Starting phenix.real_space_refine on Fri Feb 6 04:54:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m1m_63576/02_2026/9m1m_63576.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m1m_63576/02_2026/9m1m_63576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m1m_63576/02_2026/9m1m_63576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m1m_63576/02_2026/9m1m_63576.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m1m_63576/02_2026/9m1m_63576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m1m_63576/02_2026/9m1m_63576.map" } resolution = 2.21 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= 0.027 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 8 5.49 5 Mg 3 5.21 5 S 133 5.16 5 C 14242 2.51 5 N 3911 2.21 5 O 4246 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s 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: 22547 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1313 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "D" Number of atoms: 8788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 8788 Classifications: {'peptide': 1122} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 1074} Chain breaks: 1 Chain: "E" Number of atoms: 4084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4084 Classifications: {'peptide': 516} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 489} Chain breaks: 1 Chain: "G" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1467 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "a" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3416 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" 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} 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: 5.18, per 1000 atoms: 0.23 Number of scatterers: 22547 At special positions: 0 Unit cell: (177.483, 127.592, 161.943, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 133 16.00 P 8 15.00 Al 1 13.00 Mg 3 11.99 F 3 9.00 O 4246 8.00 N 3911 7.00 C 14242 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.2 seconds 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5340 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 15 sheets defined 53.6% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'C' and resid 299 through 307 removed outlier: 3.612A pdb=" N SER C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 307 " --> pdb=" O PHE C 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 42 Processing helix chain 'D' and resid 43 through 46 Processing helix chain 'D' and resid 50 through 65 removed outlier: 3.688A pdb=" N GLU D 54 " --> pdb=" O GLY D 50 " (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 77 through 90 removed outlier: 3.586A pdb=" N ILE D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 113 removed outlier: 3.688A pdb=" N VAL D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 125 through 128 Processing helix chain 'D' and resid 129 through 136 removed outlier: 3.530A pdb=" N LEU D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 139 No H-bonds generated for 'chain 'D' and resid 137 through 139' Processing helix chain 'D' and resid 146 through 160 removed outlier: 3.618A pdb=" N ARG D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 172 removed outlier: 3.868A pdb=" N LEU D 170 " --> pdb=" O ASP D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 197 removed outlier: 3.706A pdb=" N SER D 195 " --> pdb=" O GLN D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 removed outlier: 3.619A pdb=" N ALA D 206 " --> pdb=" O LYS D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 224 Processing helix chain 'D' and resid 224 through 239 Processing helix chain 'D' and resid 243 through 263 Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 272 through 284 removed outlier: 3.667A pdb=" N ARG D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 306 removed outlier: 3.571A pdb=" N LEU D 306 " --> pdb=" O GLN D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 366 removed outlier: 3.616A pdb=" N ARG D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 389 removed outlier: 3.561A pdb=" N SER D 379 " --> pdb=" O VAL D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 405 removed outlier: 3.955A pdb=" N ASP D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP D 405 " --> pdb=" O GLY D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 408 No H-bonds generated for 'chain 'D' and resid 406 through 408' Processing helix chain 'D' and resid 412 through 430 removed outlier: 3.683A pdb=" N TRP D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 435 No H-bonds generated for 'chain 'D' and resid 433 through 435' Processing helix chain 'D' and resid 436 through 448 removed outlier: 3.758A pdb=" N ALA D 442 " --> pdb=" O VAL D 438 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 473 Processing helix chain 'D' and resid 483 through 487 removed outlier: 3.685A pdb=" N VAL D 487 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 501 Processing helix chain 'D' and resid 503 through 521 Processing helix chain 'D' and resid 526 through 534 removed outlier: 3.638A pdb=" N THR D 533 " --> pdb=" O ASP D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 548 Processing helix chain 'D' and resid 548 through 555 Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 576 through 591 removed outlier: 3.580A 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: 3.549A pdb=" N ARG D 605 " --> pdb=" O GLN D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 640 removed outlier: 3.561A pdb=" N GLN D 638 " --> pdb=" O LYS D 634 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU D 639 " --> pdb=" O LEU D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 646 Processing helix chain 'D' and resid 648 through 655 Processing helix chain 'D' and resid 657 through 664 Processing helix chain 'D' and resid 671 through 689 removed outlier: 4.381A pdb=" N LEU D 675 " --> pdb=" O LEU D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 713 removed outlier: 4.382A pdb=" N ASP D 701 " --> pdb=" O ASP D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 717 Processing helix chain 'D' and resid 721 through 741 removed outlier: 3.591A pdb=" N MET D 725 " --> pdb=" O SER D 721 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR D 741 " --> pdb=" O CYS D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 764 Processing helix chain 'D' and resid 768 through 780 removed outlier: 3.750A pdb=" N ARG D 772 " --> pdb=" O GLU D 768 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 777 " --> pdb=" O CYS D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 788 removed outlier: 4.047A pdb=" N LYS D 788 " --> pdb=" O PHE D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 803 removed outlier: 3.836A pdb=" N THR D 796 " --> pdb=" O GLN D 792 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL D 801 " --> pdb=" O GLY D 797 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 830 Processing helix chain 'D' and resid 845 through 854 Processing helix chain 'D' and resid 867 through 888 removed outlier: 4.011A pdb=" N VAL D 871 " --> pdb=" O VAL D 867 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 885 " --> pdb=" O ASP D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 889 through 894 removed outlier: 6.410A pdb=" N GLU D 892 " --> pdb=" O SER D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 910 Processing helix chain 'D' and resid 914 through 930 removed outlier: 3.596A pdb=" N ARG D 918 " --> pdb=" O ILE D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 941 through 949 Processing helix chain 'D' and resid 950 through 955 removed outlier: 3.750A pdb=" N ALA D 955 " --> pdb=" O ARG D 951 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 964 Processing helix chain 'D' and resid 965 through 970 Processing helix chain 'D' and resid 971 through 974 Processing helix chain 'D' and resid 975 through 991 removed outlier: 3.962A pdb=" N TYR D 980 " --> pdb=" O PRO D 976 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N HIS D 981 " --> pdb=" O THR D 977 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL D 988 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER D 989 " --> pdb=" O GLY D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1010 Processing helix chain 'D' and resid 1015 through 1033 Processing helix chain 'D' and resid 1036 through 1054 removed outlier: 4.494A pdb=" N VAL D1041 " --> pdb=" O GLU D1037 " (cutoff:3.500A) Proline residue: D1042 - end of helix Processing helix chain 'D' and resid 1065 through 1080 removed outlier: 3.960A pdb=" N LYS D1070 " --> pdb=" O PRO D1066 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA D1073 " --> pdb=" O VAL D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1098 Processing helix chain 'D' and resid 1099 through 1101 No H-bonds generated for 'chain 'D' and resid 1099 through 1101' Processing helix chain 'D' and resid 1103 through 1118 removed outlier: 3.599A pdb=" N ARG D1107 " --> pdb=" O GLY D1103 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS D1118 " --> pdb=" O CYS D1114 " (cutoff:3.500A) Processing helix chain 'D' and resid 1121 through 1139 Processing helix chain 'D' and resid 1144 through 1148 removed outlier: 3.550A pdb=" N VAL