Starting phenix.real_space_refine on Sat Jun 6 12:13:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lwi_63446/06_2026/9lwi_63446.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lwi_63446/06_2026/9lwi_63446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lwi_63446/06_2026/9lwi_63446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lwi_63446/06_2026/9lwi_63446.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lwi_63446/06_2026/9lwi_63446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lwi_63446/06_2026/9lwi_63446.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.047 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: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 172 5.16 5 C 17837 2.51 5 N 4832 2.21 5 O 5277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28124 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3137 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 6, 'TRANS': 385} Chain breaks: 1 Chain: "B" Number of atoms: 8918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 8918 Classifications: {'peptide': 1140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 1098} Chain: "C" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 793 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "D" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1840 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 4, 'TRANS': 220} Chain breaks: 3 Chain: "E" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1787 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1928 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain: "G" Number of atoms: 5898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5898 Classifications: {'peptide': 719} Link IDs: {'PTRANS': 19, 'TRANS': 699} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 746 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "I" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3071 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 13, 'TRANS': 367} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12178 SG CYS C 61 88.909 69.483 103.013 1.00 11.24 S ATOM 12228 SG CYS C 69 91.522 67.468 104.327 1.00 9.78 S ATOM 12773 SG CYS C 137 88.115 67.744 106.253 1.00 14.58 S ATOM 17961 SG CYS F 191 68.221 82.075 29.722 1.00 65.99 S ATOM 17983 SG CYS F 194 70.234 81.858 26.907 1.00 66.98 S ATOM 18141 SG CYS F 215 72.285 83.686 29.884 1.00 61.99 S ATOM 18057 SG CYS F 204 61.062 94.755 34.253 1.00 65.17 S ATOM 18079 SG CYS F 207 58.948 93.369 31.416 1.00 59.52 S ATOM 18246 SG CYS F 228 62.633 94.286 30.855 1.00 67.60 S ATOM 18269 SG CYS F 231 59.861 96.952 31.283 1.00 63.77 S ATOM 24507 SG CYS H 42 103.456 115.893 69.666 1.00 64.24 S ATOM 24526 SG CYS H 45 100.889 116.862 66.931 1.00 66.39 S ATOM 24821 SG CYS H 83 99.648 114.934 70.038 1.00 66.89 S ATOM 24593 SG CYS H 53 95.015 116.799 69.541 1.00 67.46 S ATOM 24616 SG CYS H 56 92.748 119.683 70.149 1.00 68.85 S ATOM 24700 SG CYS H 68 96.171 119.888 71.973 1.00 66.54 S ATOM 24750 SG CYS H 75 110.853 111.289 75.920 1.00 63.66 S ATOM 24917 SG CYS H 94 108.640 109.263 74.139 1.00 62.57 S Time building chain proxies: 6.55, per 1000 atoms: 0.23 Number of scatterers: 28124 At special positions: 0 Unit cell: (152.848, 169.624, 207.836, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 172 16.00 O 5277 8.00 N 4832 7.00 C 17837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 313 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" ND1 HIS C 139 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 61 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 137 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 69 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 191 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 215 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 194 " pdb=" ZN F 302 " pdb="ZN ZN F 302 " - pdb=" SG CYS F 207 " pdb="ZN ZN F 302 " - pdb=" SG CYS F 204 " pdb="ZN ZN F 302 " - pdb=" SG CYS F 228 " pdb="ZN ZN F 302 " - pdb=" SG CYS F 231 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 42 " pdb="ZN ZN H 201 " - pdb=" ND1 HIS H 80 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 45 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 83 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" ND1 HIS H 82 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 53 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 56 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 68 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 75 " pdb="ZN ZN H 203 " - pdb=" ND1 HIS H 77 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 94 " Number of angles added : 15 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6618 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 40 sheets defined 41.0% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 