Starting phenix.real_space_refine on Sun Jul 27 21:29:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkr_14049/07_2025/7qkr_14049.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkr_14049/07_2025/7qkr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7qkr_14049/07_2025/7qkr_14049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkr_14049/07_2025/7qkr_14049.map" model { file = "/net/cci-nas-00/data/ceres_data/7qkr_14049/07_2025/7qkr_14049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkr_14049/07_2025/7qkr_14049.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.23, per 1000 atoms: 0.66 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: 2.40 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.11 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: 3.65 Time building geometry restraints manager: 2.83 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: 5466 23.63 - 47.25: 314 47.25 - 70.87: 36 70.87 - 94.50: 16 94.50 - 118.12: 3 Dihedral angle restraints: 5835 sinusoidal: 2373 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 5832 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: 1.840 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.760 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 : 15.132 118.125 3615 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.53 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (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 TRP 0.009 0.001 TRP A 316 HIS 0.005 0.001 HIS A 103 PHE 0.030 0.001 PHE A 119 TYR 0.021 0.001 TYR A 248 ARG 0.004 0.000 ARG A1274 Details of bonding type rmsd hydrogen bonds : bond 0.15003 ( 621) hydrogen bonds : angle 6.09669 ( 1836) covalent geometry : bond 0.00664 ( 9566) covalent geometry : angle 0.85612 (12954) *********************** 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 : 1.008 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: 0.2490 time to fit residues: 45.7149 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 : 1.006 ------------------------------------------------------------------------------- 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 100 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 0.0020 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3517 r_free = 0.3517 target = 0.134395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.101368 restraints weight = 11073.024| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.77 r_work: 0.2883 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9566 Z= 0.143 Angle : 0.501 5.848 12954 Z= 0.265 Chirality : 0.039 0.134 1519 Planarity : 0.004 0.037 1611 Dihedral : 9.206 109.766 1465 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.79 % Allowed : 9.30 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.24), residues: 1193 helix: 1.61 (0.18), residues: 810 sheet: -1.64 (0.65), residues: 58 loop : -0.84 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 316 HIS 0.005 0.001 HIS A 103 PHE 0.020 0.001 PHE A 119 TYR 0.023 0.001 TYR A 248 ARG 0.007 0.000 ARG A 642 Details of bonding type rmsd hydrogen bonds : bond 0.05335 ( 621) hydrogen bonds : angle 4.13554 ( 1836) covalent geometry : bond 0.00315 ( 9566) covalent geometry : angle 0.50079 (12954) *********************** 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 107 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 345 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7745 (mp) REVERT: A 405 ARG cc_start: 0.7865 (mtm-85) cc_final: 0.7659 (mtp85) REVERT: A 534 VAL cc_start: 0.8613 (p) cc_final: 0.8068 (m) REVERT: A 892 LYS cc_start: 0.8080 (ptmt) cc_final: 0.7706 (pttp) outliers start: 8 outliers final: 5 residues processed: 106 average time/residue: 0.2414 time to fit residues: 35.5449 Evaluate side-chains 94 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 636 VAL Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL 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 3 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 2 optimal weight: 0.0370 overall best weight: 1.0660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3407 r_free = 0.3407 target = 0.126757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.091328 restraints weight = 11457.940| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.89 r_work: 0.2777 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9566 Z= 0.149 Angle : 0.482 5.806 12954 Z= 0.252 Chirality : 0.039 0.134 1519 Planarity : 0.003 0.037 1611 Dihedral : 7.813 101.447 1463 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.38 % Allowed : 10.58 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1193 helix: 1.76 (0.18), residues: 814 sheet: -1.52 (0.65), residues: 58 loop : -0.75 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 316 HIS 0.004 0.001 HIS A 103 PHE 0.017 0.001 PHE A 119 TYR 0.025 0.001 TYR A 248 ARG 0.002 0.000 ARG A 810 Details of bonding type rmsd hydrogen bonds : bond 0.05004 ( 621) hydrogen bonds : angle 3.89854 ( 1836) covalent geometry : bond 0.00346 ( 9566) covalent geometry : angle 0.48189 (12954) *********************** 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 106 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 405 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7600 (mtp85) REVERT: A 449 ASP cc_start: 0.7890 (t0) cc_final: 0.7364 (m-30) REVERT: A 534 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.7945 (m) REVERT: A 941 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7931 (tpt-90) outliers start: 14 outliers final: 9 residues processed: 103 average time/residue: 0.2406 time to fit residues: 34.5633 Evaluate side-chains 95 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 575 SER 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 1048 THR Chi-restraints excluded: chain A residue 1264 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 63 optimal weight: 0.0770 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.0270 chunk 85 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3425 r_free = 0.3425 target = 0.128301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.093009 restraints weight = 11346.865| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.88 r_work: 0.2841 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9566 Z= 0.113 Angle : 0.450 6.066 12954 Z= 0.236 Chirality : 0.037 0.135 1519 Planarity : 0.003 0.038 1611 Dihedral : 7.287 100.279 1461 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.29 % Allowed : 11.47 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1193 helix: 1.93 (0.18), residues: 814 sheet: -1.45 (0.64), residues: 58 loop : -0.64 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 213 HIS 0.003 0.001 HIS A 103 PHE 0.015 0.001 PHE A 308 TYR 0.022 0.001 TYR A 248 ARG 0.006 0.000 ARG A 795 Details of bonding type rmsd hydrogen bonds : bond 0.04630 ( 621) hydrogen bonds : angle 3.76867 ( 1836) covalent geometry : bond 0.00238 ( 9566) covalent geometry : angle 0.45006 (12954) *********************** 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 107 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 405 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7549 (mtp85) REVERT: A 449 ASP cc_start: 0.7836 (t0) cc_final: 0.7362 (m-30) REVERT: A 534 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.7981 (m) REVERT: A 812 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7939 (pt0) REVERT: A 892 LYS cc_start: 0.7978 (ptmt) cc_final: 0.7548 (pttp) outliers start: 13 outliers final: 7 residues processed: 102 average time/residue: 0.2378 time to fit residues: 33.8607 Evaluate side-chains 98 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 498 TYR 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 812 GLU Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 969 LEU 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 73 optimal weight: 3.9990 chunk 52 optimal weight: 0.0060 chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3400 r_free = 0.3400 target = 0.126148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.090552 restraints weight = 11492.259| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.90 r_work: 0.2786 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9566 Z= 0.189 Angle : 0.488 5.997 12954 Z= 0.255 Chirality : 0.040 0.139 1519 Planarity : 0.003 0.037 1611 Dihedral : 7.089 94.125 1461 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.19 % Allowed : 12.17 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.24), residues: 1193 helix: 1.81 (0.18), residues: 814 sheet: -1.42 (0.65), residues: 58 loop : -0.67 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 154 HIS 0.003 0.001 HIS A 103 PHE 0.018 0.002 PHE A 979 TYR 0.026 0.001 TYR A 248 ARG 0.005 0.000 ARG A 795 Details of bonding type rmsd hydrogen bonds : bond 0.05043 ( 621) hydrogen bonds : angle 3.82165 ( 1836) covalent geometry : bond 0.00449 ( 9566) covalent geometry : angle 0.48770 (12954) *********************** 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 106 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 449 ASP cc_start: 0.7944 (t0) cc_final: 0.7426 (m-30) REVERT: A 812 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7964 (pt0) REVERT: A 941 ARG cc_start: 0.8228 (mtm-85) cc_final: 0.7976 (tpt-90) outliers start: 12 outliers final: 10 residues processed: 103 average time/residue: 0.2333 time to fit residues: 34.1126 Evaluate side-chains 101 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 523 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 812 GLU Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 969 LEU 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 48 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 100 optimal weight: 0.0980 chunk 59 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3453 r_free = 0.3453 target = 0.129575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.095257 restraints weight = 11301.353| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.83 r_work: 0.2863 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9566 Z= 0.188 Angle : 0.488 5.995 12954 Z= 0.255 Chirality : 0.039 0.139 1519 