Starting phenix.real_space_refine on Thu Jul 2 18:40:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qkr_14049/07_2026/7qkr_14049.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkr_14049/07_2026/7qkr_14049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7qkr_14049/07_2026/7qkr_14049.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qkr_14049/07_2026/7qkr_14049.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qkr_14049/07_2026/7qkr_14049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkr_14049/07_2026/7qkr_14049.map" model { file = "/net/cci-nas-00/data/ceres_data/7qkr_14049/07_2026/7qkr_14049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkr_14049/07_2026/7qkr_14049.cif" } resolution = 3.2 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= 0.006 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 47 5.16 5 C 6047 2.51 5 N 1549 2.21 5 O 1756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9403 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1199, 9299 Classifications: {'peptide': 1199} Link IDs: {'PTRANS': 27, 'TRANS': 1171} Chain breaks: 2 Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 104 Unusual residues: {' MG': 1, '9Z9': 1, 'ANP': 1, 'I6H': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.70, per 1000 atoms: 0.18 Number of scatterers: 9403 At special positions: 0 Unit cell: (137.268, 97.092, 102.951, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 3 15.00 Mg 1 11.99 O 1756 8.00 N 1549 7.00 C 6047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 211.7 milliseconds 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 5 sheets defined 71.5% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 32 through 42 Processing helix chain 'A' and resid 51 through 57 Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 61 through 80 removed outlier: 4.324A pdb=" N CYS A 65 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 66 " --> pdb=" O TRP A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 101 removed outlier: 3.923A pdb=" N LEU A 86 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 158 Processing helix chain 'A' and resid 160 through 167 Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 188 through 212 removed outlier: 3.702A pdb=" N GLY A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 230 through 261 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 270 through 326 removed outlier: 3.639A pdb=" N GLN A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 275 " --> pdb=" O HIS A 271 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP A 304 " --> pdb=" O MET A 300 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N SER A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 372 removed outlier: 3.552A pdb=" N ILE A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 355 " --> pdb=" O ILE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.734A pdb=" N VAL A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 470 Processing helix chain 'A' and resid 485 through 491 Processing helix chain 'A' and resid 492 through 494 No H-bonds generated for 'chain 'A' and resid 492 through 494' Processing helix chain 'A' and resid 502 through 517 Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.709A pdb=" N GLN A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 557 removed outlier: 4.266A pdb=" N SER A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 588 removed outlier: 3.816A pdb=" N GLY A 577 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE A 578 " --> pdb=" O ARG A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 630 through 646 Processing helix chain 'A' and resid 699 through 706 Processing helix chain 'A' and resid 707 through 712 Processing helix chain 'A' and resid 715 through 741 removed outlier: 3.617A pdb=" N ALA A 720 " --> pdb=" O CYS A 716 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 748 through 801 removed outlier: 3.575A pdb=" N VAL A 769 " --> pdb=" O MET A 765 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS A 796 " --> pdb=" O MET A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 810 removed outlier: 3.742A pdb=" N PHE A 808 " --> pdb=" O ASP A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 829 Proline residue: A 826 - end of helix Processing helix chain 'A' and resid 830 through 832 No H-bonds generated for 'chain 'A' and resid 830 through 832' Processing helix chain 'A' and resid 833 through 858 removed outlier: 3.526A pdb=" N ALA A 837 " --> pdb=" O SER A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 894 removed outlier: 4.083A pdb=" N VAL A 864 " --> pdb=" O ARG A 860 " (cutoff:3.500A) Proline residue: A 870 - end of helix removed outlier: 3.615A