82 through 93 removed outlier: 4.354A pdb=" N LEU A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.741A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 215 through 257 removed outlier: 3.600A pdb=" N MET A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 952 removed outlier: 3.848A pdb=" N GLU A 897 " --> pdb=" O ARG A 893 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1007 removed outlier: 3.565A pdb=" N PHE A 994 " --> pdb=" O GLY A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1040 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.509A pdb=" N GLN B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.652A pdb=" N SER B 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 990 Processing helix chain 'B' and resid 1044 through 1062 Processing helix chain 'B' and resid 1069 through 1075 Processing helix chain 'B' and resid 1091 through 1096 Processing helix chain 'B' and resid 1097 through 1099 No H-bonds generated for 'chain 'B' and resid 1097 through 1099' Processing helix chain 'B' and resid 1101 through 1110 Processing helix chain 'B' and resid 1125 through 1138 removed outlier: 3.618A pdb=" N ARG B1138 " --> pdb=" O GLU B1134 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 88 through 99 Processing helix chain 'C' and resid 104 through 124 Processing helix chain 'C' and resid 126 through 135 Processing helix chain 'D' and resid 26 through 54 removed outlier: 4.138A pdb=" N ASN D 54 " --> pdb=" O CYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 64 through 80 removed outlier: 4.024A pdb=" N GLY D 79 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 109 removed outlier: 4.076A pdb=" N ASN D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 Processing helix chain 'D' and resid 138 through 142 removed outlier: 4.187A pdb=" N CYS D 142 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 removed outlier: 3.726A pdb=" N PHE D 150 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 220 removed outlier: 3.962A pdb=" N ASN D 220 " --> pdb=" O ALA D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 224 Processing helix chain 'D' and resid 254 through 269 Processing helix chain 'D' and resid 311 through 322 removed outlier: 4.014A pdb=" N ASN D 316 " --> pdb=" O GLN D 312 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE D 317 " --> pdb=" O GLU D 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 100 Processing helix chain 'E' and resid 107 through 115 removed outlier: 3.903A pdb=" N ILE E 111 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N HIS E 114 " --> pdb=" O ASP E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 138 Processing helix chain 'E' and resid 176 through 189 Processing helix chain 'E' and resid 195 through 204 removed outlier: 4.166A pdb=" N ARG E 204 " --> pdb=" O ASP E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 230 removed outlier: 4.449A pdb=" N PHE E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL E 228 " --> pdb=" O THR E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 258 Processing helix chain 'E' and resid 259 through 266 removed outlier: 3.781A pdb=" N VAL E 263 " --> pdb=" O SER E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 294 removed outlier: 3.649A pdb=" N ARG E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 26 removed outlier: 3.548A pdb=" N THR F 24 " --> pdb=" O GLN F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 45 Processing helix chain 'F' and resid 52 through 65 removed outlier: 3.648A pdb=" N PHE F 56 " --> pdb=" O LYS F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 99 removed outlier: 3.621A pdb=" N MET F 97 " --> pdb=" O SER F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 119 Processing helix chain 'F' and resid 125 through 132 Processing helix chain 'F' and resid 142 through 156 Processing helix chain 'F' and resid 169 through 184 removed outlier: 5.766A pdb=" N GLN F 178 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N TYR F 179 " --> pdb=" O GLU F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 220 Processing helix chain 'G' and resid 57 through 74 Processing helix chain 'G' and resid 75 through 77 No H-bonds generated for 'chain 'G' and resid 75 through 77' Processing helix chain 'G' and resid 82 through 94 Processing helix chain 'G' and resid 98 through 122 removed outlier: 3.519A pdb=" N LEU G 102 " --> pdb=" O VAL G 98 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU G 119 " --> pdb=" O GLN G 115 " (cutoff:3.500A) Proline residue: G 120 - end of helix Processing helix chain 'G' and resid 127 through 153 Processing helix chain 'G' and resid 153 through 161 Processing helix chain 'G' and resid 169 through 182 Processing helix chain 'G' and resid 186 through 205 removed outlier: 3.888A pdb=" N SER G 190 " --> pdb=" O LYS G 186 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG G 204 " --> pdb=" O ILE G 200 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER G 205 " --> pdb=" O GLU G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 224 removed outlier: 3.532A pdb=" N LEU G 214 " --> pdb=" O ASP G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 254 removed outlier: 4.546A pdb=" N LEU G 233 " --> pdb=" O ASP G 229 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LYS G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN G 252 " --> pdb=" O GLN G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 277 Processing helix chain 'G' and resid 279 through 281 No H-bonds generated for 'chain 'G' and resid 279 through 281' Processing helix chain 'G' and resid 282 through 295 Processing helix chain 'G' and resid 298 through 305 Processing helix chain 'G' and resid 306 through 314 Processing helix chain 'G' and resid 315 through 329 removed outlier: 3.666A pdb=" N LEU G 319 " --> pdb=" O ARG G 315 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL G 329 " --> pdb=" O LEU G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 354 removed outlier: 3.544A pdb=" N ASN G 354 " --> pdb=" O ALA G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 359 removed outlier: 4.103A pdb=" N LYS G 359 " --> pdb=" O PRO G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 360 through 379 removed outlier: 3.615A pdb=" N VAL G 378 " --> pdb=" O HIS G 374 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 400 Processing helix chain 'G' and resid 403 through 418 Processing helix chain 'G' and resid 425 through 443 removed outlier: 3.711A pdb=" N LEU G 429 " --> pdb=" O THR G 425 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG G 431 " --> pdb=" O GLU G 427 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR G 432 " --> pdb=" O GLU G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 463 Processing helix chain 'G' and resid 468 through 480 removed outlier: 3.547A pdb=" N GLU G 472 " --> pdb=" O SER G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 484 through 516 removed outlier: 4.008A pdb=" N THR G 488 " --> pdb=" O GLY G 484 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN G 514 " --> pdb=" O GLN G 510 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 560 removed outlier: 3.762A pdb=" N GLY G 560 " --> pdb=" O ALA G 556 " (cutoff:3.500A) Processing helix chain 'G' and resid 593 through 602 removed outlier: 3.646A pdb=" N MET G 601 " --> pdb=" O LEU G 597 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE G 602 " --> pdb=" O VAL G 598 " (cutoff:3.500A) Processing helix chain 'G' and resid 609 through 618 Processing helix chain 'G' and resid 620 through 630 removed outlier: 3.891A pdb=" N ARG G 626 " --> pdb=" O SER G 622 " (cutoff:3.500A) Processing helix chain 'G' and resid 669 through 675 removed outlier: 3.777A pdb=" N GLN G 673 " --> pdb=" O ILE G 669 " (cutoff:3.500A) Processing helix chain 'G' and resid 677 through 707 removed outlier: 3.666A pdb=" N GLN G 681 " --> pdb=" O THR G 677 " (cutoff:3.500A) Processing helix chain 'G' and resid 711 through 723 Processing helix chain 'G' and resid 728 through 742 Processing helix chain 'H' and resid 53 through 58 Processing helix chain 'H' and resid 86 through 91 removed outlier: 4.308A pdb=" N THR H 90 " --> pdb=" O ARG H 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 96 Processing helix chain 'I' and resid 109 through 118 removed outlier: 3.564A pdb=" N PHE I 112 " --> pdb=" O LYS I 109 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS I 115 " --> pdb=" O PHE I 112 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ARG I 116 " --> pdb=" O PHE I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 169 removed outlier: 4.177A pdb=" N ALA I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU I 168 " --> pdb=" O LYS I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 178 Processing helix chain 'I' and resid 182 through 190 removed outlier: 4.175A pdb=" N GLU I 186 " --> pdb=" O ASP I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 204 removed outlier: 3.548A pdb=" N LYS I 201 " --> pdb=" O GLU I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 241 removed outlier: 3.753A pdb=" N HIS I 209 " --> pdb=" O PRO I 205 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN I 241 " --> pdb=" O GLN I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 888 through 951 removed outlier: 4.130A pdb=" N ASN I 930 " --> pdb=" O GLU I 926 " (cutoff:3.500A) Proline residue: I 931 - end of helix Processing helix chain 'I' and resid 992 through 1005 Processing helix chain 'I' and resid 1005 through 1011 removed outlier: 3.794A pdb=" N ASN I1011 " --> pdb=" O LEU I1007 " (cutoff:3.500A) Processing helix chain 'I' and resid 