Starting phenix.real_space_refine on Wed Feb 4 23:38:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m1i_63572/02_2026/9m1i_63572.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m1i_63572/02_2026/9m1i_63572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m1i_63572/02_2026/9m1i_63572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m1i_63572/02_2026/9m1i_63572.map" model { file = "/net/cci-nas-00/data/ceres_data/9m1i_63572/02_2026/9m1i_63572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m1i_63572/02_2026/9m1i_63572.cif" } resolution = 2.48 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= 0.001 sd= 0.025 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 86 5.16 5 C 8555 2.51 5 N 2356 2.21 5 O 2517 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13518 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 8710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8710 Classifications: {'peptide': 1112} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 1066} Chain breaks: 2 Chain: "G" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1395 Classifications: {'peptide': 174} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "b" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3380 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 410} Chain: "b" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.91, per 1000 atoms: 0.22 Number of scatterers: 13518 At special positions: 0 Unit cell: (105.193, 118.162, 131.131, 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 86 16.00 P 3 15.00 Mg 1 11.99 O 2517 8.00 N 2356 7.00 C 8555 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: 0.78 Conformation dependent library (CDL) restraints added in 600.4 milliseconds 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 7 sheets defined 64.8% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'D' and resid 32 through 41 removed outlier: 3.532A pdb=" N THR D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 65 removed outlier: 3.535A pdb=" N ALA D 56 " --> pdb=" O GLU D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 79 through 90 removed outlier: 3.896A pdb=" N LEU D 85 " --> pdb=" O MET D 81 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 113 removed outlier: 3.562A pdb=" N VAL D 99 " --> pdb=" O PRO D 95 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 108 " --> pdb=" O LYS D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 removed outlier: 3.648A pdb=" N LEU D 121 " --> pdb=" O PHE D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 128 removed outlier: 3.687A pdb=" N ASP D 128 " --> pdb=" O GLU D 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 125 through 128' Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.612A pdb=" N GLN D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 146 through 161 removed outlier: 3.900A pdb=" N ARG D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 196 removed outlier: 3.586A pdb=" N GLN D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 216 removed outlier: 4.393A pdb=" N ALA D 206 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA D 208 " --> pdb=" O ARG D 204 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR D 216 " --> pdb=" O SER D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 238 removed outlier: 3.936A pdb=" N PHE D 228 " --> pdb=" O LYS D 224 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU D 229 " --> pdb=" O MET D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 263 removed outlier: 3.659A pdb=" N VAL D 247 " --> pdb=" O THR D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 removed outlier: 3.657A pdb=" N LEU D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 282 removed outlier: 3.760A pdb=" N VAL D 276 " --> pdb=" O TYR D 272 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY D 282 " --> pdb=" O ARG D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 309 Processing helix chain 'D' and resid 355 through 369 Processing helix chain 'D' and resid 375 through 389 removed outlier: 3.774A pdb=" N SER D 379 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY D 389 " --> pdb=" O GLY D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 406 removed outlier: 3.542A pdb=" N ASP D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASP D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 429 Processing helix chain 'D' and resid 433 through 449 removed outlier: 3.761A pdb=" N LEU D 437 " --> pdb=" O LEU D 433 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL D 438 " --> pdb=" O PRO D 434 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP D 439 " --> pdb=" O SER D 435 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA D 442 " --> pdb=" O VAL D 438 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 478 Processing helix chain 'D' and resid 480 through 482 No H-bonds generated for 'chain 'D' and resid 480 through 482' Processing helix chain 'D' and resid 483 through 498 removed outlier: 5.024A pdb=" N SER D 492 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA D 493 " --> pdb=" O ALA D 489 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 495 " --> pdb=" O SER D 491 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE D 496 " --> pdb=" O SER D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 522 removed outlier: 3.723A pdb=" N ARG D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 534 Processing helix chain 'D' and resid 535 through 540 removed outlier: 3.885A pdb=" N GLY D 540 " --> pdb=" O TYR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 547 through 555 removed outlier: 3.641A pdb=" N VAL D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE D 552 " --> pdb=" O VAL D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 576 through 591 removed outlier: 3.854A pdb=" N ASN D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 601 Processing helix chain 'D' and resid 601 through 610 removed outlier: 4.284A pdb=" N ARG D 605 " --> pdb=" O GLN D 601 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 638 removed outlier: 3.604A pdb=" N ARG D 618 " --> pdb=" O ASP D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 657 Processing helix chain 'D' and resid 658 through 665 Processing helix chain 'D' and resid 672 through 689 removed outlier: 3.755A pdb=" N MET D 676 " --> pdb=" O GLY D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 713 removed outlier: 3.802A pdb=" N ASP D 701 " --> pdb=" O ASP D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 721 