pdb=" N GLY A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 890 " --> pdb=" O PHE A 886 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 906 Processing helix chain 'A' and resid 907 through 915 Processing helix chain 'A' and resid 916 through 971 removed outlier: 3.540A pdb=" N LYS A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG A 941 " --> pdb=" O ARG A 937 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR A 942 " --> pdb=" O SER A 938 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 945 " --> pdb=" O ARG A 941 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN A 953 " --> pdb=" O ILE A 949 " (cutoff:3.500A) Proline residue: A 954 - end of helix Processing helix chain 'A' and resid 974 through 997 removed outlier: 3.527A pdb=" N GLU A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 995 " --> pdb=" O SER A 991 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 997 " --> pdb=" O GLY A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1018 removed outlier: 3.618A pdb=" N LYS A1004 " --> pdb=" O PRO A1000 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A1006 " --> pdb=" O MET A1002 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN A1007 " --> pdb=" O GLY A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1091 removed outlier: 3.738A pdb=" N GLY A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1111 No H-bonds generated for 'chain 'A' and resid 1109 through 1111' Processing helix chain 'A' and resid 1112 through 1119 Processing helix chain 'A' and resid 1133 through 1139 Processing helix chain 'A' and resid 1140 through 1142 No H-bonds generated for 'chain 'A' and resid 1140 through 1142' Processing helix chain 'A' and resid 1153 through 1162 Processing helix chain 'A' and resid 1164 through 1170 Processing helix chain 'A' and resid 1187 through 1202 removed outlier: 4.524A pdb=" N ARG A1202 " --> pdb=" O ARG A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1233 removed outlier: 3.823A pdb=" N MET A1222 " --> pdb=" O SER A1218 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL A1223 " --> pdb=" O GLU A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1250 removed outlier: 3.528A pdb=" N GLN A1248 " --> pdb=" O SER A1245 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN A1249 " --> pdb=" O THR A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1274 removed outlier: 3.534A pdb=" N ARG A1274 " --> pdb=" O LEU A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1275 through 1288 Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 418 removed outlier: 6.765A pdb=" N SER A 412 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR A 399 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE A 414 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N PHE A 395 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU A 453 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASN A 397 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU A 451 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 471 through 474 removed outlier: 6.508A pdb=" N THR A 423 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL A 609 " --> pdb=" O THR A 423 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA A 425 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU A 611 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL A 427 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A 618 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER A 612 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE A 616 " --> pdb=" O SER A 612 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 483 through 484 removed outlier: 3.526A pdb=" N ALA A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1058 through 1067 removed outlier: 5.582A pdb=" N THR A1061 " --> pdb=" O PHE A1049 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N PHE A1049 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU A1065 " --> pdb=" O ARG A1045 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG A1045 " --> pdb=" O LEU A1065 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE A1067 " --> pdb=" O GLU A1043 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU A1043 " --> pdb=" O ILE A1067 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU A1044 " --> pdb=" O LEU A1102 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU A1102 " --> pdb=" O LEU A1044 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASP A1046 " --> pdb=" O GLN A1100 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLN A1100 " --> pdb=" O ASP A1046 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 6.685A pdb=" N ALA A1121 " --> pdb=" O LEU A1208 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ASP