1026 through 1041 removed outlier: 3.696A pdb=" N ARG I1031 " --> pdb=" O PRO I1027 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.764A pdb=" N ILE A 51 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ILE A 47 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR A 122 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE A 51 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N SER A 120 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 165 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1011 through 1012 removed outlier: 9.187A pdb=" N LEU A1065 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE A 73 " --> pdb=" O LEU A1065 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 958 through 961 Processing sheet with id=AA4, first strand: chain 'B' and resid 1004 through 1009 removed outlier: 3.804A pdb=" N VAL B1006 " --> pdb=" O GLY B1031 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER B1027 " --> pdb=" O VAL B1040 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B1040 " --> pdb=" O SER B1027 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU B1029 " --> pdb=" O GLY B1038 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY B1038 " --> pdb=" O LEU B1029 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE B1037 " --> pdb=" O ALA B 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 21 removed outlier: 3.820A pdb=" N GLY B 17 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N VAL B 43 " --> pdb=" O PRO B 51 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR B 45 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 63 through 67 removed outlier: 3.767A pdb=" N VAL B 63 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 104 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU B 90 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N THR B 102 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 92 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE B 100 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER B 94 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ILE B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 169 removed outlier: 6.708A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE B 169 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR B 177 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N VAL B 190 " --> pdb=" O TRP B 207 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N TRP B 207 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B 192 " --> pdb=" O GLY B 205 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 205 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 196 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 201 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 232 Processing sheet with id=AB1, first strand: chain 'B' and resid 258 through 263 removed outlier: 3.947A pdb=" N CYS B 260 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU B 280 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP B 299 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU B 288 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU B 297 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 318 removed outlier: 6.614A pdb=" N VAL B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER B 331 " --> pdb=" O THR B 352 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR B 352 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU B 333 " --> pdb=" O MET B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 359 through 363 removed outlier: 4.283A pdb=" N ASP B 361 " --> pdb=" O CYS B 378 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 396 through 402 removed outlier: 6.131A pdb=" N GLU B 398 " --> pdb=" O THR B 703 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR B 703 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 410 through 411 removed outlier: 3.503A pdb=" N TRP B 411 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 426 " --> pdb=" O TRP B 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 457 through 463 removed outlier: 3.684A pdb=" N SER B 488 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER B 480 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU B 486 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 500 through 503 removed outlier: 3.528A pdb=" N VAL B 500 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B 516 " --> pdb=" O HIS B 531 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS B 531 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR B 518 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.225A pdb=" N GLY B 559 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU B 541 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA B 557 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LYS B 570 