Processing helix chain 'D' and resid 722 through 741 removed outlier: 3.523A pdb=" N LYS D 726 " --> pdb=" O ARG D 722 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 761 Processing helix chain 'D' and resid 768 through 781 removed outlier: 3.651A pdb=" N ARG D 772 " --> pdb=" O GLU D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 803 Processing helix chain 'D' and resid 811 through 830 removed outlier: 3.667A pdb=" N ARG D 815 " --> pdb=" O PHE D 811 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 854 Processing helix chain 'D' and resid 868 through 889 removed outlier: 3.648A pdb=" N ALA D 874 " --> pdb=" O TRP D 870 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 888 " --> pdb=" O LEU D 884 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 889 " --> pdb=" O LEU D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 890 through 894 Processing helix chain 'D' and resid 895 through 909 Processing helix chain 'D' and resid 910 through 912 No H-bonds generated for 'chain 'D' and resid 910 through 912' Processing helix chain 'D' and resid 914 through 930 Processing helix chain 'D' and resid 941 through 949 removed outlier: 3.929A pdb=" N LYS D 947 " --> pdb=" O GLY D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 957 removed outlier: 4.073A pdb=" N VAL D 954 " --> pdb=" O ARG D 951 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ALA D 955 " --> pdb=" O SER D 952 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER D 956 " --> pdb=" O ASP D 953 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL D 957 " --> pdb=" O VAL D 954 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 970 Proline residue: D 967 - end of helix Processing helix chain 'D' and resid 971 through 975 Processing helix chain 'D' and resid 976 through 979 removed outlier: 3.562A pdb=" N ARG D 979 " --> pdb=" O PRO D 976 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 976 through 979' Processing helix chain 'D' and resid 980 through 991 removed outlier: 3.647A pdb=" N VAL D 988 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER D 989 " --> pdb=" O GLY D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1009 removed outlier: 3.600A pdb=" N ILE D 998 " --> pdb=" O THR D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1010 through 1012 No H-bonds generated for 'chain 'D' and resid 1010 through 1012' Processing helix chain 'D' and resid 1015 through 1033 removed outlier: 3.673A pdb=" N ASN D1033 " --> pdb=" O ILE D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1052 Processing helix chain 'D' and resid 1065 through 1077 removed outlier: 3.737A pdb=" N LEU D1071 " --> pdb=" O PHE D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1098 removed outlier: 3.644A pdb=" N GLU D1097 " --> pdb=" O ALA D1093 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET D1098 " --> pdb=" O VAL D1094 " (cutoff:3.500A) Processing helix chain 'D' and resid 1099 through 1102 Proline residue: D1102 - end of helix No H-bonds generated for 'chain 'D' and resid 1099 through 1102' Processing helix chain 'D' and resid 1103 through 1116 removed outlier: 3.656A pdb=" N ARG D1107 " --> pdb=" O GLY D1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 1117 through 1119 No H-bonds generated for 'chain 'D' and resid 1117 through 1119' Processing helix chain 'D' and resid 1121 through 1139 removed outlier: 3.725A pdb=" N ARG D1125 " --> pdb=" O PHE D1121 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA D1129 " --> pdb=" O ARG D1125 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU D1137 " --> pdb=" O TYR D1133 " (cutoff:3.500A) Processing helix chain 'D' and resid 1144 through 1157 removed outlier: 3.622A pdb=" N ASP D1149 " --> pdb=" O ALA D1145 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU D1150 " --> pdb=" O ASP D1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1179 removed outlier: 3.512A pdb=" N VAL D1167 " --> pdb=" O GLU D1163 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU D1169 " --> pdb=" O ALA D1165 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 14 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.786A pdb=" N THR G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 110 removed outlier: 3.835A pdb=" N CYS G 102 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 143 Processing helix chain 'G' and resid 165 through 178 removed outlier: 3.546A pdb=" N ILE G 169 " --> pdb=" O LEU G 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 25 removed outlier: 3.979A pdb=" N ALA b 18 " --> pdb=" O ASN b 14 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS b 19 " --> pdb=" O GLN b 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 43 through 50 removed outlier: 4.015A pdb=" N ARG b 46 " --> pdb=" O GLN b 43 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE b 47 " --> pdb=" O LEU b 44 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N SER b 48 " --> pdb=" O ASP b 45 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL b 49 " --> pdb=" O ARG b 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 70 through 77 removed outlier: 3.527A pdb=" N ARG b 77 " --> pdb=" O MET b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 100 through 106 removed outlier: 3.564A pdb=" N GLY b 104 " --> pdb=" O ASN b 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 108 through 127 removed outlier: 4.073A pdb=" N LEU b 112 " --> pdb=" O GLU b 108 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL b 113 " --> pdb=" O GLY b 109 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASP b 114 " --> pdb=" O ALA b 110 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER b 115 " --> pdb=" O GLU b 111 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER b 126 " --> pdb=" O LYS b 122 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS b 127 " --> pdb=" O GLU b 123 " (cutoff:3.500A) Processing helix chain 'b' and resid 142 through 159 removed outlier: 3.705A pdb=" N GLY b 146 " --> pdb=" O GLY b 142 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY b 148 " --> pdb=" O GLY b 144 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR b 149 " --> pdb=" O SER b 145 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU b 151 " --> pdb=" O MET b 147 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE b 152 " --> pdb=" O GLY b 148 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 193 removed outlier: 3.567A pdb=" N ASN b 184 " --> pdb=" O VAL b 180 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN b 