A1210 " --> pdb=" O ALA A1121 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A1123 " --> pdb=" O ASP A1210 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A1073 " --> pdb=" O THR A1239 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR A1072 " --> pdb=" O VAL A1252 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N TYR A1254 " --> pdb=" O TYR A1072 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY A1074 " --> pdb=" O TYR A1254 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N PHE A1256 " --> pdb=" O GLY A1074 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL A1076 " --> pdb=" O PHE A1256 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A1263 " --> pdb=" O VAL A1255 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASP A1257 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE A1261 " --> pdb=" O ASP A1257 " (cutoff:3.500A) 621 hydrogen bonds defined for protein. 1836 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: 1.23 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1531 1.27 - 1.40: 2263 1.40 - 1.54: 5587 1.54 - 1.67: 107 1.67 - 1.81: 78 Bond restraints: 9566 Sorted by residual: bond pdb=" N3B ANP A1302 " pdb=" PG ANP A1302 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.09e+01 bond pdb=" O3A ANP A1302 " pdb=" PB ANP A1302 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" N ILE A1042 " pdb=" CA ILE A1042 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.14e-02 7.69e+03 1.34e+01 bond pdb=" C THR A 233 " pdb=" O THR A 233 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.17e-02 7.31e+03 1.03e+01 bond pdb=" N ILE A1033 " pdb=" CA ILE A1033 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.24e-02 6.50e+03 9.80e+00 ... (remaining 9561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 12291 1.97 - 3.94: 592 3.94 - 5.91: 64 5.91 - 7.88: 6 7.88 - 9.85: 1 Bond angle restraints: 12954 Sorted by residual: angle pdb=" CA ARG A1260 " pdb=" C ARG A1260 " pdb=" O ARG A1260 " ideal model delta sigma weight residual 121.11 116.58 4.53 1.17e+00 7.31e-01 1.50e+01 angle pdb=" N ILE A 234 " pdb=" CA ILE A 234 " pdb=" C ILE A 234 " ideal model delta sigma weight residual 110.53 106.91 3.62 9.40e-01 1.13e+00 1.49e+01 angle pdb=" CA ILE A 756 " pdb=" C ILE A 756 " pdb=" O ILE A 756 " ideal model delta sigma weight residual 121.27 117.28 3.99 1.04e+00 9.25e-01 1.47e+01 angle pdb=" CA VAL A1262 " pdb=" C VAL A1262 " pdb=" O VAL A1262 " ideal model delta sigma weight residual 120.85 116.80 4.05 1.06e+00 8.90e-01 1.46e+01 angle pdb=" N GLY A 620 " pdb=" CA GLY A 620 " pdb=" C GLY A 620 " ideal model delta sigma weight residual 110.45 115.34 -4.89 1.30e+00 5.92e-01 1.42e+01 ... (remaining 12949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.63: 5378 23.63 - 47.25: 307 47.25 - 70.87: 28 70.87 - 94.50: 8 94.50 - 118.12: 3 Dihedral angle restraints: 5724 sinusoidal: 2262 harmonic: 3462 Sorted by residual: dihedral pdb=" C23 9Z9 A1304 " pdb=" C21 9Z9 A1304 " pdb=" C22 9Z9 A1304 " pdb=" O20 9Z9 A1304 " ideal model delta sinusoidal sigma weight residual 177.26 59.14 118.12 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C22 9Z9 A1304 " pdb=" C23 9Z9 A1304 " pdb=" C48 9Z9 A1304 " pdb=" O49 9Z9 A1304 " ideal model delta sinusoidal sigma weight residual 177.15 -65.26 -117.59 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" C22 9Z9 A1304 " pdb=" C23 9Z9 A1304 " pdb=" C24 9Z9 A1304 " pdb=" O25 9Z9 A1304 " ideal model delta sinusoidal sigma weight residual -163.69 -61.22 -102.47 1 3.00e+01 1.11e-03 1.30e+01 ... (remaining 5721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1341 0.084 - 0.169: 149 0.169 - 0.253: 22 0.253 - 0.338: 6 0.338 - 0.422: 1 Chirality restraints: 1519 Sorted by residual: chirality pdb=" C3' ANP A1302 " pdb=" C2' ANP A1302 " pdb=" C4' ANP A1302 " pdb=" O3' ANP A1302 " both_signs ideal model delta sigma weight residual False -2.36 -2.78 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA THR A 231 " pdb=" N THR A 231 " pdb=" C THR A 231 " pdb=" CB THR A 231 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA PHE A 341 " pdb=" N PHE A 341 " pdb=" C PHE A 341 " pdb=" CB PHE A 341 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1516 not shown) Planarity restraints: 1611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1193 " 0.202 9.50e-02 1.11e+02 9.04e-02 5.01e+00 pdb=" NE ARG A1193 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A1193 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A1193 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A1193 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1216 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C LEU A1216 