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU B 576 " --> pdb=" O LYS B 570 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 588 through 595 removed outlier: 4.392A pdb=" N HIS B 600 " --> pdb=" O LEU B 616 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 588 through 595 removed outlier: 4.392A pdb=" N HIS B 600 " --> pdb=" O LEU B 616 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 637 through 642 removed outlier: 3.530A pdb=" N VAL B 637 " --> pdb=" O CYS B 652 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N THR B 647 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER B 661 " --> pdb=" O THR B 647 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 720 through 727 removed outlier: 6.345A pdb=" N SER B 738 " --> pdb=" O PRO B 721 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS B 723 " --> pdb=" O LEU B 736 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 720 through 727 removed outlier: 6.345A pdb=" N SER B 738 " --> pdb=" O PRO B 721 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS B 723 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS B 803 " --> pdb=" O ILE B 793 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ASP B 795 " --> pdb=" O VAL B 801 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL B 801 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER B 762 " --> pdb=" O ALA B 804 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N GLN B 806 " --> pdb=" O SER B 762 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER B 764 " --> pdb=" O GLN B 806 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 811 through 819 removed outlier: 5.290A pdb=" N ALA B 813 " --> pdb=" O ALA B 834 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA B 834 " --> pdb=" O ALA B 813 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 815 " --> pdb=" O GLY B 832 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 862 " --> pdb=" O VAL B 850 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLN B 852 " --> pdb=" O THR B 860 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N THR B 860 " --> pdb=" O GLN B 852 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 873 through 876 removed outlier: 6.323A pdb=" N VAL B 888 " --> pdb=" O ASN B 904 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASN B 904 " --> pdb=" O VAL B 888 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU B 890 " --> pdb=" O GLU B 902 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 913 through 917 removed outlier: 3.842A pdb=" N TYR B 913 " --> pdb=" O GLY B 924 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL B 930 " --> pdb=" O ASP B 948 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 946 " --> pdb=" O LEU B 932 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ALA B 934 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLU B 944 " --> pdb=" O ALA B 934 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS B 936 " --> pdb=" O PHE B 942 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE B 942 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 954 through 958 removed outlier: 6.489A pdb=" N ALA B 968 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL B 957 " --> pdb=" O LEU B 966 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 966 " --> pdb=" O VAL B 957 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B 973 " --> pdb=" O GLU B 969 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 996 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLN B 978 " --> pdb=" O GLU B 994 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLU B 994 " --> pdb=" O GLN B 978 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 58 through 59 removed outlier: 3.965A pdb=" N LEU C 58 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 140 through 144 removed outlier: 3.672A pdb=" N VAL E 143 " --> pdb=" O ILE E 153 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 193 through 194 removed outlier: 3.820A pdb=" N ARG E 236 " --> pdb=" O GLU E 247 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 27 through 29 removed outlier: 3.784A pdb=" N ALA F 85 " --> pdb=" O LYS F 72 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS F 72 " --> pdb=" O ALA F 85 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 159 through 162 Processing sheet with id=AD5, first strand: chain 'F' and resid 201 through 203 Processing sheet with id=AD6, first strand: chain 'G' and resid 522 through 529 removed outlier: 3.660A pdb=" N ALA H 29 " --> pdb=" O THR G 524 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N PHE H 22 " --> pdb=" O LEU G 578 " (cutoff:3.500A) removed outlier: 10.055A pdb=" N LEU G 578 " --> pdb=" O PHE H 22 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N VAL H 24 " --> pdb=" O ALA G 576 " (cutoff:3.500A) removed outlier: 10.760A pdb=" N