191 " --> pdb=" O LEU b 187 " (cutoff:3.500A) Processing helix chain 'b' and resid 204 through 213 Processing helix chain 'b' and resid 221 through 237 removed outlier: 3.664A pdb=" N LEU b 225 " --> pdb=" O THR b 221 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU b 228 " --> pdb=" O ASP b 224 " (cutoff:3.500A) Processing helix chain 'b' and resid 249 through 258 removed outlier: 3.532A pdb=" N VAL b 258 " --> pdb=" O ALA b 254 " (cutoff:3.500A) Processing helix chain 'b' and resid 285 through 293 Processing helix chain 'b' and resid 295 through 299 Processing helix chain 'b' and resid 322 through 334 removed outlier: 3.562A pdb=" N VAL b 326 " --> pdb=" O SER b 322 " (cutoff:3.500A) Processing helix chain 'b' and resid 371 through 373 No H-bonds generated for 'chain 'b' and resid 371 through 373' Processing helix chain 'b' and resid 374 through 390 removed outlier: 3.569A pdb=" N PHE b 378 " --> pdb=" O ILE b 374 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET b 388 " --> pdb=" O GLN b 384 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 400 removed outlier: 3.562A pdb=" N THR b 399 " --> pdb=" O LEU b 395 " (cutoff:3.500A) Processing helix chain 'b' and resid 404 through 425 removed outlier: 3.703A pdb=" N PHE b 408 " --> pdb=" O ASP b 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.768A pdb=" N CYS G 153 " --> pdb=" O LEU G 120 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE G 122 " --> pdb=" O CYS G 153 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN G 155 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU G 87 " --> pdb=" O LEU G 121 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE G 123 " --> pdb=" O LEU G 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.768A pdb=" N CYS G 153 " --> pdb=" O LEU G 120 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE G 122 " --> pdb=" O CYS G 153 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN G 155 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL G 91 " --> pdb=" O ASN G 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 452 through 454 removed outlier: 3.622A pdb=" N CYS D 457 " --> pdb=" O ARG D 454 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 861 through 862 removed outlier: 3.602A pdb=" N ASP D 862 " --> pdb=" O GLY D 865 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY D 865 " --> pdb=" O ASP D 862 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 19 through 21 removed outlier: 6.592A pdb=" N LEU G 19 " --> pdb=" O TRP G 65 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL G 67 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N MET G 21 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP G 66 " --> pdb=" O ASN G 51 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN G 51 " --> pdb=" O ASP G 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 90 through 92 removed outlier: 8.370A pdb=" N VAL b 91 " --> pdb=" O ALA b 63 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU b 65 " --> pdb=" O VAL b 91 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU b 3 " --> pdb=" O LEU b 130 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY b 132 " --> pdb=" O GLU b 3 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL b 5 " --> pdb=" O GLY b 132 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLN b 131 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N ASN b 165 " --> pdb=" O GLN b 131 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE b 133 " --> pdb=" O ASN b 165 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N PHE b 167 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU b 135 " --> pdb=" O PHE b 167 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU b 198 " --> pdb=" O MET b 164 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR b 199 " --> pdb=" O PHE b 266 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY b 369 " --> pdb=" O MET b 267 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE b 367 " --> pdb=" O GLY b 269 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA b 271 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL b 365 " --> pdb=" O ALA b 271 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA b 364 " --> pdb=" O ARG b 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 169 through 170 675 hydrogen bonds defined for protein. 1983 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2265 1.31 - 1.43: 3485 1.43 - 1.56: 7897 1.56 - 1.69: 5 1.69 - 1.81: 132 Bond restraints: 13784 Sorted by residual: bond pdb=" C VAL D 99 " pdb=" N HIS D 100 " ideal model delta sigma weight residual 1.335 1.274 0.061 1.34e-02 5.57e+03 2.06e+01 bond pdb=" N GLU b 69 " pdb=" CA GLU b 69 " ideal model delta sigma weight residual 1.453 1.491 -0.038 8.30e-03 1.45e+04 2.04e+01 bond pdb=" C PRO b 61 " pdb=" O PRO b 61 " ideal model delta sigma weight residual 1.233 1.180 0.053 1.24e-02 6.50e+03 1.85e+01 bond pdb=" N VAL b 60 " pdb=" CA VAL b 60 " ideal model delta sigma weight residual 1.456 1.493 -0.037 8.70e-03 1.32e+04 1.81e+01 bond pdb=" N VAL D 939 " pdb=" CA VAL D 939 " ideal model delta sigma weight residual 1.460 1.490 -0.030 7.60e-03 1.73e+04 1.58e+01 ... (remaining 13779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.93: 18620 4.93 - 9.87: 60 9.87 - 14.80: 1 14.80 - 19.73: 1 19.73 - 24.66: 1 Bond angle restraints: 18683 Sorted by residual: angle pdb=" PB GTP b1500 " pdb=" O3B GTP b1500 " pdb=" PG GTP b1500 " ideal model delta sigma weight residual 120.50 145.16 -24.66 3.00e+00 1.11e-01 6.76e+01 angle pdb=" PA GTP b1500 " pdb=" O3A GTP b1500 " pdb=" PB GTP b1500 " ideal model delta sigma weight residual 120.50 139.12 -18.62 3.00e+00 1.11e-01 3.85e+01 angle pdb=" N ARG D1038 " pdb=" CA ARG D1038 " pdb=" C ARG D1038 " ideal model delta sigma weight residual 113.28 107.27 6.01 1.22e+00 6.72e-01 2.43e+01 angle pdb=" N LYS D 571 " pdb=" CA LYS D 571 " pdb=" C LYS D 571 " ideal model delta sigma weight residual 113.28 119.14 -5.86 1.22e+00 6.72e-01 2.30e+01 angle pdb=" CA GLY b 141 " pdb=" C GLY b 141 " pdb=" O GLY b 141 " ideal model delta sigma weight residual 122.28 117.54 4.74 1.00e+00 1.00e+00 2.25e+01 ... (remaining 18678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.96: 8244 32.96 - 65.91: 55 65.91 - 98.87: 2 98.87 - 131.83: 1 131.83 - 164.78: 3 Dihedral angle restraints: 8305 sinusoidal: 3339 harmonic: 4966 Sorted by residual: dihedral pdb=" C5' GTP b1500 " pdb=" O5' GTP b1500 " pdb=" PA GTP b1500 " pdb=" O3A GTP b1500 " ideal model delta sinusoidal