D1147 " --> pdb=" O GLY D1144 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU D1148 " --> pdb=" O ALA D1145 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1144 through 1148' Processing helix chain 'D' and resid 1150 through 1158 removed outlier: 3.842A pdb=" N VAL D1154 " --> pdb=" O GLU D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1179 removed outlier: 4.030A pdb=" N GLU D1169 " --> pdb=" O ALA D1165 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN D1170 " --> pdb=" O VAL D1166 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 47 Processing helix chain 'E' and resid 80 through 89 Processing helix chain 'E' and resid 115 through 124 Processing helix chain 'E' and resid 125 through 129 removed outlier: 3.534A pdb=" N LYS E 128 " --> pdb=" O GLN E 125 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 129 " --> pdb=" O LEU E 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 125 through 129' Processing helix chain 'E' and resid 146 through 152 Processing helix chain 'E' and resid 168 through 178 removed outlier: 3.628A pdb=" N ILE E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN E 177 " --> pdb=" O HIS E 173 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 178 " --> pdb=" O ILE E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 225 removed outlier: 3.715A pdb=" N ARG E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 228 No H-bonds generated for 'chain 'E' and resid 226 through 228' Processing helix chain 'E' and resid 266 through 271 Processing helix chain 'E' and resid 272 through 274 No H-bonds generated for 'chain 'E' and resid 272 through 274' Processing helix chain 'E' and resid 322 through 329 removed outlier: 3.552A pdb=" N GLU E 329 " --> pdb=" O PHE E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 350 No H-bonds generated for 'chain 'E' and resid 348 through 350' Processing helix chain 'E' and resid 351 through 362 removed outlier: 3.967A pdb=" N LEU E 357 " --> pdb=" O THR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 396 removed outlier: 5.386A pdb=" N ASN E 391 " --> pdb=" O LYS E 387 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU E 392 " --> pdb=" O ALA E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 415 removed outlier: 3.801A pdb=" N LEU E 412 " --> pdb=" O SER E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 425 Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.569A pdb=" N LEU E 433 " --> pdb=" O ASP E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 443 Processing helix chain 'E' and resid 470 through 483 Processing helix chain 'E' and resid 485 through 489 removed outlier: 3.504A pdb=" N LEU E 489 " --> pdb=" O VAL E 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 15 Processing helix chain 'G' and resid 28 through 38 removed outlier: 3.791A pdb=" N LEU G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN G 37 " --> pdb=" O LEU G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 81 removed outlier: 3.703A pdb=" N PHE G 81 " --> pdb=" O ARG G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 111 removed outlier: 3.868A pdb=" N CYS G 102 " --> pdb=" O ARG G 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN G 103 " --> pdb=" O MET G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 142 Processing helix chain 'G' and resid 164 through 178 removed outlier: 3.617A pdb=" N GLY G 168 " --> pdb=" O ASN G 164 " (cutoff:3.500A) Processing helix chain 'a' and resid 10 through 29 Processing helix chain 'a' and resid 48 through 51 removed outlier: 3.869A pdb=" N THR a 51 " --> pdb=" O SER a 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 48 through 51' Processing helix chain 'a' and resid 71 through 80 removed outlier: 4.194A pdb=" N ILE a 75 " --> pdb=" O GLU a 71 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU a 77 " --> pdb=" O THR a 73 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL a 78 " --> pdb=" O VAL a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 88 through 90 No H-bonds generated for 'chain 'a' and resid 88 through 90' Processing helix chain 'a' and resid 102 through 108 removed outlier: 3.542A pdb=" N GLY a 106 " --> pdb=" O ASN a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 110 through 129 removed outlier: 3.684A pdb=" N ILE a 114 " --> pdb=" O ILE a 110 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP a 116 " --> pdb=" O LYS a 112 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU a 117 " --> pdb=" O GLU a 113 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN a 128 " --> pdb=" O LYS a 124 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N CYS a 129 " --> pdb=" O LEU a 125 " (cutoff:3.500A) Processing helix chain 'a' and resid 147 through 161 removed outlier: 3.882A pdb=" N VAL a 159 " --> pdb=" O GLU a 155 " (cutoff:3.500A) Processing helix chain 'a' and resid 182 through 194 Processing helix chain 'a' and resid 205 through 216 Processing helix chain 'a' and resid 223 through 244 removed outlier: 3.569A pdb=" N LEU a 230 " --> pdb=" O ASN a 226 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER a 241 " --> pdb=" O SER a 237 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU a 242 " --> pdb=" O ILE a 238 " (cutoff:3.500A) Processing helix chain 'a' and resid 252 through 259 removed outlier: 4.043A pdb=" N GLN a 256 " --> pdb=" O LEU a 252 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR a 257 " --> pdb=" O THR a 253 " (cutoff:3.500A) Processing helix chain 'a' and resid 297 through 301 Processing helix chain 'a' and resid 324 through 339 Processing helix chain 'a' and resid 383 through 400 removed outlier: 4.122A pdb=" N ALA a 387 " --> pdb=" O ALA a 383 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP a 388 " --> pdb=" O ILE a 384 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU a 391 " --> pdb=" O ALA a 387 " (cutoff:3.500A) Processing helix chain 'a' and resid 405 through 410 Processing helix chain 'a' and resid 415 through 437 removed outlier: 4.029A pdb=" N SER a 419 " --> pdb=" O GLU a 415 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 29 removed outlier: 3.704A pdb=" N ASP b 26 " --> pdb=" O GLU b 22 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU b 27 " --> pdb=" O VAL b 23 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 49 removed outlier: 3.938A pdb=" N ARG b 46 " --> pdb=" O GLN b 43 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE b 47 " --> pdb=" O LEU b 44 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N SER b 48 " --> pdb=" O ASP b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 55 through 57 No H-bonds generated for 'chain 'b' and resid 55 through 57' Processing helix chain 'b' and resid 70 through 78 Processing helix chain 'b' and resid 86 through 88 No H-bonds generated for 'chain 'b' and resid 86 through 88' Processing helix chain 'b' and resid 100 through 106 Processing helix chain 'b' and resid 107 through 125 removed outlier: 4.628A pdb=" N ASP b 114 " --> pdb=" O ALA b 110 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER b 115 " --> pdb=" O GLU b 111 " (cutoff:3.500A) Processing helix chain 'b' and resid 141 through 159 removed outlier: 3.779A pdb=" N SER b 145 " --> pdb=" O GLY b 141 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 195 removed outlier: 3.615A pdb=" N ASN b 184 " --> pdb=" O VAL b 180 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU b 194 " --> pdb=" O HIS b 190 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 214 Processing helix chain 'b' and resid 222 through 237 removed outlier: 3.676A pdb=" N HIS b 227 " --> pdb=" O GLY b 223 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU b 228 " --> pdb=" O ASP b 224 " (cutoff:3.500A) Processing helix chain 'b' and resid 237 through 242 Processing helix chain 'b' and resid 249 through 258 Processing helix chain 'b' and resid 285 through 294 Processing helix chain 'b' and resid 295 through 299 Processing helix chain 'b' and resid 322 through 334 removed outlier: 3.638A pdb=" N VAL b 326 " --> pdb=" O SER b 322 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN b 334 " --> pdb=" O MET b 330 " (cutoff:3.500A) Processing helix chain 'b' and resid 373 through 387 removed outlier: 4.283A pdb=" N LEU b 377 " --> pdb=" O ALA b 373 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE b 381 " --> pdb=" O LEU b 377 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER b 382 " --> pdb=" O PHE b 378 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN b 384 " --> pdb=" O ARG b 380 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 400 Processing helix chain 'b' and resid 404 through 426 removed outlier: 3.669A pdb=" N PHE b 408 " --> pdb=" O ASP b 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 184 through 187 removed outlier: 6.378A pdb=" N CYS C 184 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N THR C 209 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE C 186 " --> pdb=" O THR C 209 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU C 211 " --> pdb=" O PHE C 186 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 206 " --> pdb=" O ARG C 226 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N THR C 228 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU C 208 