ALA G 576 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 12.379A pdb=" N LYS H 26 " --> pdb=" O GLY G 574 " (cutoff:3.500A) removed outlier: 11.201A pdb=" N GLY G 574 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 10.499A pdb=" N ASN H 28 " --> pdb=" O THR G 572 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N THR G 572 " --> pdb=" O ASN H 28 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL H 30 " --> pdb=" O GLN G 570 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA G 576 " --> pdb=" O VAL G 591 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE G 589 " --> pdb=" O LEU G 578 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 639 through 641 Processing sheet with id=AD8, first strand: chain 'G' and resid 745 through 748 removed outlier: 4.996A pdb=" N GLN G 754 " --> pdb=" O ASP G 748 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 70 through 72 Processing sheet with id=AE1, first strand: chain 'I' and resid 52 through 57 removed outlier: 5.951A pdb=" N ILE I 53 " --> pdb=" O PHE I 128 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE I 128 " --> pdb=" O ILE I 53 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG I 55 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY I 121 " --> pdb=" O ILE I 140 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE I 136 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU I 127 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU I 134 " --> pdb=" O LEU I 127 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 1052 through 1053 removed outlier: 6.250A pdb=" N ILE I 78 " --> pdb=" O THR I1053 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 974 through 975 removed outlier: 3.848A pdb=" N VAL I 975 " --> pdb=" O HIS I 984 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS I 984 " --> pdb=" O VAL I 975 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'I' and resid 1015 through 1017 1329 hydrogen bonds defined for protein. 3855 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: 6.07 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4768 1.29 - 1.43: 7053 1.43 - 1.56: 16534 1.56 - 1.69: 17 1.69 - 1.82: 270 Bond restraints: 28642 Sorted by residual: bond pdb=" C LEU A 939 " pdb=" O LEU A 939 " ideal model delta sigma weight residual 1.236 1.160 0.076 1.29e-02 6.01e+03 3.44e+01 bond pdb=" N LEU F 213 " pdb=" CA LEU F 213 " ideal model delta sigma weight residual 1.459 1.514 -0.055 1.04e-02 9.25e+03 2.75e+01 bond pdb=" N LEU G 54 " pdb=" CA LEU G 54 " ideal model delta sigma weight residual 1.457 1.497 -0.041 9.10e-03 1.21e+04 1.99e+01 bond pdb=" N VAL D 80 " pdb=" CA VAL D 80 " ideal model delta sigma weight residual 1.456 1.510 -0.053 1.19e-02 7.06e+03 1.99e+01 bond pdb=" N MET F 211 " pdb=" CA MET F 211 " ideal model delta sigma weight residual 1.454 1.509 -0.055 1.23e-02 6.61e+03 1.98e+01 ... (remaining 28637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 36824 2.11 - 4.23: 1572 4.23 - 6.34: 182 6.34 - 8.46: 26 8.46 - 10.57: 9 Bond angle restraints: 38613 Sorted by residual: angle pdb=" N GLU B 619 " pdb=" CA GLU B 619 " pdb=" C GLU B 619 " ideal model delta sigma weight residual 110.97 102.37 8.60 1.09e+00 8.42e-01 6.22e+01 angle pdb=" N LEU A 216 " pdb=" CA LEU A 216 " pdb=" C LEU A 216 " ideal model delta sigma weight residual 112.89 103.57 9.32 1.24e+00 6.50e-01 5.64e+01 angle pdb=" N ASN C 84 " pdb=" CA ASN C 84 " pdb=" C ASN C 84 " ideal model delta sigma weight residual 112.86 104.62 8.24 1.22e+00 6.72e-01 4.56e+01 angle pdb=" N GLU B 525 " pdb=" CA GLU B 525 " pdb=" C GLU B 525 " ideal model delta sigma weight residual 108.55 119.12 -10.57 1.62e+00 3.81e-01 4.26e+01 angle pdb=" N ALA C 102 " pdb=" CA ALA C 102 " pdb=" C ALA C 102 " ideal model delta sigma weight residual 112.92 105.07 7.85 1.23e+00 6.61e-01 4.07e+01 ... (remaining 38608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16070 17.95 - 35.90: 1100 35.90 - 53.85: 218 53.85 - 71.80: 48 71.80 - 89.75: 26 Dihedral angle restraints: 17462 sinusoidal: 7254 harmonic: 10208 Sorted by residual: dihedral pdb=" N THR B 532 " pdb=" C THR B 532 " pdb=" CA THR B 532 " pdb=" CB THR B 532 " ideal model delta harmonic sigma weight residual 123.40 133.22 -9.82 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" N ASN G 47 " pdb=" C ASN G 47 " pdb=" CA ASN G 47 " pdb=" CB ASN G 47 " ideal model delta harmonic sigma weight residual 122.80 113.13 9.67 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" N LEU B 76 " pdb=" C LEU B 76 " pdb=" CA LEU B 76 " pdb=" CB LEU B 76 " ideal model delta harmonic sigma weight residual 122.80 113.44 9.36 0 2.50e+00 1.60e-01 1.40e+01 ... (remaining 17459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3585 0.071 - 0.143: 576 0.143 - 0.214: 107 0.214 - 0.285: 33 0.285 - 0.357: 9 Chirality