sigma weight residual 69.27 -125.95 -164.78 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C8 GTP b1500 " pdb=" C1' GTP b1500 " pdb=" N9 GTP b1500 " pdb=" O4' GTP b1500 " ideal model delta sinusoidal sigma weight residual 104.59 -43.39 147.98 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O5' GTP b1500 " pdb=" O3A GTP b1500 " pdb=" PA GTP b1500 " pdb=" PB GTP b1500 " ideal model delta sinusoidal sigma weight residual 274.12 130.51 143.61 1 2.00e+01 2.50e-03 4.33e+01 ... (remaining 8302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1469 0.045 - 0.089: 337 0.089 - 0.134: 212 0.134 - 0.179: 87 0.179 - 0.224: 20 Chirality restraints: 2125 Sorted by residual: chirality pdb=" CA ILE D1058 " pdb=" N ILE D1058 " pdb=" C ILE D1058 " pdb=" CB ILE D1058 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE b 64 " pdb=" N ILE b 64 " pdb=" C ILE b 64 " pdb=" CB ILE b 64 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ILE b 202 " pdb=" N ILE b 202 " pdb=" C ILE b 202 " pdb=" CB ILE b 202 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 2122 not shown) Planarity restraints: 2407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D1046 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C THR D1046 " -0.049 2.00e-02 2.50e+03 pdb=" O THR D1046 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU D1047 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 363 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.00e+00 pdb=" C GLU D 363 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU D 363 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN D 364 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 960 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C SER D 960 " -0.040 2.00e-02 2.50e+03 pdb=" O SER D 960 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA D 961 " 0.013 2.00e-02 2.50e+03 ... (remaining 2404 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 5108 2.90 - 3.40: 13966 3.40 - 3.90: 21693 3.90 - 4.40: 24630 4.40 - 4.90: 41737 Nonbonded interactions: 107134 Sorted by model distance: nonbonded pdb=" OD1 ASN G 79 " pdb=" O GLU G 82 " model vdw 2.405 3.040 nonbonded pdb=" OE1 GLN D 290 " pdb=" OD2 ASP b 88 " model vdw 2.472 3.040 nonbonded pdb=" OG1 THR D1052 " pdb=" OE2 GLU D1097 " model vdw 2.476 3.040 nonbonded pdb=" OD1 ASN b 52 " pdb=" NH1 ARG b 62 " model vdw 2.487 3.120 nonbonded pdb=" O LEU D 306 " pdb=" NH1 ARG D 390 " model vdw 2.493 3.120 ... (remaining 107129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.430 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.030 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 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 0.065 13784 Z= 0.554 Angle : 1.028 24.663 18683 Z= 0.734 Chirality : 0.059 0.224 2125 Planarity : 0.003 0.028 2407 Dihedral : 8.921 164.782 5093 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.07 % Allowed : 2.94 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -2.25 (0.20), residues: 1705 helix: -0.63 (0.16), residues: 990 sheet: -3.39 (0.46), residues: 82 loop : -2.54 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 62 TYR 0.014 0.001 TYR D 859 PHE 0.009 0.001 PHE D1067 TRP 0.026 0.001 TRP G 152 HIS 0.006 0.001 HIS G 150 Details of bonding type rmsd covalent geometry : bond 0.00734 (13784) covalent geometry : angle 1.02813 (18683) hydrogen bonds : bond 0.22302 ( 672) hydrogen bonds : angle 6.59542 ( 1983) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 476 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: D 166 ASP cc_start: 0.6820 (t0) cc_final: 0.6492 (t0) REVERT: D 570 MET cc_start: 0.7580 (mmt) cc_final: 0.7364 (mmt) REVERT: D 1131 GLN cc_start: 0.7190 (mm-40) cc_final: 0.6966 (mm-40) REVERT: b 27 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7801 (mt-10) REVERT: b 67 ASP cc_start: 0.8513 (t0) cc_final: 0.8088 (t0) outliers start: 1 outliers final: 1 residues processed: 477 average time/residue: 0.5723 time to fit residues: 296.4453 Evaluate side-chains 381 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 380 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1104 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0000 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.3980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 242 GLN D 255 GLN D 417 HIS D 515 GLN D 619 HIS D 653 GLN D 657 GLN D 660 GLN D 759 GLN D 766 ASN D1081 ASN D1100 GLN D1112 GLN G 37 ASN G 70 GLN ** b 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN b 99 ASN b 165 ASN b 256 ASN b 279 GLN b 291 GLN b 307 HIS b 329 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.135127 restraints weight = 17039.982| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.55 r_work: 0.3633 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13784 Z= 0.144 Angle : 0.570 8.053 18683 Z= 0.292 Chirality : 0.040 0.222 2125 Planarity : 0.005 0.052 2407 Dihedral : 7.549 178.695 1879 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.21 % Allowed : 12.83 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.33 (0.21), residues: 1705 helix: 0.86 (0.17), residues: 998 sheet: -1.79 (0.47), residues: 96 loop : -1.74 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 665 TYR 0.015 0.002 TYR D 107 PHE 0.025 0.002 PHE D 308 TRP 0.015 0.002 TRP G 152 HIS 0.006 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00304 (13784) covalent geometry : angle 0.57005 (18683) hydrogen bonds : bond 0.04872 ( 672) hydrogen bonds : angle 3.48066 ( 1983) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 384 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: D 152 MET cc_start: 0.8780 (mmm) cc_final: 0.8545 (mmm) REVERT: D 166 ASP cc_start: 0.7125 (t0) cc_final: 0.6770 (t0) REVERT: D 183 MET cc_start: 0.6422 (mmm) cc_final: 0.6201 (mmm) REVERT: D 302 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8317 (pt0) REVERT: D 391 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7818 (pt) REVERT: D 944 GLU cc_start: 0.7365 (mp0) cc_final: 0.7149 (mp0) REVERT: D 1078 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7493 (tp30) REVERT: D 1172 ASN cc_start: 0.7423 (OUTLIER) cc_final: 0.7048 (m110) REVERT: G 21 MET cc_start: 0.7749 (ttp) cc_final: 0.7512 (ttp) REVERT: b 205 GLU cc_start: 0.7729 (tt0) cc_final: 0.7480 (tt0) REVERT: b 312 THR cc_start: 0.8256 (m) cc_final: 0.7906 (p) REVERT: b 335 ASN cc_start: 0.7372 (t0) cc_final: 0.7139 (t0) outliers start: 47 outliers final: 17 residues processed: 403 average time/residue: 