718 (tmm) cc_final: 0.8454 (tmm) REVERT: A 278 MET cc_start: 0.7341 (mmm) cc_final: 0.7093 (mmm) REVERT: A 723 ARG cc_start: 0.9086 (mtp-110) cc_final: 0.8588 (mtt-85) outliers start: 24 outliers final: 12 residues processed: 99 average time/residue: 0.2119 time to fit residues: 30.6375 Evaluate side-chains 85 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1436 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 112 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 95 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.069594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.052188 restraints weight = 105400.340| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.96 r_work: 0.2752 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 11698 Z= 0.138 Angle : 0.474 5.054 15932 Z= 0.234 Chirality : 0.036 0.142 1723 Planarity : 0.003 0.038 2041 Dihedral : 7.750 71.865 1662 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.39 % Favored : 95.40 % Rotamer: Outliers : 2.41 % Allowed : 18.85 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.99 (0.24), residues: 1390 helix: 2.40 (0.20), residues: 661 sheet: -1.43 (0.33), residues: 241 loop : -0.63 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 656 TYR 0.012 0.001 TYR A1064 PHE 0.012 0.001 PHE A 103 TRP 0.007 0.001 TRP A 595 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00334 (11695) covalent geometry : angle 0.47424 (15930) SS BOND : bond 0.00110 ( 1) SS BOND : angle 0.48094 ( 2) hydrogen bonds : bond 0.03236 ( 552) hydrogen bonds : angle 4.21075 ( 1605) Misc. bond : bond 0.08754 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: A 723 ARG cc_start: 0.9093 (mtp-110) cc_final: 0.8593 (mtt-85) outliers start: 29 outliers final: 20 residues processed: 100 average time/residue: 0.2182 time to fit residues: 32.1378 Evaluate side-chains 92 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1333 ASN Chi-restraints excluded: chain A residue 1376 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 135 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 chunk 116 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.069665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.052200 restraints weight = 105114.049| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.92 r_work: 0.2752 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 11698 Z= 0.127 Angle : 0.473 4.824 15932 Z= 0.232 Chirality : 0.036 0.143 1723 Planarity : 0.003 0.036 2041 Dihedral : 7.627 66.089 1662 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.82 % Favored : 94.96 % Rotamer: Outliers : 2.24 % Allowed : 19.35 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.05 (0.24), residues: 1390 helix: 2.48 (0.20), residues: 661 sheet: -1.45 (0.33), residues: 241 loop : -0.62 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 656 TYR 0.012 0.001 TYR A1064 PHE 0.011 0.001 PHE A 103 TRP 0.007 0.001 TRP A 595 HIS 0.004 0.000 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00311 (11695) covalent geometry : angle 0.47310 (15930) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.42080 ( 2) hydrogen bonds : bond 0.03097 ( 552) hydrogen bonds : angle 4.12084 ( 1605) Misc. bond : bond 0.08326 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8133 (pm20) REVERT: A 653 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8474 (tp30) REVERT: A 723 ARG cc_start: 0.9099 (mtp-110) cc_final: 0.8592 (mmt180) outliers start: 27 outliers final: 20 residues processed: 102 average time/residue: 0.2341 time to fit residues: 34.9056 Evaluate side-chains 95 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1333 ASN Chi-restraints excluded: chain A residue 1376 ASN Chi-restraints excluded: chain A residue 1436 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.069159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.051664 restraints weight = 104856.773| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.91 r_work: 0.2744 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 11698 Z= 0.139 Angle : 0.476 4.753 15932 Z= 0.233 Chirality : 0.036 0.142 1723 Planarity : 0.003 0.038 2041 Dihedral : 7.573 61.453 1662 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.53 % Favored : 95.25 % Rotamer: Outliers : 2.33 % Allowed : 19.52 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.07 (0.24), residues: 1390 helix: 2.50 (0.20), residues: 660 sheet: -1.41 (0.33), residues: 241 loop : -0.65 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 656 TYR 0.012 0.001 TYR A1064 PHE 0.009 0.001 PHE A 103 TRP 0.008 0.001 TRP A 283 HIS 0.004 0.000 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00337 (11695) covalent geometry : angle 0.47636 (15930) SS BOND : bond 0.00095 ( 1) SS BOND : angle 0.46419 ( 2) hydrogen bonds : bond 0.03111 ( 552) hydrogen bonds : angle 4.10789 ( 1605) Misc. bond : bond 0.08658 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8135 (pm20) REVERT: A 723 ARG cc_start: 0.9091 (mtp-110) cc_final: 0.8593 (mmt180) outliers start: 28 outliers final: 21 residues processed: 103 average time/residue: 0.2373 time to fit residues: 35.4909 Evaluate side-chains 97 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1064 TYR Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1333 ASN Chi-restraints excluded: chain A residue 1376 ASN Chi-restraints excluded: chain A residue 1436 SER Chi-restraints excluded: chain A residue 1442 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 78 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.067586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.049866 restraints weight = 105654.505| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.93 r_work: 0.2695 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.180 11698 Z= 0.231 Angle : 0.552 6.277 15932 Z= 0.275 Chirality : 0.038 0.139 1723 Planarity : 0.004 0.032 2041 Dihedral : 8.163 65.118 1662 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.47 % Favored : 94.39 % Rotamer: Outliers : 2.66 % Allowed : 19.44 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.77 (0.23), residues: 1390 helix: 2.19 (0.20), residues: 661 sheet: -1.62 (0.32), residues: 240 loop : -0.66 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 656 TYR 0.014 0.002 TYR A 522 PHE 0.014 0.001 PHE A1195 TRP 0.009 0.001 TRP A 595 HIS 0.008 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00537 (11695) covalent geometry : angle 0.55217 (15930) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.40885 ( 2) hydrogen bonds : bond 0.03552 ( 552) hydrogen bonds : angle 4.37963 ( 1605) Misc. bond : bond 0.12776 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.9414 (t0) cc_final: 0.8876 (t0) REVERT: A 653 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8763 (tp30) REVERT: A 723 ARG cc_start: 0.9102 (mtp-110) cc_final: 0.8572 (mmt180) outliers start: 32 outliers final: 22 residues processed: 110 average time/residue: 0.2604 time to fit residues: 40.5297 Evaluate side-chains 103 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1064 TYR Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1333 ASN Chi-restraints excluded: chain A residue 1376 ASN Chi-restraints excluded: chain A residue 1436 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.068651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.051108 restraints weight = 105033.231| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.91 r_work: 0.2725 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 11698 Z= 0.118 Angle : 0.494 6.095 15932 Z= 0.242 Chirality : 0.036 0.145 1723 Planarity : 0.003 0.035 2041 Dihedral : 7.743 63.886 1662 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.53 % Favored : 95.32 % Rotamer: Outliers : 1.99 % Allowed : 20.27 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.96 (0.24), residues: 1390 helix: 2.41 (0.21), residues: 659 sheet: -1.48 (0.33), residues: 242 loop : -0.67 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 656 TYR 0.011 0.001 TYR A1064 PHE 0.011 0.001 PHE A 103 TRP 0.010 0.001 TRP A 689 HIS 0.003 0.000 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00290 (11695) covalent geometry : angle 0.49446 (15930) SS BOND : bond 0.00039 ( 1) SS BOND : angle 0.59074 ( 2) hydrogen bonds : bond 0.03186 ( 552) hydrogen bonds : angle 4.11658 ( 1605) Misc. bond : bond 0.08553 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.9404 (t0) cc_final: 0.8869 (t0) REVERT: A 232 MET cc_start: 0.8948 (tmm) cc_final: 0.8509 (tmm) REVERT: A 293 MET cc_start: 0.9350 (tmm) cc_final: 0.9104 (tmm) REVERT: A 723 ARG cc_start: 0.9070 (mtp-110) cc_final: 0.8556 (mmt180) outliers start: 24 outliers final: 23 residues processed: 107 average time/residue: 0.2488 time to fit residues: 37.6483 Evaluate side-chains 104 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1064 TYR Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1333 ASN Chi-restraints excluded: chain A residue 1376 ASN Chi-restraints excluded: chain A residue 1436 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 37 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.050611 restraints weight = 105773.897| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.93 r_work: 0.2714 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 11698 Z= 0.169 Angle : 0.508 7.170 15932 Z= 0.251 Chirality : 0.037 0.142 1723 Planarity : 0.003 0.033 2041 Dihedral : 7.803 68.009 1662 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.11 % Favored : 94.75 % Rotamer: Outliers : 2.16 % Allowed : 20.02 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.92 (0.24), residues: 1390 helix: 2.37 (0.20), residues: 660 sheet: -1.52 (0.32), residues: 242 loop : -0.66 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 656 TYR 0.012 0.001 TYR A1064 PHE 0.012 0.001 PHE A 103 TRP 0.007 0.001 TRP A 595 HIS 0.005 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00402 (11695) covalent geometry : angle 0.50768 (15930) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.43129 ( 2) hydrogen bonds : bond 0.03230 ( 552) hydrogen bonds : angle 4.17269 ( 1605) Misc. bond : bond 0.10096 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.9408 (t0) cc_final: 0.8866 (t0) REVERT: A 293 MET cc_start: 0.9369 (tmm) cc_final: 0.9123 (tmm) REVERT: A 595 TRP cc_start: 0.9199 (OUTLIER) cc_final: 0.8144 (m100) REVERT: A 653 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8568 (tp30) REVERT: A 723 ARG cc_start: 0.9071 (mtp-110) cc_final: 0.8550 (mmt180) outliers start: 26 outliers final: 22 residues processed: 108 average time/residue: 0.2787 time to fit residues: 42.4854 Evaluate side-chains 104 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1064 TYR Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1333 ASN Chi-restraints excluded: chain A residue 1376 ASN Chi-restraints excluded: chain A residue 1436 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 43 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.068504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.050903 restraints weight = 104057.268| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.89 r_work: 0.2724 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 11698 Z= 0.150 Angle : 0.495 6.668 15932 Z= 0.244 Chirality : 0.037 0.143 1723 Planarity : 0.003 0.033 2041 Dihedral : 7.746 72.691 1662 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.53 % Favored : 95.32 % Rotamer: Outliers : 2.16 % Allowed : 20.02 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.97 (0.24), residues: 1390 helix: 2.40 (0.21), residues: 660 sheet: -1.49 (0.33), residues: 240 loop : -0.65 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 656 TYR 0.012 0.001 TYR A1064 PHE 0.008 0.001 PHE A1195 TRP 0.008 0.001 TRP A 283 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00361 (11695) covalent geometry : angle 0.49538 (15930) SS BOND : bond 0.00061 ( 1) SS BOND : angle 0.57446 ( 2) hydrogen bonds : bond 0.03119 ( 552) hydrogen bonds : angle 4.10453 ( 1605) Misc. bond : bond 0.09056 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4547.44 seconds wall clock time: 78 minutes 5.22 seconds (4685.22 seconds total)