Planarity : 0.003 0.037 1611 Dihedral : 7.097 94.125 1461 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.09 % Allowed : 12.76 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.24), residues: 1193 helix: 1.81 (0.18), residues: 814 sheet: -1.42 (0.65), residues: 58 loop : -0.67 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 154 HIS 0.003 0.001 HIS A 103 PHE 0.018 0.002 PHE A 979 TYR 0.026 0.001 TYR A 248 ARG 0.005 0.000 ARG A 795 Details of bonding type rmsd hydrogen bonds : bond 0.05042 ( 621) hydrogen bonds : angle 3.82169 ( 1836) covalent geometry : bond 0.00449 ( 9566) covalent geometry : angle 0.48768 (12954) *********************** 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 101 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 449 ASP cc_start: 0.7915 (t0) cc_final: 0.7449 (m-30) REVERT: A 812 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7971 (pt0) outliers start: 11 outliers final: 10 residues processed: 98 average time/residue: 0.2371 time to fit residues: 32.7713 Evaluate side-chains 102 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 523 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 812 GLU Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 969 LEU 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 61 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 108 optimal weight: 0.0770 chunk 90 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3407 r_free = 0.3407 target = 0.127137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.091489 restraints weight = 11552.937| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.92 r_work: 0.2833 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1595 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= 0.115 Angle : 0.447 6.499 12954 Z= 0.234 Chirality : 0.037 0.135 1519 Planarity : 0.003 0.037 1611 Dihedral : 6.896 92.770 1461 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.48 % Allowed : 12.46 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.24), residues: 1193 helix: 2.06 (0.18), residues: 809 sheet: -1.34 (0.66), residues: 58 loop : -0.51 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 213 HIS 0.003 0.001 HIS A 103 PHE 0.014 0.001 PHE A 308 TYR 0.023 0.001 TYR A 248 ARG 0.007 0.000 ARG A 795 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 621) hydrogen bonds : angle 3.71428 ( 1836) covalent geometry : bond 0.00248 ( 9566) covalent geometry : angle 0.44663 (12954) *********************** 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 109 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 449 ASP cc_start: 0.7844 (t0) cc_final: 0.7376 (m-30) REVERT: A 812 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7917 (pt0) REVERT: A 892 LYS cc_start: 0.8001 (ptmt) cc_final: 0.7555 (pttp) REVERT: A 1266 LYS cc_start: 0.7444 (mttm) cc_final: 0.7134 (mmmt) outliers start: 15 outliers final: 10 residues processed: 104 average time/residue: 0.2459 time to fit residues: 35.4511 Evaluate side-chains 97 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1201 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 117 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 99 optimal weight: 0.2980 chunk 50 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3403 r_free = 0.3403 target = 0.126862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.091169 restraints weight = 11657.281| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.92 r_work: 0.2814 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9566 Z= 0.132 Angle : 0.458 6.551 12954 Z= 0.238 Chirality : 0.038 0.135 1519 Planarity : 0.003 0.036 1611 Dihedral : 6.778 92.852 1460 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.58 % Allowed : 12.96 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.24), residues: 1193 helix: 2.06 (0.18), residues: 809 sheet: -1.34 (0.66), residues: 58 loop : -0.49 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 213 HIS 0.002 0.001 HIS A 103 PHE 0.016 0.001 PHE A 308 TYR 0.022 0.001 TYR A 248 ARG 0.006 0.000 ARG A 795 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 621) hydrogen bonds : angle 3.71107 ( 1836) covalent geometry : bond 0.00303 ( 9566) covalent geometry : angle 0.45751 (12954) *********************** 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 103 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.9148 (mmt) cc_final: 0.8876 (mmt) REVERT: A 366 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8555 (mp) REVERT: A 449 ASP cc_start: 0.7853 (t0) cc_final: 0.7379 (m-30) REVERT: A 812 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7924 (pt0) REVERT: A 892 LYS cc_start: 0.8011 (ptmt) cc_final: 0.7578 (pttp) REVERT: A 1266 LYS cc_start: 0.7427 (mttm) cc_final: 0.7108 (mmmt) outliers start: 16 outliers final: 12 residues processed: 99 average time/residue: 0.2927 time to fit residues: 40.2843 Evaluate side-chains 101 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 523 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 812 GLU Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1201 