restraints: 4310 Sorted by residual: chirality pdb=" CB VAL C 83 " pdb=" CA VAL C 83 " pdb=" CG1 VAL C 83 " pdb=" CG2 VAL C 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA TYR B 837 " pdb=" N TYR B 837 " pdb=" C TYR B 837 " pdb=" CB TYR B 837 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA MET B 835 " pdb=" N MET B 835 " pdb=" C MET B 835 " pdb=" CB MET B 835 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 4307 not shown) Planarity restraints: 4967 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 395 " 0.026 2.00e-02 2.50e+03 5.34e-02 2.85e+01 pdb=" C GLY B 395 " -0.092 2.00e-02 2.50e+03 pdb=" O GLY B 395 " 0.036 2.00e-02 2.50e+03 pdb=" N ILE B 396 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 59 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C THR G 59 " -0.070 2.00e-02 2.50e+03 pdb=" O THR G 59 " 0.026 2.00e-02 2.50e+03 pdb=" N GLN G 60 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 937 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C LEU A 937 " 0.070 2.00e-02 2.50e+03 pdb=" O LEU A 937 " -0.026 2.00e-02 2.50e+03 pdb=" N THR A 938 " -0.024 2.00e-02 2.50e+03 ... (remaining 4964 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 979 2.72 - 3.26: 29421 3.26 - 3.81: 45285 3.81 - 4.35: 56381 4.35 - 4.90: 95900 Nonbonded interactions: 227966 Sorted by model distance: nonbonded pdb=" OD1 ASP B 166 " pdb=" N VAL B 167 " model vdw 2.171 3.120 nonbonded pdb=" O PRO E 174 " pdb=" OG1 THR E 175 " model vdw 2.172 3.040 nonbonded pdb=" O ILE G 548 " pdb=" OE1 GLU G 552 " model vdw 2.210 3.040 nonbonded pdb=" O GLN G 248 " pdb=" NE2 GLN G 252 " model vdw 2.226 3.120 nonbonded pdb=" O GLU B 675 " pdb=" ND2 ASN B 695 " model vdw 2.227 3.120 ... (remaining 227961 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: 12.820 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: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.650 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 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 : 0.006 0.244 28665 Z= 0.429 Angle : 0.863 13.006 38630 Z= 0.602 Chirality : 0.058 0.357 4310 Planarity : 0.004 0.053 4967 Dihedral : 13.135 89.754 10841 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.64 % Allowed : 2.88 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.15), residues: 3474 helix: 2.90 (0.14), residues: 1317 sheet: 0.66 (0.21), residues: 673 loop : -0.89 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 96 TYR 0.023 0.001 TYR B 812 PHE 0.022 0.001 PHE B 67 TRP 0.017 0.001 TRP G 139 HIS 0.010 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.43 (28642) covalent geometry : angle 0.85679 / 0.60 (38613) SS BOND : bond 0.00058 / 0.03 ( 1) SS BOND : angle 0.03042 / 0.02 ( 2) hydrogen bonds : bond 0.16796 / 11.18 ( 1312) hydrogen bonds : angle 6.89960 / 4.99 ( 3855) metal coordination : bond 0.05514 / 3.07 ( 22) metal coordination : angle 5.17015 / 3.37 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 400 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 166 ASP cc_start: 0.6128 (t0) cc_final: 0.5765 (t70) REVERT: F 141 MET cc_start: 0.2342 (ttm) cc_final: -0.0725 (mmt) REVERT: G 505 MET cc_start: 0.2498 (ttp) cc_final: 0.2105 (ttp) REVERT: H 86 ARG cc_start: 0.1665 (mtt180) cc_final: 0.1275 (mmm160) REVERT: I 208 MET cc_start: -0.1257 (tpt) cc_final: -0.1642 (mtp) REVERT: I 230 LYS cc_start: 0.4991 (mmmt) cc_final: 0.4741 (mttm) outliers start: 20 outliers final: 3 residues processed: 413 average time/residue: 0.1869 time to fit residues: 123.4774 Evaluate side-chains 281 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 278 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 962 HIS B 4 ASN B 149 ASN B 156 ASN B 186 GLN B 189 HIS B 240 HIS B 261 HIS B 337 ASN B 462 ASN B 617 ASN B 743 GLN B 796 GLN B 803 HIS B 852 GLN B 990 GLN C 86 HIS C 87 GLN D 64 ASN E 135 GLN F 15 HIS F 25 HIS F 39 HIS ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 ASN G 164 ASN G 514 ASN ** G 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.229179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.181392 restraints weight = 39302.319| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 2.77 r_work: 0.3511 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.451 28665 Z= 0.264 Angle : 0.696 21.296 38630 Z= 0.354 Chirality : 0.047 0.249 4310 Planarity : 0.005 0.052 4967 Dihedral : 4.254 33.395 3785 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.73 % Allowed : 8.86 % Favored : 89.41 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.14), residues: 3474 helix: 2.50 (0.14), residues: 1330 sheet: -0.03 (0.20), residues: 680 loop : -0.92 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 263 TYR 0.028 0.002 TYR B 613 PHE 0.035 0.002 PHE B1030 TRP 0.015 0.002 TRP C 120 HIS 0.017 