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA C 230 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N GLU C 210 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU C 225 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU C 261 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLU C 282 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE C 263 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA C 279 " --> pdb=" O ASP C 319 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 215 through 217 Processing sheet with id=AA3, first strand: chain 'C' and resid 253 through 254 removed outlier: 5.957A pdb=" N LYS C 267 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLN C 288 " --> pdb=" O LYS C 267 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR C 269 " --> pdb=" O GLN C 288 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 452 through 454 removed outlier: 3.757A pdb=" N CYS D 457 " --> pdb=" O ARG D 454 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 13 through 16 removed outlier: 6.652A pdb=" N GLY E 38 " --> pdb=" O ARG E 24 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ALA E 26 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N TRP E 36 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 52 through 53 Processing sheet with id=AA7, first strand: chain 'E' and resid 105 through 106 removed outlier: 3.573A pdb=" N ILE E 106 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE a 351 " --> pdb=" O PRO E 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU E 112 " --> pdb=" O PHE a 351 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL a 353 " --> pdb=" O GLU E 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 157 through 159 removed outlier: 6.613A pdb=" N VAL E 158 " --> pdb=" O ASN E 185 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU E 184 " --> pdb=" O VAL E 210 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU E 209 " --> pdb=" O TYR E 235 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU E 234 " --> pdb=" O ASP E 258 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU E 257 " --> pdb=" O ILE E 283 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU E 312 " --> pdb=" O SER E 338 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 337 " --> pdb=" O THR E 367 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 461 through 466 removed outlier: 3.592A pdb=" N LEU E 461 " --> pdb=" O ILE E 450 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N LEU E 523 " --> pdb=" O THR E 447 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS E 449 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL E 525 " --> pdb=" O LYS E 449 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS E 451 " --> pdb=" O VAL E 525 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER E 492 " --> pdb=" O LEU E 524 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG E 526 " --> pdb=" O LEU E 490 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR E 493 " --> pdb=" O ILE E 503 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE E 503 " --> pdb=" O TYR E 493 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N SER E 495 " --> pdb=" O ARG E 501 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG E 501 " --> pdb=" O SER E 495 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 50 through 57 removed outlier: 7.332A pdb=" N LEU G 17 " --> pdb=" O ASN G 63 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N TRP G 65 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU G 19 " --> pdb=" O TRP G 65 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N VAL G 67 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N MET G 21 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU G 87 " --> pdb=" O LEU G 121 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE G 123 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP G 89 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN G 125 " --> pdb=" O TRP G 89 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL G 91 " --> pdb=" O ASN G 125 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLN G 155 " --> pdb=" O LEU G 120 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE G 122 " --> pdb=" O GLN G 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 92 through 93 removed outlier: 8.392A pdb=" N ILE a 93 " --> pdb=" O ALA a 65 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE a 67 " --> pdb=" O ILE a 93 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLU a 3 " --> pdb=" O GLY a 134 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N LEU a 136 " --> pdb=" O GLU a 3 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE a 5 " --> pdb=" O LEU a 136 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N PHE a 138 " --> pdb=" O ILE a 5 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE a 7 " --> pdb=" O PHE a 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'b' and resid 90 through 91 removed outlier: 6.425A pdb=" N LEU b 65 " --> pdb=" O VAL b 91 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL b 66 " --> pdb=" O HIS b 6 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN b 8 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLU b 3 " --> pdb=" O GLN b 131 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE b 133 " --> pdb=" O GLU b 3 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL b 5 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU b 135 " --> pdb=" O VAL b 5 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE b 7 " --> pdb=" O LEU b 135 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE b 163 " --> pdb=" O GLN b 131 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N MET b 164 " --> pdb=" O GLU b 198 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N TYR b 200 " --> pdb=" O MET b 164 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR b 166 " --> pdb=" O TYR b 200 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR b 199 " --> pdb=" O PHE b 266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 51 through 53 removed outlier: 3.616A pdb=" N VAL b 60 " --> pdb=" O ASN b 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 169 through 170 991 hydrogen bonds defined for protein. 2862 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: 4.83 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3801 1.30 - 1.43: 5728 1.43 - 1.56: 13261 1.56 - 1.69: 13 1.69 - 1.81: 198 Bond restraints: 23001 Sorted by residual: bond pdb=" F1 AF3 G1501 " pdb="AL AF3 G1501 " ideal model delta sigma weight residual 1.637 1.792 -0.155 2.00e-02 2.50e+03 6.03e+01 bond pdb=" F2 AF3 G1501 " pdb="AL AF3 G1501 " ideal model delta sigma weight residual 1.637 1.778 -0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" F3 AF3 G1501 " pdb="AL AF3 G1501 " ideal model delta sigma weight residual 1.637 1.754 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C SER D 492 " pdb=" O SER D 492 " ideal model delta sigma weight residual 1.237 1.178 0.058 1.19e-02 7.06e+03 2.39e+01 bond pdb=" C VAL E 313 " pdb=" O VAL E 313 " ideal model delta sigma weight residual 1.237 1.184 0.053 1.10e-02 8.26e+03 2.30e+01 ... (remaining 22996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.67: 31095 4.67 - 9.33: 96 9.33 - 14.00: 8 14.00 - 18.66: 1 18.66 - 23.33: 1 Bond angle restraints: 31201 Sorted by residual: angle pdb=" PB GTP a1500 " pdb=" O3B GTP a1500 " pdb=" PG GTP a1500 " ideal model delta sigma weight residual 120.50 143.83 -23.33 3.00e+00 1.11e-01 6.05e+01 angle pdb=" PB GTP b1500 " pdb=" O3B GTP b1500 " pdb=" PG GTP b1500 " ideal model delta sigma weight residual 120.50 137.38 -16.88 3.00e+00 1.11e-01 3.17e+01 angle pdb=" N GLU b 405 " pdb=" CA GLU b 405 " pdb=" C GLU b 405 " ideal model delta sigma weight residual 113.01 107.14 5.87 1.20e+00 6.94e-01 2.39e+01 angle pdb=" CA LYS D 265 " pdb=" C LYS D 265 " pdb=" O LYS D 265 " ideal model delta sigma weight residual 121.55 116.46 5.09 1.06e+00 8.90e-01 2.31e+01 angle pdb=" N GLU E 347 " pdb=" CA GLU E 347 " pdb=" C GLU E 347 " ideal model delta sigma weight residual 113.16 107.33 5.83 1.24e+00 6.50e-01 2.21e+01 ... (remaining 31196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.67: 13590 34.67 - 69.34: 251 69.34 - 104.02: 19 104.02 - 138.69: 4 138.69 - 173.36: 5 Dihedral angle restraints: 13869 sinusoidal: 5608 harmonic: 8261 Sorted by residual: dihedral pdb=" C5' GTP a1500 " pdb=" O5' GTP a1500 " pdb=" PA GTP a1500 " pdb=" O3A GTP a1500 " ideal model delta sinusoidal sigma weight residual 69.27 -117.37 -173.36 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O5' GTP a1500 " pdb=" O3A GTP a1500 " pdb=" PA GTP a1500 " pdb=" PB GTP a1500 " ideal model delta sinusoidal sigma weight residual 274.12 108.72 165.41 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C8 GTP a1500 " pdb=" C1' GTP a1500 " pdb=" N9 GTP a1500 " pdb=" O4' GTP a1500 " ideal model delta sinusoidal sigma weight residual 104.59 -56.41 161.00 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 13866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2687 0.058 - 0.116: 619 0.116 - 0.174: 185 0.174 - 0.232: 39 0.232 - 0.290: 1 Chirality restraints: 3531 Sorted by residual: chirality pdb=" CA ASP C 248 " pdb=" N ASP C 248 " pdb=" C ASP C 248 " pdb=" CB ASP