0.5715 time to fit residues: 249.3502 Evaluate side-chains 374 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 353 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 406 CYS Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 903 MET Chi-restraints excluded: chain D residue 915 ASP Chi-restraints excluded: chain D residue 928 LEU Chi-restraints excluded: chain D residue 960 SER Chi-restraints excluded: chain D residue 1078 GLU Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1172 ASN Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 353 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 100 optimal weight: 0.6980 chunk 116 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 66 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 94 optimal weight: 0.0980 chunk 112 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 HIS D 235 ASN D 759 GLN D 793 GLN D1036 ASN D1108 GLN G 63 ASN b 14 ASN b 99 ASN b 131 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.144871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.127187 restraints weight = 16745.747| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.55 r_work: 0.3517 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13784 Z= 0.119 Angle : 0.499 9.082 18683 Z= 0.253 Chirality : 0.039 0.214 2125 Planarity : 0.004 0.036 2407 Dihedral : 7.455 179.304 1877 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.80 % Allowed : 15.84 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.41 (0.21), residues: 1705 helix: 1.39 (0.17), residues: 1013 sheet: -1.08 (0.48), residues: 107 loop : -1.45 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 665 TYR 0.017 0.001 TYR b 159 PHE 0.017 0.002 PHE D1006 TRP 0.013 0.001 TRP G 152 HIS 0.007 0.001 HIS D 619 Details of bonding type rmsd covalent geometry : bond 0.00251 (13784) covalent geometry : angle 0.49946 (18683) hydrogen bonds : bond 0.04758 ( 672) hydrogen bonds : angle 3.17435 ( 1983) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 353 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: D 52 GLU cc_start: 0.7138 (mp0) cc_final: 0.6707 (mp0) REVERT: D 183 MET cc_start: 0.6436 (mmm) cc_final: 0.6201 (mmm) REVERT: D 390 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.8178 (mmt90) REVERT: D 391 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7771 (pt) REVERT: D 570 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7237 (mpt) REVERT: D 643 VAL cc_start: 0.7768 (t) cc_final: 0.7550 (p) REVERT: D 944 GLU cc_start: 0.7339 (mp0) cc_final: 0.7106 (mp0) REVERT: D 1078 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7446 (tp30) REVERT: D 1172 ASN cc_start: 0.7459 (OUTLIER) cc_final: 0.7091 (m110) REVERT: b 415 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8335 (ttp) outliers start: 41 outliers final: 14 residues processed: 370 average time/residue: 0.6285 time to fit residues: 251.4054 Evaluate side-chains 357 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 338 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 406 CYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 903 MET Chi-restraints excluded: chain D residue 1078 GLU Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1172 ASN Chi-restraints excluded: chain G residue 15 ARG Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 415 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.0270 chunk 76 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 107 optimal weight: 0.0980 chunk 91 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 235 ASN D 417 HIS D 589 ASN D 759 GLN D 793 GLN D1108 GLN G 63 ASN G 155 GLN b 52 ASN b 131 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.139397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.121666 restraints weight = 16503.267| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.52 r_work: 0.3444 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13784 Z= 0.119 Angle : 0.505 9.852 18683 Z= 0.257 Chirality : 0.039 0.151 2125 Planarity : 0.004 0.054 2407 Dihedral : 7.570 178.719 1877 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.94 % Allowed : 16.59 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.74 (0.21), residues: 1705 helix: 1.60 (0.17), residues: 1019 sheet: -0.87 (0.47), residues: 113 loop : -1.26 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 665 TYR 0.015 0.001 TYR D 668 PHE 0.014 0.002 PHE D 775 TRP 0.012 0.001 TRP D 575 HIS 0.006 0.001 HIS D 574 Details of bonding type rmsd covalent geometry : bond 0.00256 (13784) covalent geometry : angle 0.50493 (18683) hydrogen bonds : bond 0.04964 ( 672) hydrogen bonds : angle 3.14739 ( 1983) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 344 time to evaluate : 0.491 Fit side-chains REVERT: D 52 GLU cc_start: 0.7280 (mp0) cc_final: 0.6833 (mp0) REVERT: D 183 MET cc_start: 0.6565 (mmm) cc_final: 0.6336 (mmm) REVERT: D 391 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7809 (pt) REVERT: D 558 GLU cc_start: 0.7487 (pt0) cc_final: 0.7277 (pm20) REVERT: D 570 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7181 (mpt) REVERT: D 944 GLU cc_start: 0.7401 (mp0) cc_final: 0.6856 (mp0) REVERT: D 1172 ASN cc_start: 0.7469 (OUTLIER) cc_final: 0.7124 (m110) REVERT: b 35 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8291 (m) REVERT: b 415 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8432 (ttp) outliers start: 43 outliers final: 18 residues processed: 360 average time/residue: 0.6073 time to fit residues: 236.6574 Evaluate side-chains 361 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 338 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 406 CYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 903 MET Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1172 ASN Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 339 SER Chi-restraints excluded: chain b residue 414 ASN Chi-restraints excluded: chain b residue 415 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 76 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 156 optimal weight: 0.0980 chunk 52 optimal weight: 0.0670 chunk 120 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 302 GLN D 364 GLN D 759 GLN D 793 GLN D1000 HIS D1108 GLN G 63 ASN b 99 ASN b 131 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.138923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120847 restraints weight = 16509.371| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.62 r_work: 0.3424 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13784 