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU A1216 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP A1217 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 228 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C LEU A 228 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU A 228 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 229 " 0.011 2.00e-02 2.50e+03 ... (remaining 1608 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 56 2.65 - 3.21: 8919 3.21 - 3.77: 14402 3.77 - 4.34: 20353 4.34 - 4.90: 33623 Nonbonded interactions: 77353 Sorted by model distance: nonbonded pdb=" O3G ANP A1302 " pdb="MG MG A1303 " model vdw 2.084 2.170 nonbonded pdb=" OG SER A 435 " pdb="MG MG A1303 " model vdw 2.127 2.170 nonbonded pdb=" OD1 ASN A 706 " pdb=" NZ LYS A 791 " model vdw 2.310 3.120 nonbonded pdb=" N GLY A1040 " pdb=" OD2 ASP A1104 " model vdw 2.344 3.120 nonbonded pdb=" OE2 GLU A 142 " pdb=" NH2 ARG A 889 " model vdw 2.348 3.120 ... (remaining 77348 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.190 Find NCS groups from input model: 0.020 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 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 : 0.007 0.168 9566 Z= 0.450 Angle : 0.856 9.852 12954 Z= 0.599 Chirality : 0.057 0.422 1519 Planarity : 0.005 0.090 1611 Dihedral : 14.487 118.125 3504 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.40 % Allowed : 3.86 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.24), residues: 1193 helix: 0.85 (0.19), residues: 802 sheet: -1.67 (0.74), residues: 48 loop : -1.15 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1274 TYR 0.021 0.001 TYR A 248 PHE 0.030 0.001 PHE A 119 TRP 0.009 0.001 TRP A 316 HIS 0.005 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.45 ( 9566) covalent geometry : angle 0.85612 / 0.60 (12954) hydrogen bonds : bond 0.15003 / 10.20 ( 621) hydrogen bonds : angle 6.09669 / 4.40 ( 1836) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.242 Fit side-chains REVERT: A 322 MET cc_start: 0.8410 (mtp) cc_final: 0.8075 (mtp) REVERT: A 345 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7478 (mp) REVERT: A 534 VAL cc_start: 0.8751 (p) cc_final: 0.8357 (m) outliers start: 4 outliers final: 3 residues processed: 135 average time/residue: 0.0904 time to fit residues: 16.9179 Evaluate side-chains 96 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 865 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.0020 chunk 49 optimal weight: 0.0870 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.0970 chunk 117 optimal weight: 0.9990 overall best weight: 0.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN A1137 ASN A1192 GLN A1282 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.133321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.099689 restraints weight = 11184.570| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.82 r_work: 0.2912 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9566 Z= 0.119 Angle : 0.477 6.128 12954 Z= 0.254 Chirality : 0.038 0.137 1519 Planarity : 0.004 0.038 1611 Dihedral : 7.556 99.388 1354 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.69 % Allowed : 9.00 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.32 (0.24), residues: 1193 helix: 1.73 (0.18), residues: 814 sheet: -1.67 (0.64), residues: 58 loop : -0.79 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 642 TYR 0.020 0.001 TYR A 248 PHE 0.019 0.001 PHE A 119 TRP 0.008 0.001 TRP A 316 HIS 0.004 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 ( 9566) covalent geometry : angle 0.47654 / 0.25 (12954) hydrogen bonds : bond 0.04978 / 3.33 ( 621) hydrogen bonds : angle 4.06281 / 2.94 ( 1836) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 345 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7714 (mp) REVERT: A 405 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7602 (mtp85) REVERT: A 534 VAL cc_start: 0.8618 (p) cc_final: 0.8084 (m) REVERT: A 820 THR cc_start: 0.8315 (m) cc_final: 0.7895 (p) REVERT: A 892 LYS cc_start: 0.7911 (ptmt) cc_final: 0.7538 (pttp) outliers start: 7 outliers final: 3 residues processed: 113 average time/residue: 0.0909 time to fit residues: 14.1970 Evaluate side-chains 96 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 1048 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 51 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 110 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1137 ASN A1282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.129740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.095069 restraints weight = 11313.680| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.86 r_work: 0.2889 