C 248 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA ILE D 192 " pdb=" N ILE D 192 " pdb=" C ILE D 192 " pdb=" CB ILE D 192 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL D 298 " pdb=" N VAL D 298 " pdb=" C VAL D 298 " pdb=" CB VAL D 298 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 3528 not shown) Planarity restraints: 4022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 932 " 0.016 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C ASP D 932 " -0.054 2.00e-02 2.50e+03 pdb=" O ASP D 932 " 0.020 2.00e-02 2.50e+03 pdb=" N SER D 933 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 333 " 0.029 2.00e-02 2.50e+03 1.93e-02 9.35e+00 pdb=" CG TRP C 333 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP C 333 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP C 333 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP C 333 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 333 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 333 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 333 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 333 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP C 333 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 162 " -0.014 2.00e-02 2.50e+03 3.05e-02 9.28e+00 pdb=" C LEU D 162 " 0.053 2.00e-02 2.50e+03 pdb=" O LEU D 162 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE D 163 " -0.018 2.00e-02 2.50e+03 ... (remaining 4019 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 7887 2.87 - 3.38: 22409 3.38 - 3.89: 37103 3.89 - 4.39: 43580 4.39 - 4.90: 72386 Nonbonded interactions: 183365 Sorted by model distance: nonbonded pdb=" OG1 THR G 30 " pdb="MG MG G1502 " model vdw 2.365 2.170 nonbonded pdb=" NE2 GLN a 15 " pdb=" O6 GTP a1500 " model vdw 2.384 3.120 nonbonded pdb=" CG2 THR b 399 " pdb=" OE2 GLU b 405 " model vdw 2.389 3.460 nonbonded pdb=" OG SER E 492 " pdb=" O ILE E 503 " model vdw 2.441 3.040 nonbonded pdb=" OH TYR E 493 " pdb=" O TYR E 515 " model vdw 2.444 3.040 ... (remaining 183360 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: 0.000 Normalize map: mean=0, sd=1: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.680 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 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 0.191 23002 Z= 0.530 Angle : 0.961 23.329 31201 Z= 0.669 Chirality : 0.056 0.290 3531 Planarity : 0.003 0.031 4022 Dihedral : 14.122 173.361 8529 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.04 % Allowed : 5.97 % Favored : 93.99 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.46 % 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: -2.41 (0.15), residues: 2838 helix: -1.01 (0.14), residues: 1355 sheet: -2.42 (0.25), residues: 345 loop : -1.90 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 501 TYR 0.032 0.001 TYR E 493 PHE 0.016 0.001 PHE C 289 TRP 0.051 0.001 TRP C 333 HIS 0.004 0.000 HIS b 37 Details of bonding type rmsd covalent geometry : bond 0.00707 (23001) covalent geometry : angle 0.96074 (31201) hydrogen bonds : bond 0.19121 ( 991) hydrogen bonds : angle 6.83453 ( 2862) Misc. bond : bond 0.19077 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 788 time to evaluate : 0.888 Fit side-chains REVERT: C 234 LYS cc_start: 0.7085 (ttmt) cc_final: 0.6857 (tttm) REVERT: C 235 LEU cc_start: 0.6848 (tp) cc_final: 0.6506 (tm) REVERT: D 186 MET cc_start: 0.7326 (ttm) cc_final: 0.7038 (ttm) REVERT: D 363 GLU cc_start: 0.6736 (tm-30) cc_final: 0.6387 (tm-30) REVERT: D 425 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7158 (mm-30) REVERT: D 501 ASP cc_start: 0.7044 (t0) cc_final: 0.6828 (t70) REVERT: D 503 ASP cc_start: 0.6341 (m-30) cc_final: 0.6019 (m-30) REVERT: D 523 THR cc_start: 0.7648 (p) cc_final: 0.7334 (t) REVERT: D 603 PHE cc_start: 0.7153 (t80) cc_final: 0.6906 (t80) REVERT: D 687 LEU cc_start: 0.7254 (mt) cc_final: 0.7007 (mp) REVERT: D 727 ASP cc_start: 0.7722 (m-30) cc_final: 0.7515 (m-30) REVERT: D 743 LYS cc_start: 0.6895 (tttt) cc_final: 0.6559 (tttt) REVERT: D 832 LYS cc_start: 0.8139 (tttt) cc_final: 0.7800 (ttpp) REVERT: D 1010 LYS cc_start: 0.7136 (ttmm) cc_final: 0.6875 (ttpp) REVERT: D 1079 ILE cc_start: 0.7324 (tp) cc_final: 0.7103 (pt) REVERT: D 1084 ASP cc_start: 0.6595 (t0) cc_final: 0.6355 (t0) REVERT: D 1107 ARG cc_start: 0.7086 (mtm-85) cc_final: 0.6676 (mtt90) REVERT: E 1 MET cc_start: 0.1135 (mtt) cc_final: 0.0930 (mtt) REVERT: E 15 GLU cc_start: 0.6120 (tt0) cc_final: 0.5826 (tt0) REVERT: E 40 GLU cc_start: 0.5872 (tt0) cc_final: 0.5603 (tt0) REVERT: E 180 HIS cc_start: 0.6820 (m-70) cc_final: 0.6401 (m170) REVERT: E 190 LYS cc_start: 0.7142 (mttt) cc_final: 0.6895 (ttmm) REVERT: E 207 LYS cc_start: 0.6311 (mttt) cc_final: 0.5719 (mmtm) REVERT: E 235 TYR cc_start: 0.6681 (m-80) cc_final: 0.6417 (m-80) REVERT: E 267 GLU cc_start: 0.6092 (pt0) cc_final: 0.5882 (pt0) REVERT: E 310 LYS cc_start: 0.6897 (mtpp) cc_final: 0.6692 (mtmm) REVERT: E 362 ILE cc_start: 0.5571 (mt) cc_final: 0.5276 (mp) REVERT: E 420 PHE cc_start: 0.6475 (t80) cc_final: 0.6036 (t80) REVERT: E 480 ARG cc_start: 0.6916 (mtp-110) cc_final: 0.6688 (mtp-110) REVERT: G 61 LYS cc_start: 0.7393 (mttt) cc_final: 0.7152 (mttt) REVERT: a 1 MET cc_start: 0.3835 (ppp) cc_final: 0.3050 (ppp) REVERT: a 31 GLN cc_start: 0.7024 (mp10) cc_final: 0.6611 (mp10) REVERT: a 60 LYS cc_start: 0.6960 (ttmm) cc_final: 0.6647 (ttmm) REVERT: a 69 ASP cc_start: 0.6363 (t0) cc_final: 0.5786 (t0) REVERT: a 97 GLU cc_start: 0.5999 (tt0) cc_final: 0.5776 (tt0) REVERT: a 112 LYS cc_start: 0.6585 (ttpp) cc_final: 0.6377 (ttpp) REVERT: a 124 LYS cc_start: 0.6629 (tptt) cc_final: 0.6349 (tptt) REVERT: a 133 GLN cc_start: 0.6626 (mt0) cc_final: 0.6420 (mt0) REVERT: a 155 GLU cc_start: 0.6137 (tp30) cc_final: 0.5866 (tp30) REVERT: a 216 ASN cc_start: 0.7441 (m-40) cc_final: 0.7202 (m-40) REVERT: a 245 ASP cc_start: 0.6655 (t0) cc_final: 0.6377 (t0) REVERT: a 276 ILE cc_start: 0.6901 (mm) cc_final: 0.6699 (mp) REVERT: a 326 LYS cc_start: 0.5990 (tttt) cc_final: 0.5764 (tttt) REVERT: a 386 GLU cc_start: 0.6738 (tt0) cc_final: 0.6480 (tt0) REVERT: b 8 GLN cc_start: 0.7889 (pt0) cc_final: 0.7680 (pt0) REVERT: b 24 ILE cc_start: 0.6148 (pt) cc_final: 0.4917 (mm) REVERT: b 161 ASP cc_start: 0.6466 (p0) cc_final: 0.6120 (p0) REVERT: b 334 GLN cc_start: 0.7157 (mt0) cc_final: 0.6900 (mt0) outliers start: 1 outliers final: 0 residues processed: 789 average time/residue: 0.7021 time to fit residues: 625.4633 Evaluate side-chains 629 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 629 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 ASN C 221 ASN C 223 ASN C 259 GLN C 322 ASN D 90 GLN D 235 ASN D 245 GLN D 255 GLN D 302 GLN D 364 GLN D 505 ASN D 515 GLN D 541 ASN D 574 HIS ** D 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN ** D 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 723 GLN D 759 GLN D 844 ASN D 909 GLN D 941 HIS D1013 GLN D1119 HIS D1170 GLN D1172 ASN E 189 ASN E 212 ASN E 252 GLN E 369 ASN E 405 ASN E 436 GLN E 472 GLN a 15 GLN a 139 HIS a 186 ASN a 233 GLN a 380 ASN b 8 GLN b 11 GLN b 43 GLN b 99 ASN b 134 GLN b 184 ASN b 256 ASN b 384 GLN b 423 GLN b 426 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.165669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.148364 restraints weight = 26219.269| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.36 r_work: 0.3816 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23002 Z= 0.156 Angle : 0.570 10.040 31201 Z= 0.290 Chirality : 0.042 0.185 3531 Planarity : 0.004 0.046 4022 Dihedral : 8.571 176.337 3128 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.05 % Allowed : 12.55 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: -0.64 (0.16), residues: 2838 helix: 0.44 (0.14), residues: 1381 sheet: -1.38 (0.26), residues: 342 loop : -1.10 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 53 TYR 0.016 0.002 TYR C 219 PHE 0.024 0.002 PHE a 141 TRP 0.020 0.002 TRP D 80 HIS 0.013 0.001 HIS D 920 Details of bonding type rmsd covalent geometry : bond 0.00341 (23001) covalent geometry : angle 0.57027 (31201) hydrogen bonds : bond 0.04683 ( 991) hydrogen bonds : angle 3.81115 ( 2862) Misc. bond : bond 0.00143 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 663 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 543 SER cc_start: 0.8426 (OUTLIER) cc_final: 0.8220 (t) REVERT: D 553 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7899 (mm) REVERT: D 630 TYR cc_start: 0.7926 (t80) cc_final: 0.7710 (t80) REVERT: D 1092 ILE cc_start: 0.8263 (mt) cc_final: 0.8040 (mt) REVERT: E 318 GLN cc_start: 0.7556 (mm-40) cc_final: 0.7258 (mm110) REVERT: G 170 ASP cc_start: 0.7533 (m-30) cc_final: 0.7297 (m-30) REVERT: a 1 MET cc_start: 0.4366 (ppp) cc_final: 0.3377 (ppp) REVERT: a 31 GLN cc_start: 0.7846 (mp10) cc_final: 0.7580 (mp10) REVERT: a 109 THR cc_start: 0.8052 (m) cc_final: 0.7155 (p) REVERT: a 243 ARG cc_start: 0.7979 (mtm110) cc_final: 0.7665 (mtm110) REVERT: a 245 ASP cc_start: 0.6972 (t0) cc_final: 0.6747 (t0) REVERT: b 84 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8126 (pp) REVERT: b 414 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8073 (t0) outliers start: 75 outliers final: 19 residues processed: 692 average