Z= 0.112 Angle : 0.482 10.223 18683 Z= 0.246 Chirality : 0.039 0.213 2125 Planarity : 0.004 0.041 2407 Dihedral : 7.585 178.566 1877 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.07 % Allowed : 16.79 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.21), residues: 1705 helix: 1.79 (0.17), residues: 1013 sheet: -0.61 (0.47), residues: 112 loop : -1.15 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 53 TYR 0.012 0.001 TYR D 668 PHE 0.017 0.001 PHE D1006 TRP 0.011 0.001 TRP D 231 HIS 0.006 0.001 HIS D 619 Details of bonding type rmsd covalent geometry : bond 0.00243 (13784) covalent geometry : angle 0.48155 (18683) hydrogen bonds : bond 0.04737 ( 672) hydrogen bonds : angle 3.13447 ( 1983) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 338 time to evaluate : 0.335 Fit side-chains REVERT: D 52 GLU cc_start: 0.7279 (mp0) cc_final: 0.6833 (mp0) REVERT: D 183 MET cc_start: 0.6640 (mmm) cc_final: 0.6413 (mmm) REVERT: D 391 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7783 (pt) REVERT: D 558 GLU cc_start: 0.7462 (pt0) cc_final: 0.7237 (pm20) REVERT: D 570 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7154 (mpt) REVERT: D 880 MET cc_start: 0.8410 (ttm) cc_final: 0.8190 (ttp) REVERT: D 944 GLU cc_start: 0.7436 (mp0) cc_final: 0.7222 (mp0) REVERT: D 1172 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.7134 (m110) REVERT: b 415 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8459 (ttp) outliers start: 45 outliers final: 28 residues processed: 355 average time/residue: 0.5789 time to fit residues: 222.6991 Evaluate side-chains 359 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 327 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 406 CYS Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 429 ARG Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 793 GLN Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 903 MET Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1172 ASN Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 339 SER Chi-restraints excluded: chain b residue 388 MET Chi-restraints excluded: chain b residue 414 ASN Chi-restraints excluded: chain b residue 415 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 7 optimal weight: 0.0010 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 0.0070 chunk 10 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 154 optimal weight: 0.4980 chunk 168 optimal weight: 0.0980 overall best weight: 0.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN D 759 GLN D1108 GLN G 63 ASN b 131 GLN b 426 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.139775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121336 restraints weight = 16455.280| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.61 r_work: 0.3436 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13784 Z= 0.094 Angle : 0.447 9.075 18683 Z= 0.228 Chirality : 0.037 0.178 2125 Planarity : 0.004 0.040 2407 Dihedral : 7.531 179.264 1877 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.46 % Allowed : 17.75 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.25 (0.21), residues: 1705 helix: 1.98 (0.17), residues: 1015 sheet: -0.35 (0.48), residues: 104 loop : -1.03 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 53 TYR 0.012 0.001 TYR b 159 PHE 0.013 0.001 PHE D1006 TRP 0.013 0.001 TRP D 231 HIS 0.004 0.001 HIS D 619 Details of bonding type rmsd covalent geometry : bond 0.00196 (13784) covalent geometry : angle 0.44659 (18683) hydrogen bonds : bond 0.04078 ( 672) hydrogen bonds : angle 3.03823 ( 1983) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 330 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: D 52 GLU cc_start: 0.7297 (mp0) cc_final: 0.6835 (mp0) REVERT: D 183 MET cc_start: 0.6692 (mmm) cc_final: 0.6455 (mmm) REVERT: D 391 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7765 (pt) REVERT: D 558 GLU cc_start: 0.7428 (pt0) cc_final: 0.7198 (pm20) REVERT: D 570 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7158 (mpt) REVERT: D 880 MET cc_start: 0.8456 (ttm) cc_final: 0.8248 (ttp) REVERT: D 944 GLU cc_start: 0.7447 (mp0) cc_final: 0.7215 (mp0) REVERT: D 1133 TYR cc_start: 0.7303 (t80) cc_final: 0.6870 (t80) REVERT: D 1172 ASN cc_start: 0.7486 (OUTLIER) cc_final: 0.7147 (m110) REVERT: G 99 MET cc_start: 0.6807 (mmt) cc_final: 0.6589 (mmt) REVERT: b 35 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8284 (m) REVERT: b 328 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7075 (mt-10) REVERT: b 415 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8474 (ttp) REVERT: b 424 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7855 (tt0) outliers start: 36 outliers final: 19 residues processed: 347 average time/residue: 0.5888 time to fit residues: 220.8968 Evaluate side-chains 346 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 321 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 406 CYS Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 429 ARG Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 903 MET Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1172 ASN Chi-restraints excluded: chain G residue 10 MET Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 339 SER Chi-restraints excluded: chain b residue 414 ASN Chi-restraints excluded: chain b residue 415 MET Chi-restraints excluded: chain b residue 424 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 73 optimal weight: 0.0570 chunk 12 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 137 optimal weight: 0.0370 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 364 GLN D 793 GLN D1081 ASN D1108 GLN G 63 ASN b 131 GLN b 426 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.134899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.116135 restraints weight = 16274.936| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.62 r_work: 0.3364 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13784 Z= 0.140 Angle : 0.519 10.324 18683 Z= 0.267 Chirality : 0.040 0.166 2125 Planarity : 0.004 0.043 2407 Dihedral : 7.711 178.355 1877 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.14 % Allowed : 17.54 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.11 (0.21), residues: 1705 helix: 1.81 (0.17), residues: 1023 sheet: -0.24 (0.47), residues: 103 loop : -1.05 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 309 TYR 0.014 0.002 TYR D 668 PHE 0.018 0.002 PHE D 775 TRP 0.011 0.001 TRP D 231 HIS 0.008 0.001 HIS D 619 Details of bonding type rmsd covalent