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9566 Z= 0.129 Angle : 0.466 5.940 12954 Z= 0.246 Chirality : 0.038 0.137 1519 Planarity : 0.003 0.035 1611 Dihedral : 7.091 93.524 1350 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.99 % Allowed : 9.79 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.53 (0.24), residues: 1193 helix: 1.90 (0.18), residues: 812 sheet: -1.52 (0.65), residues: 58 loop : -0.74 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 642 TYR 0.022 0.001 TYR A 248 PHE 0.016 0.001 PHE A 308 TRP 0.007 0.001 TRP A 213 HIS 0.004 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 9566) covalent geometry : angle 0.46625 / 0.25 (12954) hydrogen bonds : bond 0.04916 / 3.28 ( 621) hydrogen bonds : angle 3.91180 / 2.83 ( 1836) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 345 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7719 (mp) REVERT: A 405 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7560 (mtp85) REVERT: A 449 ASP cc_start: 0.7811 (t0) cc_final: 0.7384 (m-30) REVERT: A 534 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8109 (m) REVERT: A 892 LYS cc_start: 0.7925 (ptmt) cc_final: 0.7550 (pttp) outliers start: 10 outliers final: 7 residues processed: 105 average time/residue: 0.0814 time to fit residues: 12.1298 Evaluate side-chains 100 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1048 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1137 ASN A1282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.128891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.094090 restraints weight = 11479.201| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.88 r_work: 0.2846 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9566 Z= 0.129 Angle : 0.466 5.940 12954 Z= 0.246 Chirality : 0.038 0.137 1519 Planarity : 0.003 0.035 1611 Dihedral : 7.091 93.524 1350 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.89 % Allowed : 10.09 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.53 (0.24), residues: 1193 helix: 1.90 (0.18), residues: 812 sheet: -1.52 (0.65), residues: 58 loop : -0.74 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 642 TYR 0.022 0.001 TYR A 248 PHE 0.016 0.001 PHE A 308 TRP 0.007 0.001 TRP A 213 HIS 0.004 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 9566) covalent geometry : angle 0.46625 / 0.25 (12954) hydrogen bonds : bond 0.04916 / 3.28 ( 621) hydrogen bonds : angle 3.91180 / 2.83 ( 1836) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 345 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7718 (mp) REVERT: A 405 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7550 (mtp85) REVERT: A 449 ASP cc_start: 0.7828 (t0) cc_final: 0.7370 (m-30) REVERT: A 534 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8085 (m) REVERT: A 892 LYS cc_start: 0.7918 (ptmt) cc_final: 0.7537 (pttp) outliers start: 9 outliers final: 7 residues processed: 98 average time/residue: 0.0830 time to fit residues: 11.3454 Evaluate side-chains 100 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1048 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 89 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 79 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1137 ASN A1282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.094019 restraints weight = 11436.674| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.88 r_work: 0.2862 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9566 Z= 0.129 Angle : 0.463 5.782 12954 Z= 0.244 Chirality : 0.038 0.135 1519 Planarity : 0.003 0.034 1611 Dihedral : 7.042 91.501 1350 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.99 % Allowed : 10.19 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.24), residues: 1193 helix: 1.91 (0.18), residues: 814 sheet: -1.55 (0.64), residues: 58 loop : -0.67 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1193 TYR 0.022 0.001 TYR A 248 PHE 0.018 0.001 PHE A 308 TRP 0.007 0.001 TRP A 213 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9566) covalent geometry : angle 0.46313 / 0.24 (12954) hydrogen bonds : bond 0.04881 / 3.25 ( 621) hydrogen bonds : angle 3.87718 / 2.81 ( 1836) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 345 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7718 (mp) REVERT: A 449 ASP cc_start: 0.7820 (t0) cc_final: 0.7361 (m-30) REVERT: A 534 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8101 (m) REVERT: A 892 LYS cc_start: 0.7924 (ptmt) cc_final: 0.7537 (pttp) outliers start: 10 outliers final: 7 residues processed: 101 average time/residue: 0.0848 time to fit residues: 12.1655 Evaluate side-chains 100 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1048 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.093175 