time/residue: 0.7175 time to fit residues: 558.7658 Evaluate side-chains 626 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 603 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 770 MET Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1014 SER Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 38 SER Chi-restraints excluded: chain a residue 73 THR Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 223 THR Chi-restraints excluded: chain a residue 236 SER Chi-restraints excluded: chain a residue 242 LEU Chi-restraints excluded: chain a residue 361 THR Chi-restraints excluded: chain b residue 69 GLU Chi-restraints excluded: chain b residue 84 ILE Chi-restraints excluded: chain b residue 414 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 42 optimal weight: 0.5980 chunk 276 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 264 optimal weight: 0.4980 chunk 249 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 228 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 ASN ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 HIS D 646 HIS D 674 GLN ** D 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 847 GLN D 941 HIS D 958 ASN D1036 ASN D1049 HIS E 180 HIS E 415 HIS E 472 GLN G 79 ASN G 127 GLN G 136 ASN a 101 ASN a 216 ASN a 258 ASN ** a 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 ASN b 6 HIS b 8 GLN b 11 GLN b 99 ASN b 134 GLN b 256 ASN b 307 HIS b 384 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.156334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.138191 restraints weight = 24965.089| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.36 r_work: 0.3680 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23002 Z= 0.144 Angle : 0.552 10.555 31201 Z= 0.280 Chirality : 0.043 0.206 3531 Planarity : 0.004 0.060 4022 Dihedral : 8.527 175.898 3128 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.68 % Allowed : 15.55 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 0.17 (0.16), residues: 2838 helix: 0.99 (0.14), residues: 1375 sheet: -0.58 (0.27), residues: 346 loop : -0.66 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 585 TYR 0.014 0.002 TYR b 159 PHE 0.023 0.002 PHE a 141 TRP 0.017 0.001 TRP D 80 HIS 0.010 0.001 HIS D 920 Details of bonding type rmsd covalent geometry : bond 0.00329 (23001) covalent geometry : angle 0.55207 (31201) hydrogen bonds : bond 0.04895 ( 991) hydrogen bonds : angle 3.72504 ( 2862) Misc. bond : bond 0.00164 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 640 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: D 553 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7952 (mm) REVERT: D 769 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7134 (tp30) REVERT: D 903 MET cc_start: 0.8813 (mmm) cc_final: 0.8104 (mmm) REVERT: E 170 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6540 (mt-10) REVERT: E 342 ASN cc_start: 0.7911 (m-40) cc_final: 0.7428 (m-40) REVERT: E 425 TYR cc_start: 0.6926 (m-80) cc_final: 0.6690 (m-80) REVERT: a 1 MET cc_start: 0.4367 (ppp) cc_final: 0.3427 (ppp) REVERT: a 3 GLU cc_start: 0.7838 (mp0) cc_final: 0.7272 (mp0) REVERT: a 27 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6363 (tt0) REVERT: a 35 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7823 (mm110) REVERT: a 398 MET cc_start: 0.7399 (tpp) cc_final: 0.6963 (mpp) REVERT: b 414 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8172 (t0) outliers start: 66 outliers final: 21 residues processed: 661 average time/residue: 0.7397 time to fit residues: 549.6412 Evaluate side-chains 632 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 608 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 769 GLU Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1014 SER Chi-restraints excluded: chain D residue 1123 LEU Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 38 SER Chi-restraints excluded: chain a residue 73 THR Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 223 THR Chi-restraints excluded: chain a residue 242 LEU Chi-restraints excluded: chain b residue 69 GLU Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 306 ARG Chi-restraints excluded: chain b residue 414 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 271 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 250 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 115 optimal weight: 0.1980 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 227 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN C 259 GLN ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 HIS ** D 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 941 HIS D1013 GLN D1049 HIS D1112 GLN E 177 GLN E 180 HIS E 269 GLN E 315 ASN E 321 GLN E 472 GLN G 155 GLN a 216 ASN a 300 ASN ** a 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 ASN b 131 GLN b 134 GLN b 256 ASN b 292 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.153041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.134677 restraints weight = 24831.834| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.37 r_work: 0.3629 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23002 Z= 0.149 Angle : 0.545 11.948 31201 Z= 0.278 Chirality : 0.043 0.165 3531 Planarity : 0.004 0.045 4022 Dihedral : 8.567 178.983 3128 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.80 % Allowed : 16.36 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 0.48 (0.16), residues: 2838 helix: 1.17 (0.14), residues: 1377 sheet: -0.13 (0.28), residues: 344 loop : -0.51 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 480 TYR 0.017 0.002 TYR D1139 PHE 0.023 0.002 PHE a 141 TRP 0.018 0.002 TRP D 80 HIS 0.008 0.001 HIS D 920 Details of bonding type rmsd covalent geometry : bond 0.00349 (23001) covalent geometry : angle 0.54502 (31201) hydrogen bonds : bond 0.04932 ( 991) hydrogen bonds : angle 3.73209 ( 2862) Misc. bond : bond 0.00154 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 640 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 192 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: C 320 ASP cc_start: 0.8009 (t0) cc_final: 0.7801 (t0) REVERT: D 553 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7960 (mm) REVERT: D 570 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7420 (mtm) REVERT: D 712 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8022 (mtm110) REVERT: D 892 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: D 1170 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7870 (mm110) REVERT: E 170 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6693 (mt-10) REVERT: E 286 ASP cc_start: 0.7472 (t0) cc_final: 0.7208 (t0) REVERT: E 342 ASN cc_start: 0.8085 (m-40) cc_final: 0.7513 (m-40) REVERT: a 1 MET cc_start: 0.4325 (ppp) cc_final: 0.3237 (ppp) REVERT: a 3 GLU cc_start: 0.7975 (mp0) cc_final: 0.7568 (mp0) REVERT: a 27 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6770 (tt0) REVERT: a 398 MET cc_start: 0.7453 (tpp) cc_final: 0.7065 (mpp) REVERT: b 375 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.5981 (pp30) REVERT: b 414 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8202 (t0) outliers start: 69 outliers final: 31 residues processed: 664 average time/residue: 0.7505 time to fit residues: 556.7408 Evaluate side-chains 659 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 621 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 544 ASN Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 860 THR Chi-restraints excluded: chain D residue 892 GLU Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1123 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 155 GLN Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 38 SER Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 242 LEU Chi-restraints excluded: chain a residue 277 SER Chi-restraints excluded: chain b residue 69 GLU Chi-restraints excluded: chain b residue 128 ASP Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain b residue 306 ARG Chi-restraints excluded: chain b residue 375 GLN Chi-restraints excluded: chain b residue 414 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 46 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 221 ASN C 223 ASN C 314 ASN D 68 GLN ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 HIS ** D 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 890 GLN D 941 HIS D1013 GLN D1049 HIS E 180 HIS E 293 HIS E 472 GLN G 79 ASN a 15 GLN a 35 GLN a 216 ASN ** a 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 ASN b 11 GLN b 134 GLN b 165 ASN b 256 ASN b 292 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.149819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.131440 restraints weight = 24270.610| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.34 r_work: 0.3583 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23002 Z= 0.206 Angle : 0.614 12.865 31201 Z= 0.315 Chirality : 0.046 0.182 3531 Planarity : 0.005 0.048 4022 Dihedral : 8.896 179.624 3128 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.21 % Allowed : 16.61 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 0.45 (0.16), residues: 2838 helix: 1.06 (0.14), residues: 1390 sheet: 0.15 (0.28), residues: 328 loop : -0.52 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 2 TYR 0.022 0.002 TYR E 425 