geometry : bond 0.00317 (13784) covalent geometry : angle 0.51923 (18683) hydrogen bonds : bond 0.05754 ( 672) hydrogen bonds : angle 3.26239 ( 1983) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 333 time to evaluate : 0.539 Fit side-chains REVERT: D 52 GLU cc_start: 0.7335 (mp0) cc_final: 0.6878 (mp0) REVERT: D 183 MET cc_start: 0.6808 (mmm) cc_final: 0.6557 (mmm) REVERT: D 391 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7804 (pt) REVERT: D 570 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7197 (mpt) REVERT: D 661 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.7075 (mt0) REVERT: D 880 MET cc_start: 0.8497 (ttm) cc_final: 0.8257 (ttp) REVERT: D 912 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7264 (mm-30) REVERT: D 944 GLU cc_start: 0.7479 (mp0) cc_final: 0.6885 (mp0) REVERT: D 1133 TYR cc_start: 0.7342 (t80) cc_final: 0.6909 (t80) REVERT: D 1172 ASN cc_start: 0.7515 (OUTLIER) cc_final: 0.7145 (m110) REVERT: G 85 ASP cc_start: 0.7849 (m-30) cc_final: 0.7581 (m-30) REVERT: b 328 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7023 (mt-10) REVERT: b 415 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8392 (ttp) REVERT: b 424 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7962 (tt0) outliers start: 46 outliers final: 26 residues processed: 354 average time/residue: 0.6017 time to fit residues: 231.1057 Evaluate side-chains 363 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 331 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 406 CYS Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 661 GLN Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 903 MET Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain D residue 1172 ASN Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 339 SER Chi-restraints excluded: chain b residue 388 MET Chi-restraints excluded: chain b residue 414 ASN Chi-restraints excluded: chain b residue 415 MET Chi-restraints excluded: chain b residue 424 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 65 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 793 GLN D1108 GLN G 63 ASN G 97 GLN G 155 GLN b 99 ASN b 131 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.115811 restraints weight = 16339.128| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.56 r_work: 0.3363 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13784 Z= 0.146 Angle : 0.543 12.133 18683 Z= 0.278 Chirality : 0.041 0.168 2125 Planarity : 0.004 0.048 2407 Dihedral : 7.774 178.145 1877 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.80 % Allowed : 17.95 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.02 (0.21), residues: 1705 helix: 1.71 (0.17), residues: 1023 sheet: -0.09 (0.46), residues: 108 loop : -1.06 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 585 TYR 0.017 0.002 TYR D 115 PHE 0.018 0.002 PHE D 775 TRP 0.011 0.002 TRP D 231 HIS 0.008 0.001 HIS D 619 Details of bonding type rmsd covalent geometry : bond 0.00335 (13784) covalent geometry : angle 0.54286 (18683) hydrogen bonds : bond 0.05863 ( 672) hydrogen bonds : angle 3.34662 ( 1983) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 345 time to evaluate : 0.470 Fit side-chains REVERT: D 52 GLU cc_start: 0.7345 (mp0) cc_final: 0.6892 (mp0) REVERT: D 183 MET cc_start: 0.6855 (mmm) cc_final: 0.6626 (mmm) REVERT: D 391 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7799 (pt) REVERT: D 570 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7194 (mpt) REVERT: D 661 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7056 (mt0) REVERT: D 880 MET cc_start: 0.8535 (ttm) cc_final: 0.8295 (ttp) REVERT: D 912 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7217 (mm-30) REVERT: D 944 GLU cc_start: 0.7422 (mp0) cc_final: 0.7147 (mp0) REVERT: D 1133 TYR cc_start: 0.7317 (t80) cc_final: 0.6902 (t80) REVERT: D 1172 ASN cc_start: 0.7549 (OUTLIER) cc_final: 0.7179 (m110) REVERT: G 85 ASP cc_start: 0.7945 (m-30) cc_final: 0.7738 (m-30) REVERT: b 318 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8306 (mtt180) REVERT: b 328 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7023 (mt-10) REVERT: b 415 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8413 (ttp) REVERT: b 424 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7965 (tt0) outliers start: 41 outliers final: 27 residues processed: 363 average time/residue: 0.6090 time to fit residues: 238.8836 Evaluate side-chains 369 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 335 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 406 CYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 661 GLN Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 793 GLN Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 903 MET Chi-restraints excluded: chain D residue 928 LEU Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain D residue 1172 ASN Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 318 ARG Chi-restraints excluded: chain b residue 339 SER Chi-restraints excluded: chain b residue 414 ASN Chi-restraints excluded: chain b residue 415 MET Chi-restraints excluded: chain b residue 424 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 84 optimal weight: 1.9990 chunk 136 optimal weight: 0.4980 chunk 69 optimal weight: 0.3980 chunk 142 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 102 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 HIS D 541 ASN D 640 ASN D 793 GLN D1108 GLN G 63 ASN b 99 ASN b 131 GLN b 426 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.135009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117166 restraints weight = 16367.763| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.54 r_work: 0.3373 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13784 Z= 0.127 Angle : 0.512 11.301 18683 Z= 0.263 Chirality : 0.040 0.156 2125 Planarity : 0.004 0.049 2407 Dihedral : 7.751 178.397 1877 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.46 % Allowed : 18.29 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.10 (0.21), residues: 1705 helix: 1.77 (0.17), residues: 1024 sheet: 0.00 (0.47), residues: 108 loop : -1.05 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 53 TYR 0.020 0.002 TYR D 115 PHE 0.015 0.001 PHE D 775 TRP 0.012 0.001 TRP D 231 HIS 0.007 0.001 HIS D 619 Details of bonding type rmsd covalent geometry : bond 0.00285 (13784) covalent geometry : angle 0.51172 (18683) hydrogen bonds : bond 0.05334 ( 672) hydrogen bonds : angle 3.29656 ( 1983) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 