restraints weight = 11430.540| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.88 r_work: 0.2845 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9566 Z= 0.129 Angle : 0.463 5.782 12954 Z= 0.244 Chirality : 0.038 0.135 1519 Planarity : 0.003 0.034 1611 Dihedral : 7.042 91.501 1350 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.89 % Allowed : 10.58 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.24), residues: 1193 helix: 1.91 (0.18), residues: 814 sheet: -1.55 (0.64), residues: 58 loop : -0.67 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1193 TYR 0.022 0.001 TYR A 248 PHE 0.018 0.001 PHE A 308 TRP 0.007 0.001 TRP A 213 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9566) covalent geometry : angle 0.46313 / 0.24 (12954) hydrogen bonds : bond 0.04881 / 3.25 ( 621) hydrogen bonds : angle 3.87718 / 2.81 ( 1836) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 345 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7709 (mp) REVERT: A 449 ASP cc_start: 0.7824 (t0) cc_final: 0.7354 (m-30) REVERT: A 534 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8097 (m) REVERT: A 892 LYS cc_start: 0.7914 (ptmt) cc_final: 0.7526 (pttp) outliers start: 9 outliers final: 7 residues processed: 98 average time/residue: 0.0906 time to fit residues: 12.3210 Evaluate side-chains 100 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1048 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 50 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 92 optimal weight: 0.0040 chunk 71 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.128690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.093885 restraints weight = 11432.301| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.87 r_work: 0.2845 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9566 Z= 0.129 Angle : 0.463 5.782 12954 Z= 0.244 Chirality : 0.038 0.135 1519 Planarity : 0.003 0.034 1611 Dihedral : 7.042 91.501 1350 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.89 % Allowed : 10.58 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.24), residues: 1193 helix: 1.91 (0.18), residues: 814 sheet: -1.55 (0.64), residues: 58 loop : -0.67 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1193 TYR 0.022 0.001 TYR A 248 PHE 0.018 0.001 PHE A 308 TRP 0.007 0.001 TRP A 213 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9566) covalent geometry : angle 0.46313 / 0.24 (12954) hydrogen bonds : bond 0.04881 / 3.25 ( 621) hydrogen bonds : angle 3.87718 / 2.81 ( 1836) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 345 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7719 (mp) REVERT: A 449 ASP cc_start: 0.7829 (t0) cc_final: 0.7360 (m-30) REVERT: A 534 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8094 (m) REVERT: A 892 LYS cc_start: 0.7926 (ptmt) cc_final: 0.7540 (pttp) outliers start: 9 outliers final: 7 residues processed: 98 average time/residue: 0.0967 time to fit residues: 13.2028 Evaluate side-chains 100 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1048 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 62 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 101 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.093260 restraints weight = 11382.970| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.88 r_work: 0.2856 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9566 Z= 0.123 Angle : 0.460 6.985 12954 Z= 0.240 Chirality : 0.038 0.143 1519 Planarity : 0.003 0.035 1611 Dihedral : 6.795 93.353 1350 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.99 % Allowed : 10.68 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.66 (0.24), residues: 1193 helix: 1.96 (0.18), residues: 814 sheet: -1.53 (0.63), residues: 58 loop : -0.58 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 396 TYR 0.022 0.001 TYR A 248 PHE 0.016 0.001 PHE A 308 TRP 0.008 0.001 TRP A 213 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9566) covalent geometry : angle 0.46019 / 0.24 (12954) hydrogen bonds : bond 0.04683 / 3.12 ( 621) hydrogen bonds : angle 3.77838 / 2.74 ( 1836) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 345 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7748 (mp) REVERT: A 449 ASP cc_start: 0.7828 (t0) cc_final: 0.7355 (m-30) REVERT: A 534 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8012 (m) REVERT: A 892 LYS cc_start: 0.7929 (ptmt) cc_final: 0.7526 (pttp) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.0944 time to fit residues: 13.6307 Evaluate side-chains 101 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1048 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1137 ASN