PHE 0.022 0.002 PHE a 141 TRP 0.018 0.002 TRP D 80 HIS 0.008 0.002 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00499 (23001) covalent geometry : angle 0.61396 (31201) hydrogen bonds : bond 0.05983 ( 991) hydrogen bonds : angle 3.95364 ( 2862) Misc. bond : bond 0.00106 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 652 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 192 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7726 (mt0) REVERT: C 320 ASP cc_start: 0.8066 (t0) cc_final: 0.7855 (t0) REVERT: D 553 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8005 (mm) REVERT: D 570 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7305 (mtm) REVERT: D 712 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8012 (mtm110) REVERT: D 769 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6631 (tm-30) REVERT: D 944 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: D 1170 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7886 (mm110) REVERT: E 140 SER cc_start: 0.8345 (p) cc_final: 0.7809 (p) REVERT: E 170 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6864 (mt-10) REVERT: E 179 ARG cc_start: 0.7427 (mmt-90) cc_final: 0.7221 (mmt-90) REVERT: E 286 ASP cc_start: 0.7462 (t0) cc_final: 0.7179 (t0) REVERT: E 501 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7494 (ttm170) REVERT: G 15 ARG cc_start: 0.6564 (ttm110) cc_final: 0.6325 (ttm110) REVERT: a 1 MET cc_start: 0.4424 (ppp) cc_final: 0.3250 (ppp) REVERT: a 3 GLU cc_start: 0.8162 (mp0) cc_final: 0.7929 (mp0) REVERT: a 27 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7036 (tt0) REVERT: a 166 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8096 (mtpt) REVERT: a 398 MET cc_start: 0.7451 (tpp) cc_final: 0.7220 (tpp) REVERT: b 375 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.6060 (pp30) REVERT: b 414 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8055 (t0) outliers start: 79 outliers final: 42 residues processed: 686 average time/residue: 0.7714 time to fit residues: 591.4892 Evaluate side-chains 690 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 638 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 482 GLU Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 544 ASN Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 769 GLU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 860 THR Chi-restraints excluded: chain D residue 944 GLU Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1014 SER Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain D residue 1079 ILE Chi-restraints excluded: chain D residue 1137 LEU Chi-restraints excluded: chain D residue 1158 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 255 LYS Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 501 ARG Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 38 SER Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 166 LYS Chi-restraints excluded: chain a residue 242 LEU Chi-restraints excluded: chain a residue 250 VAL Chi-restraints excluded: chain a residue 277 SER Chi-restraints excluded: chain a residue 361 THR Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 114 ASP Chi-restraints excluded: chain b residue 306 ARG Chi-restraints excluded: chain b residue 375 GLN Chi-restraints excluded: chain b residue 414 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 119 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 259 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 267 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN C 314 ASN D 47 HIS ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 890 GLN D 941 HIS D1013 GLN E 180 HIS E 342 ASN E 472 GLN G 63 ASN G 155 GLN a 31 GLN a 35 GLN a 216 ASN a 256 GLN ** a 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 ASN b 11 GLN b 134 GLN b 165 ASN b 256 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.151038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.132827 restraints weight = 24612.502| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.34 r_work: 0.3605 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23002 Z= 0.138 Angle : 0.531 11.475 31201 Z= 0.273 Chirality : 0.042 0.167 3531 Planarity : 0.005 0.072 4022 Dihedral : 8.607 177.306 3128 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.00 % Allowed : 17.21 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 0.73 (0.16), residues: 2838 helix: 1.31 (0.14), residues: 1390 sheet: 0.30 (0.29), residues: 331 loop : -0.44 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 226 TYR 0.015 0.001 TYR E 425 PHE 0.016 0.002 PHE b 367 TRP 0.019 0.002 TRP D 80 HIS 0.004 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00323 (23001) covalent geometry : angle 0.53062 (31201) hydrogen bonds : bond 0.04848 ( 991) hydrogen bonds : angle 3.79610 ( 2862) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 630 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: C 192 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7684 (mt0) REVERT: D 90 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.7042 (mt0) REVERT: D 553 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7959 (mm) REVERT: D 712 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8007 (mtm110) REVERT: D 769 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6429 (tm-30) REVERT: D 941 HIS cc_start: 0.8468 (m-70) cc_final: 0.8040 (m90) REVERT: D 944 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: D 1009 MET cc_start: 0.8600 (mmp) cc_final: 0.8381 (tpp) REVERT: D 1170 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7946 (mm110) REVERT: E 140 SER cc_start: 0.8364 (p) cc_final: 0.7818 (p) REVERT: E 179 ARG cc_start: 0.7415 (mmt-90) cc_final: 0.7189 (mmt-90) REVERT: E 330 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7958 (mttp) REVERT: E 450 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8125 (mm) REVERT: E 501 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7269 (ttt180) REVERT: a 1 MET cc_start: 0.4391 (ppp) cc_final: 0.3107 (ppp) REVERT: a 3 GLU cc_start: 0.8120 (mp0) cc_final: 0.7783 (mp0) REVERT: a 27 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6948 (tt0) REVERT: a 166 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8065 (mtpt) REVERT: b 46 ARG cc_start: 0.7766 (mtp180) cc_final: 0.7399 (mtp180) REVERT: b 375 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.5849 (pp30) REVERT: b 379 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8142 (mtpp) REVERT: b 414 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.8045 (t0) outliers start: 74 outliers final: 39 residues processed: 662 average time/residue: 0.7817 time to fit residues: 577.8788 Evaluate side-chains 679 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 629 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 482 GLU Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 769 GLU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 860 THR Chi-restraints excluded: chain D residue 944 GLU Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1123 LEU Chi-restraints excluded: chain D residue 1137 LEU Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 501 ARG Chi-restraints excluded: chain E residue 506 GLU Chi-restraints excluded: chain G residue 12 GLN Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 155 GLN Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 38 SER Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 166 LYS Chi-restraints excluded: chain a residue 250 VAL Chi-restraints excluded: chain a residue 277 SER Chi-restraints excluded: chain a residue 384 ILE Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 114 ASP Chi-restraints excluded: chain b residue 306 ARG Chi-restraints excluded: chain b residue 363 MET Chi-restraints excluded: chain b residue 375 GLN Chi-restraints excluded: chain b residue 414 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 233 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 196 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 267 optimal weight: 0.0670 chunk 174 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN C 314 ASN C 322 ASN D 259 GLN D 566 HIS ** D 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 GLN E 180 HIS E 472 GLN G 63 ASN G 79 ASN G 127 GLN a 35 GLN a 101 ASN a 216 ASN a 226 ASN ** a 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 ASN b 11 GLN b 134 GLN b 256 ASN b 396 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.150004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131753 restraints weight = 24426.124| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.34 r_work: 0.3586 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23002 Z= 0.171 Angle : 0.568 11.513 31201 Z= 0.292 Chirality : 0.044 0.172 3531 Planarity : 0.005 0.059 4022 Dihedral : 8.673 176.788 3128 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.13 % Allowed : 17.42 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 0.72 (0.16), residues: 2838 helix: 1.29 (0.14), residues: 1388 sheet: 0.36 (0.29), residues: 324 loop : -0.43 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 226 TYR 0.017 0.002 TYR E 425 PHE 0.016 0.002 PHE D 241 TRP 0.018 0.002 TRP D 80 HIS 0.006 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00411 (23001) covalent geometry : angle 