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3411 r_free = 0.3411 target = 0.127350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.091889 restraints weight = 11437.073| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.89 r_work: 0.2816 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9566 Z= 0.132 Angle : 0.458 6.551 12954 Z= 0.238 Chirality : 0.038 0.135 1519 Planarity : 0.003 0.036 1611 Dihedral : 6.778 92.852 1460 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.38 % Allowed : 12.96 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.24), residues: 1193 helix: 2.06 (0.18), residues: 809 sheet: -1.34 (0.66), residues: 58 loop : -0.49 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 213 HIS 0.002 0.001 HIS A 103 PHE 0.016 0.001 PHE A 308 TYR 0.022 0.001 TYR A 248 ARG 0.006 0.000 ARG A 795 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 621) hydrogen bonds : angle 3.71107 ( 1836) covalent geometry : bond 0.00303 ( 9566) covalent geometry : angle 0.45751 (12954) *********************** 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 101 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.9145 (mmt) cc_final: 0.8871 (mmt) REVERT: A 366 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8560 (mp) REVERT: A 449 ASP cc_start: 0.7854 (t0) cc_final: 0.7384 (m-30) REVERT: A 812 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7929 (pt0) REVERT: A 892 LYS cc_start: 0.8018 (ptmt) cc_final: 0.7588 (pttp) REVERT: A 1266 LYS cc_start: 0.7449 (mttm) cc_final: 0.7132 (mmmt) outliers start: 14 outliers final: 12 residues processed: 97 average time/residue: 0.2444 time to fit residues: 33.3408 Evaluate side-chains 101 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 523 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 812 GLU Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1201 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3411 r_free = 0.3411 target = 0.127345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.091802 restraints weight = 11582.561| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.91 r_work: 0.2814 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9566 Z= 0.132 Angle : 0.458 6.551 12954 Z= 0.238 Chirality : 0.038 0.135 1519 Planarity : 0.003 0.036 1611 Dihedral : 6.778 92.852 1460 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.38 % Allowed : 12.96 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.24), residues: 1193 helix: 2.06 (0.18), residues: 809 sheet: -1.34 (0.66), residues: 58 loop : -0.49 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 213 HIS 0.002 0.001 HIS A 103 PHE 0.016 0.001 PHE A 308 TYR 0.022 0.001 TYR A 248 ARG 0.006 0.000 ARG A 795 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 621) hydrogen bonds : angle 3.71107 ( 1836) covalent geometry : bond 0.00303 ( 9566) covalent geometry : angle 0.45751 (12954) ********************** 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 101 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.9148 (mmt) cc_final: 0.8876 (mmt) REVERT: A 366 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8560 (mp) REVERT: A 449 ASP cc_start: 0.7853 (t0) cc_final: 0.7380 (m-30) REVERT: A 812 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7927 (pt0) REVERT: A 892 LYS cc_start: 0.8015 (ptmt) cc_final: 0.7585 (pttp) REVERT: A 1266 LYS cc_start: 0.7423 (mttm) cc_final: 0.7105 (mmmt) outliers start: 14 outliers final: 12 residues processed: 97 average time/residue: 0.2569 time to fit residues: 34.6440 Evaluate side-chains 101 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 523 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 812 GLU Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1201 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 107 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 0.0060 chunk 49 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 92 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3411 r_free = 0.3411 target = 0.127348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.091830 restraints weight = 11542.309| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.91 r_work: 0.2815 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9566 Z= 0.132 Angle : 0.458 6.551 12954 Z= 0.238 Chirality : 0.038 0.135 1519 Planarity : 0.003 0.036 1611 Dihedral : 6.778 92.852 1460 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.38 % Allowed : 12.96 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.24), residues: 1193 helix: 2.06 (0.18), residues: 809 sheet: -1.34 (0.66), residues: 58 loop : -0.49 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 213 HIS 0.002 0.001 HIS A 103 PHE 0.016 0.001 PHE A 308 TYR 0.022 0.001 TYR A 248 ARG 0.006 0.000 ARG A 795 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 621) hydrogen bonds : angle 3.71107 ( 1836) covalent geometry : bond 0.00303 ( 9566) covalent geometry : angle 0.45751 (12954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5569.74 seconds wall clock time: 97 minutes 25.19 seconds (5845.19 seconds total)