A1282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.127055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.091667 restraints weight = 11471.557| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.90 r_work: 0.2818 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9566 Z= 0.152 Angle : 0.482 6.923 12954 Z= 0.251 Chirality : 0.039 0.143 1519 Planarity : 0.003 0.035 1611 Dihedral : 6.569 97.035 1350 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.89 % Allowed : 11.18 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.64 (0.24), residues: 1193 helix: 1.93 (0.18), residues: 813 sheet: -1.49 (0.64), residues: 58 loop : -0.56 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 396 TYR 0.025 0.001 TYR A 248 PHE 0.016 0.002 PHE A 979 TRP 0.007 0.001 TRP A 213 HIS 0.004 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 9566) covalent geometry : angle 0.48201 / 0.25 (12954) hydrogen bonds : bond 0.04857 / 3.25 ( 621) hydrogen bonds : angle 3.79531 / 2.76 ( 1836) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 449 ASP cc_start: 0.7917 (t0) cc_final: 0.7413 (m-30) REVERT: A 534 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.7984 (m) REVERT: A 1266 LYS cc_start: 0.7447 (mttm) cc_final: 0.7106 (mmmt) outliers start: 9 outliers final: 6 residues processed: 102 average time/residue: 0.0937 time to fit residues: 13.1428 Evaluate side-chains 99 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1048 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 76 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 46 optimal weight: 0.0370 chunk 79 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 88 optimal weight: 0.0040 chunk 109 optimal weight: 8.9990 overall best weight: 0.3670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.095300 restraints weight = 11338.922| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.81 r_work: 0.2916 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9566 Z= 0.104 Angle : 0.453 7.534 12954 Z= 0.236 Chirality : 0.037 0.132 1519 Planarity : 0.003 0.053 1611 Dihedral : 6.250 97.624 1350 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.79 % Allowed : 11.57 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.25), residues: 1193 helix: 2.20 (0.18), residues: 808 sheet: -1.36 (0.65), residues: 58 loop : -0.43 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 795 TYR 0.018 0.001 TYR A 248 PHE 0.014 0.001 PHE A 119 TRP 0.012 0.001 TRP A 213 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 9566) covalent geometry : angle 0.45266 / 0.24 (12954) hydrogen bonds : bond 0.04245 / 2.82 ( 621) hydrogen bonds : angle 3.65934 / 2.67 ( 1836) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 345 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7807 (mp) REVERT: A 449 ASP cc_start: 0.7818 (t0) cc_final: 0.7390 (m-30) REVERT: A 534 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8070 (m) REVERT: A 700 LEU cc_start: 0.9042 (tp) cc_final: 0.8331 (pt) REVERT: A 820 THR cc_start: 0.8311 (m) cc_final: 0.7883 (p) REVERT: A 892 LYS cc_start: 0.7884 (ptmt) cc_final: 0.7484 (pttp) REVERT: A 1266 LYS cc_start: 0.7317 (mttm) cc_final: 0.7055 (mmmt) outliers start: 8 outliers final: 5 residues processed: 110 average time/residue: 0.1069 time to fit residues: 16.4164 Evaluate side-chains 105 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1048 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 67 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 89 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 111 optimal weight: 0.0570 chunk 99 optimal weight: 0.3980 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.130132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.095263 restraints weight = 11274.825| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.87 r_work: 0.2930 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9566 Z= 0.105 Angle : 0.459 7.629 12954 Z= 0.235 Chirality : 0.037 0.133 1519 Planarity : 0.003 0.039 1611 Dihedral : 5.869 93.000 1349 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.79 % Allowed : 12.36 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.25), residues: 1193 helix: 2.32 (0.18), residues: 807 sheet: -1.28 (0.64), residues: 58 loop : -0.35 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 795 TYR 0.021 0.001 TYR A 248 PHE 0.016 0.001 PHE A1049 TRP 0.010 0.001 TRP A 213 HIS 0.003 0.000 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 9566) covalent geometry : angle 0.45862 / 0.24 (12954) hydrogen bonds : bond 0.04192 / 2.79 ( 621) hydrogen bonds : angle 3.62975 / 2.64 ( 1836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2236.34 seconds wall clock time: 39 minutes 0.56 seconds (2340.56 seconds total)