0.56759 (31201) hydrogen bonds : bond 0.05382 ( 991) hydrogen bonds : angle 3.87722 ( 2862) Misc. bond : bond 0.00103 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 641 time to evaluate : 0.985 Fit side-chains REVERT: C 192 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7689 (mt0) REVERT: D 90 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7144 (mt0) REVERT: D 553 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7982 (mm) REVERT: D 712 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8012 (mtm110) REVERT: D 768 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6520 (tm-30) REVERT: D 769 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6246 (tm-30) REVERT: D 944 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: D 1170 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7944 (mm110) REVERT: E 40 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7071 (tm-30) REVERT: E 179 ARG cc_start: 0.7481 (mmt-90) cc_final: 0.7226 (mmt-90) REVERT: E 330 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7932 (mttp) REVERT: E 501 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7484 (ttm170) REVERT: G 114 ARG cc_start: 0.8113 (mtt180) cc_final: 0.7892 (mmt180) REVERT: a 1 MET cc_start: 0.4433 (ppp) cc_final: 0.3096 (ppp) REVERT: a 3 GLU cc_start: 0.8184 (mp0) cc_final: 0.7850 (mp0) REVERT: a 27 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7023 (tt0) REVERT: a 166 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8068 (mtpt) REVERT: b 156 ARG cc_start: 0.8364 (mmt180) cc_final: 0.8151 (mmp-170) REVERT: b 375 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.5967 (pp30) REVERT: b 414 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8029 (t0) outliers start: 77 outliers final: 45 residues processed: 674 average time/residue: 0.8059 time to fit residues: 606.4800 Evaluate side-chains 684 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 628 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 482 GLU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 742 MET Chi-restraints excluded: chain D residue 768 GLU Chi-restraints excluded: chain D residue 769 GLU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 860 THR Chi-restraints excluded: chain D residue 944 GLU Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain D residue 1137 LEU Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 501 ARG Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 38 SER Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 166 LYS Chi-restraints excluded: chain a residue 250 VAL Chi-restraints excluded: chain a residue 277 SER Chi-restraints excluded: chain a residue 335 ILE Chi-restraints excluded: chain a residue 384 ILE Chi-restraints excluded: chain b residue 69 GLU Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 114 ASP Chi-restraints excluded: chain b residue 128 ASP Chi-restraints excluded: chain b residue 306 ARG Chi-restraints excluded: chain b residue 375 GLN Chi-restraints excluded: chain b residue 414 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 264 optimal weight: 0.0270 chunk 116 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 268 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 216 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN C 314 ASN ** D 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 HIS E 472 GLN G 63 ASN G 127 GLN G 155 GLN a 35 GLN a 216 ASN a 226 ASN a 301 GLN ** a 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 ASN b 11 GLN b 134 GLN b 256 ASN b 264 HIS b 426 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.150539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.132361 restraints weight = 24414.715| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.34 r_work: 0.3596 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23002 Z= 0.146 Angle : 0.541 10.828 31201 Z= 0.280 Chirality : 0.043 0.161 3531 Planarity : 0.005 0.052 4022 Dihedral : 8.551 175.962 3128 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.25 % Allowed : 17.21 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.16), residues: 2838 helix: 1.34 (0.14), residues: 1405 sheet: 0.43 (0.29), residues: 323 loop : -0.39 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 226 TYR 0.015 0.001 TYR E 425 PHE 0.017 0.002 PHE b 367 TRP 0.019 0.002 TRP D 80 HIS 0.005 0.001 HIS a 61 Details of bonding type rmsd covalent geometry : bond 0.00344 (23001) covalent geometry : angle 0.54066 (31201) hydrogen bonds : bond 0.04970 ( 991) hydrogen bonds : angle 3.82447 ( 2862) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 636 time to evaluate : 0.769 Fit side-chains REVERT: C 192 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7661 (mt0) REVERT: D 90 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7173 (mt0) REVERT: D 553 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7972 (mm) REVERT: D 712 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8005 (mtm110) REVERT: D 768 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6484 (tm-30) REVERT: D 769 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6188 (tm-30) REVERT: D 944 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: D 1170 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7929 (mm110) REVERT: E 40 GLU cc_start: 0.7371 (tm-30) cc_final: 0.7051 (tm-30) REVERT: E 179 ARG cc_start: 0.7430 (mmt-90) cc_final: 0.7174 (mmt-90) REVERT: E 450 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8141 (mm) REVERT: E 501 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7290 (ttt180) REVERT: G 4 LEU cc_start: 0.7462 (mt) cc_final: 0.7172 (mt) REVERT: G 12 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6618 (mp-120) REVERT: a 1 MET cc_start: 0.4373 (ppp) cc_final: 0.1862 (ppp) REVERT: a 3 GLU cc_start: 0.8176 (mp0) cc_final: 0.7906 (mp0) REVERT: a 27 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6949 (tt0) REVERT: a 166 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8091 (mtpt) REVERT: b 46 ARG cc_start: 0.7746 (mtp180) cc_final: 0.7345 (mtp180) REVERT: b 156 ARG cc_start: 0.8382 (mmt180) cc_final: 0.8169 (mmp-170) REVERT: b 375 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.5910 (pp30) REVERT: b 414 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8141 (t0) outliers start: 80 outliers final: 53 residues processed: 672 average time/residue: 0.7718 time to fit residues: 580.1301 Evaluate side-chains 698 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 632 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 482 GLU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 544 ASN Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 742 MET Chi-restraints excluded: chain D residue 768 GLU Chi-restraints excluded: chain D residue 769 GLU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 860 THR Chi-restraints excluded: chain D residue 944 GLU Chi-restraints excluded: chain D residue 977 THR Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1079 ILE Chi-restraints excluded: chain D residue 1137 LEU Chi-restraints excluded: chain D residue 1158 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 501 ARG Chi-restraints excluded: chain E residue 506 GLU Chi-restraints excluded: chain G residue 12 GLN Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 155 GLN Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 38 SER Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 166 LYS Chi-restraints excluded: chain a residue 250 VAL Chi-restraints excluded: chain a residue 253 THR Chi-restraints excluded: chain a residue 277 SER Chi-restraints excluded: chain a residue 335 ILE Chi-restraints excluded: chain a residue 384 ILE Chi-restraints excluded: chain b residue 69 GLU Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 114 ASP Chi-restraints excluded: chain b residue 306 ARG Chi-restraints excluded: chain b residue 375 GLN Chi-restraints excluded: chain b residue 409 THR Chi-restraints excluded: chain b residue 414 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 173 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 259 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN C 314 ASN D 259 GLN ** D 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1049 HIS E 180 HIS E 472 GLN G 63 ASN G 127 GLN a 35 GLN a 216 ASN ** a 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 ASN b 11 GLN b 37 HIS b 134 GLN b 256 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.149571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.131314 restraints weight = 24357.674| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.35 r_work: 0.3582 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23002 Z= 0.186 Angle : 0.591 11.143 31201 Z= 0.305 Chirality : 0.045 0.166 3531 Planarity : 0.005 0.053 4022 Dihedral : 8.687 177.069 3128 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.80 % Allowed : 17.99 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 0.70 (0.16), residues: 2838 helix: 1.23 (0.14), residues: 1406 sheet: 0.40 (0.29), residues: 324 loop : -0.42 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 390 TYR 0.017 0.002 TYR E 425 PHE 0.017 0.002 PHE D 241 TRP 0.019 0.002 TRP D 575 HIS 0.008 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00450 (23001) covalent