332 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: D 52 GLU cc_start: 0.7369 (mp0) cc_final: 0.6931 (mp0) REVERT: D 166 ASP cc_start: 0.7211 (t0) cc_final: 0.6941 (t70) REVERT: D 183 MET cc_start: 0.6829 (mmm) cc_final: 0.6596 (mmm) REVERT: D 391 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7797 (pt) REVERT: D 570 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.7181 (mpt) REVERT: D 661 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.7052 (mt0) REVERT: D 880 MET cc_start: 0.8534 (ttm) cc_final: 0.8293 (ttp) REVERT: D 912 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7233 (mm-30) REVERT: D 944 GLU cc_start: 0.7408 (mp0) cc_final: 0.6855 (mp0) REVERT: D 1172 ASN cc_start: 0.7546 (OUTLIER) cc_final: 0.7179 (m110) REVERT: G 10 MET cc_start: 0.7864 (mpp) cc_final: 0.7659 (mpt) REVERT: G 85 ASP cc_start: 0.7950 (m-30) cc_final: 0.7722 (m-30) REVERT: b 318 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8269 (mtt180) REVERT: b 328 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6998 (mt-10) REVERT: b 415 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8397 (ttp) REVERT: b 424 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7923 (tt0) outliers start: 36 outliers final: 22 residues processed: 349 average time/residue: 0.6393 time to fit residues: 241.0377 Evaluate side-chains 359 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 330 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 406 CYS Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 661 GLN Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 903 MET Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain D residue 1172 ASN Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 176 SER Chi-restraints excluded: chain b residue 318 ARG Chi-restraints excluded: chain b residue 339 SER Chi-restraints excluded: chain b residue 366 THR Chi-restraints excluded: chain b residue 414 ASN Chi-restraints excluded: chain b residue 415 MET Chi-restraints excluded: chain b residue 424 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 123 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 793 GLN G 63 ASN b 99 ASN b 131 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.134236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.115699 restraints weight = 16293.809| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.62 r_work: 0.3352 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13784 Z= 0.136 Angle : 0.528 11.718 18683 Z= 0.271 Chirality : 0.040 0.165 2125 Planarity : 0.004 0.051 2407 Dihedral : 7.775 178.219 1877 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.32 % Allowed : 18.57 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.21), residues: 1705 helix: 1.74 (0.17), residues: 1024 sheet: 0.02 (0.47), residues: 110 loop : -1.05 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 585 TYR 0.020 0.002 TYR D 115 PHE 0.017 0.002 PHE D 775 TRP 0.011 0.002 TRP D 231 HIS 0.007 0.001 HIS D 619 Details of bonding type rmsd covalent geometry : bond 0.00309 (13784) covalent geometry : angle 0.52846 (18683) hydrogen bonds : bond 0.05682 ( 672) hydrogen bonds : angle 3.32608 ( 1983) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 334 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: D 52 GLU cc_start: 0.7340 (mp0) cc_final: 0.6968 (mp0) REVERT: D 183 MET cc_start: 0.6891 (mmm) cc_final: 0.6638 (mmm) REVERT: D 391 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7802 (pt) REVERT: D 570 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7194 (mpt) REVERT: D 661 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7053 (mt0) REVERT: D 880 MET cc_start: 0.8538 (ttm) cc_final: 0.8300 (ttp) REVERT: D 912 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7256 (mm-30) REVERT: D 944 GLU cc_start: 0.7438 (mp0) cc_final: 0.7176 (mp0) REVERT: D 1172 ASN cc_start: 0.7568 (OUTLIER) cc_final: 0.7210 (m110) REVERT: b 318 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8296 (mtt180) REVERT: b 328 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6989 (mt-10) REVERT: b 415 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8440 (ttp) REVERT: b 424 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7954 (tt0) outliers start: 34 outliers final: 25 residues processed: 351 average time/residue: 0.6764 time to fit residues: 256.1410 Evaluate side-chains 365 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 333 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 406 CYS Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 661 GLN Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 903 MET Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain D residue 1172 ASN Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 176 SER Chi-restraints excluded: chain b residue 293 VAL Chi-restraints excluded: chain b residue 318 ARG Chi-restraints excluded: chain b residue 339 SER Chi-restraints excluded: chain b residue 366 THR Chi-restraints excluded: chain b residue 414 ASN Chi-restraints excluded: chain b residue 415 MET Chi-restraints excluded: chain b residue 424 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 130 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 152 optimal weight: 0.0070 chunk 160 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 793 GLN D1108 GLN G 63 ASN b 99 ASN b 131 GLN b 337 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.134915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116405 restraints weight = 16244.514| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.62 r_work: 0.3358 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13784 Z= 0.129 Angle : 0.516 11.349 18683 Z= 0.264 Chirality : 0.040 0.157 2125 Planarity : 0.004 0.050 2407 Dihedral : 7.764 178.505 1877 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.39 % Allowed : 18.77 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.13 (0.21), residues: 1705 helix: 1.77 (0.17), residues: 1026 sheet: 0.10 (0.47), residues: 110 loop : -1.01 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 585 TYR 0.020 0.002 TYR D 115 PHE 0.015 0.002 PHE D 775 TRP 0.012 0.001 TRP D 231 HIS 0.007 0.001 HIS D 619 Details of bonding type rmsd covalent geometry : bond 0.00290 (13784) covalent geometry : angle 0.51584 (18683) hydrogen bonds : bond 0.05371 ( 672) hydrogen bonds : angle 3.29221 ( 1983) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6036.05 seconds wall clock time: 102 minutes 57.71 seconds (6177.71 seconds total)