geometry : angle 0.59050 (31201) hydrogen bonds : bond 0.05574 ( 991) hydrogen bonds : angle 3.95310 ( 2862) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 639 time to evaluate : 0.888 Fit side-chains REVERT: C 192 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7752 (mt0) REVERT: D 90 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7212 (mt0) REVERT: D 553 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8007 (mm) REVERT: D 712 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8012 (mtm110) REVERT: D 768 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6603 (tm-30) REVERT: D 769 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6297 (tm-30) REVERT: D 944 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: D 1170 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7919 (mm110) REVERT: E 40 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7058 (tm-30) REVERT: E 450 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8155 (mm) REVERT: E 501 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7312 (ttt180) REVERT: G 12 GLN cc_start: 0.7017 (mp-120) cc_final: 0.6635 (mp-120) REVERT: a 1 MET cc_start: 0.4410 (ppp) cc_final: 0.1885 (ppp) REVERT: a 3 GLU cc_start: 0.8236 (mp0) cc_final: 0.7951 (mp0) REVERT: a 27 GLU cc_start: 0.7547 (mt-10) cc_final: 0.6927 (mt-10) REVERT: a 166 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8097 (mtpt) REVERT: b 46 ARG cc_start: 0.7758 (mtp180) cc_final: 0.7355 (mtp180) REVERT: b 156 ARG cc_start: 0.8403 (mmt180) cc_final: 0.8185 (mmp-170) REVERT: b 375 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.6013 (pp30) REVERT: b 414 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.7997 (t0) outliers start: 69 outliers final: 49 residues processed: 671 average time/residue: 0.7884 time to fit residues: 589.5190 Evaluate side-chains 690 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 629 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 482 GLU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 544 ASN Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 742 MET Chi-restraints excluded: chain D residue 768 GLU Chi-restraints excluded: chain D residue 769 GLU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 860 THR Chi-restraints excluded: chain D residue 944 GLU Chi-restraints excluded: chain D residue 977 THR Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1079 ILE Chi-restraints excluded: chain D residue 1137 LEU Chi-restraints excluded: chain D residue 1158 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 501 ARG Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 38 SER Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 166 LYS Chi-restraints excluded: chain a residue 250 VAL Chi-restraints excluded: chain a residue 253 THR Chi-restraints excluded: chain a residue 277 SER Chi-restraints excluded: chain a residue 335 ILE Chi-restraints excluded: chain a residue 384 ILE Chi-restraints excluded: chain b residue 69 GLU Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 114 ASP Chi-restraints excluded: chain b residue 306 ARG Chi-restraints excluded: chain b residue 375 GLN Chi-restraints excluded: chain b residue 409 THR Chi-restraints excluded: chain b residue 414 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 246 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 245 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN C 314 ASN D 259 GLN D1049 HIS D1081 ASN E 180 HIS E 472 GLN G 63 ASN G 127 GLN ** a 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 ASN b 11 GLN b 134 GLN b 256 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.148562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130265 restraints weight = 24277.573| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.33 r_work: 0.3565 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 23002 Z= 0.225 Angle : 0.643 11.249 31201 Z= 0.333 Chirality : 0.047 0.182 3531 Planarity : 0.005 0.056 4022 Dihedral : 8.932 179.933 3128 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.80 % Allowed : 18.55 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 0.58 (0.16), residues: 2838 helix: 1.12 (0.14), residues: 1397 sheet: 0.39 (0.28), residues: 326 loop : -0.48 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 241 TYR 0.019 0.002 TYR E 425 PHE 0.021 0.002 PHE D 241 TRP 0.019 0.002 TRP D 575 HIS 0.009 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00553 (23001) covalent geometry : angle 0.64341 (31201) hydrogen bonds : bond 0.06201 ( 991) hydrogen bonds : angle 4.09448 ( 2862) Misc. bond : bond 0.00059 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5676 Ramachandran restraints generated. 2838 Oldfield, 0 Emsley, 2838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 642 time to evaluate : 0.889 Fit side-chains REVERT: C 192 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7784 (mt0) REVERT: D 90 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7274 (mt0) REVERT: D 553 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8014 (mm) REVERT: D 712 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8024 (mtm110) REVERT: D 769 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6560 (tm-30) REVERT: D 944 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: D 1170 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7927 (mm110) REVERT: E 40 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7091 (tm-30) REVERT: E 450 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8177 (mm) REVERT: E 501 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7494 (ttm170) REVERT: G 12 GLN cc_start: 0.7045 (mp-120) cc_final: 0.6669 (mp-120) REVERT: a 1 MET cc_start: 0.4420 (ppp) cc_final: 0.1832 (ppp) REVERT: a 27 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7035 (mt-10) REVERT: a 166 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8107 (mtpt) REVERT: b 46 ARG cc_start: 0.7753 (mtp180) cc_final: 0.7346 (mtp180) REVERT: b 156 ARG cc_start: 0.8415 (mmt180) cc_final: 0.8201 (mmp-170) REVERT: b 375 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.6067 (pp30) REVERT: b 414 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8097 (t0) outliers start: 69 outliers final: 50 residues processed: 675 average time/residue: 0.7910 time to fit residues: 595.8466 Evaluate side-chains 700 residues out of total 2463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 639 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 482 GLU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 544 ASN Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 712 ARG Chi-restraints excluded: chain D residue 742 MET Chi-restraints excluded: chain D residue 769 GLU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 860 THR Chi-restraints excluded: chain D residue 944 GLU Chi-restraints excluded: chain D residue 977 THR Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain D residue 1079 ILE Chi-restraints excluded: chain D residue 1137 LEU Chi-restraints excluded: chain D residue 1158 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 255 LYS Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 501 ARG Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 38 SER Chi-restraints excluded: chain a residue 74 VAL Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 166 LYS Chi-restraints excluded: chain a residue 253 THR Chi-restraints excluded: chain a residue 277 SER Chi-restraints excluded: chain a residue 302 MET Chi-restraints excluded: chain a residue 384 ILE Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 114 ASP Chi-restraints excluded: chain b residue 375 GLN Chi-restraints excluded: chain b residue 409 THR Chi-restraints excluded: chain b residue 414 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 97 optimal weight: 1.9990 chunk 253 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 262 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN C 314 ASN D 259 GLN D1049 HIS E 180 HIS E 239 ASN E 443 ASN E 472 GLN G 63 ASN G 127 GLN a 226 ASN ** a 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 11 GLN b 134 GLN b 256 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.149017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.130790 restraints weight = 24295.710| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.34 r_work: 0.3572 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23002 Z= 0.198 Angle : 0.614 10.973 31201 Z= 0.318 Chirality : 0.046 0.175 3531 Planarity : 0.005 0.058 4022 Dihedral : 8.860 179.929 3128 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.76 % Allowed : 18.80 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 0.61 (0.16), residues: 2838 helix: 1.15 (0.14), residues: 1397 sheet: 0.44 (0.28), residues: 324 loop : -0.46 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 2 TYR 0.018 0.002 TYR E 425 PHE 0.017 0.002 PHE D 241 TRP 0.024 0.002 TRP D 575 HIS 0.008 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00481 (23001) covalent geometry : angle 0.61424 (31201) hydrogen bonds : bond 0.05760 ( 991) hydrogen bonds : angle 4.04686 ( 2862) Misc. bond : bond 0.00065 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14781.35 seconds wall clock time: 250 minutes 42.76 seconds (15042.76 seconds total)