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.26 (28642) covalent geometry : angle 0.68059 / 0.35 (38613) SS BOND : bond 0.00304 / 0.16 ( 1) SS BOND : angle 1.58784 / 1.06 ( 2) hydrogen bonds : bond 0.04440 / 2.97 ( 1312) hydrogen bonds : angle 5.19060 / 3.78 ( 3855) metal coordination : bond 0.09654 / 5.11 ( 22) metal coordination : angle 7.31972 / 5.01 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 293 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7980 (mmp80) cc_final: 0.7733 (mmp80) REVERT: B 497 ASN cc_start: 0.7961 (t0) cc_final: 0.7708 (t0) REVERT: B 993 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7644 (mm-40) REVERT: D 124 PHE cc_start: 0.7823 (m-80) cc_final: 0.7621 (m-80) REVERT: D 130 ASN cc_start: 0.6842 (t0) cc_final: 0.6595 (m-40) REVERT: F 141 MET cc_start: 0.0792 (ttm) cc_final: -0.1675 (mmt) REVERT: G 505 MET cc_start: 0.0659 (ttp) cc_final: 0.0457 (ttp) REVERT: G 554 PHE cc_start: 0.6825 (t80) cc_final: 0.6520 (t80) REVERT: G 745 MET cc_start: 0.5225 (mpp) cc_final: 0.4953 (mpp) REVERT: I 122 MET cc_start: 0.5072 (mpp) cc_final: 0.4818 (mpp) outliers start: 54 outliers final: 32 residues processed: 336 average time/residue: 0.1862 time to fit residues: 100.4134 Evaluate side-chains 275 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 944 GLU Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1071 SER Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 136 ASN Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 548 ILE Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 235 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 56 optimal weight: 0.0470 chunk 204 optimal weight: 5.9990 chunk 84 optimal weight: 0.4980 chunk 308 optimal weight: 9.9990 chunk 157 optimal weight: 0.2980 chunk 282 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 166 optimal weight: 6.9990 chunk 304 optimal weight: 20.0000 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN B 189 HIS D 64 ASN E 156 ASN E 271 HIS F 20 GLN ** F 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 261 ASN G 444 HIS ** G 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.230723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.181592 restraints weight = 39605.179| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 2.81 r_work: 0.3543 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 28665 Z= 0.123 Angle : 0.540 13.297 38630 Z= 0.280 Chirality : 0.041 0.177 4310 Planarity : 0.004 0.059 4967 Dihedral : 3.973 32.850 3780 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.63 % Allowed : 10.66 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.14), residues: 3474 helix: 2.47 (0.14), residues: 1329 sheet: -0.13 (0.20), residues: 668 loop : -0.90 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 935 TYR 0.018 0.001 TYR G 757 PHE 0.036 0.001 PHE G 495 TRP 0.025 0.001 TRP D 161 HIS 0.013 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (28642) covalent geometry : angle 0.53228 / 0.28 (38613) SS BOND : bond 0.00040 / 0.02 ( 1) SS BOND : angle 0.45244 / 0.30 ( 2) hydrogen bonds : bond 0.03645 / 2.42 ( 1312) hydrogen bonds : angle 4.77791 / 3.47 ( 3855) metal coordination : bond 0.03278 / 1.80 ( 22) metal coordination : angle 4.77207 / 3.28 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 283 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7546 (tpp) cc_final: 0.7277 (tpp) REVERT: A 154 TYR cc_start: 0.5642 (m-80) cc_final: 0.5364 (m-80) REVERT: B 497 ASN cc_start: 0.7916 (t0) cc_final: 0.7647 (t0) REVERT: B 1113 GLN cc_start: 0.7111 (tp40) cc_final: 0.6828 (tp-100) REVERT: D 130 ASN cc_start: 0.6794 (t0) cc_final: 0.6562 (m-40) REVERT: E 197 GLU cc_start: 0.7855 (mp0) cc_final: 0.7568 (mp0) REVERT: F 12 THR cc_start: 0.6043 (OUTLIER) cc_final: 0.5696 (m) REVERT: F 141 MET cc_start: 0.0880 (ttm) cc_final: -0.1564 (mmt) REVERT: F 227 ARG cc_start: 0.5608 (mpt-90) cc_final: 0.5385 (mtm110) REVERT: G 354 ASN cc_start: 0.7445 (t0) cc_final: 0.7198 (t0) REVERT: G 456 ASP cc_start: 0.8428 (t0) cc_final: 0.8161 (t0) REVERT: G 505 MET cc_start: 0.0775 (ttp) cc_final: 0.0030 (tpp) REVERT: G 554 PHE cc_start: 0.6890 (t80) cc_final: 0.6568 (t80) REVERT: G 745 MET cc_start: 0.5349 (mpp) cc_final: 0.5042 (mpp) REVERT: H 86 ARG cc_start: 0.2132 (mtt180) cc_final: 0.1234 (mmm160) REVERT: I 230 LYS cc_start: 0.6190 (mmmt) cc_final: 0.5623 (mttm) REVERT: I 896 ARG cc_start: 0.4587 (tpp80) cc_final: 0.2837 (ttp-110) REVERT: I 1005 MET cc_start: 0.3618 (ttt) cc_final: 0.3314 (ptm) outliers start: 51 outliers final: 30 residues processed: 322 average time/residue: 0.1795 time to fit residues: 94.2577 Evaluate side-chains 273 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 944 GLU Chi-restraints excluded: chain B residue 1071 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 136 ASN Chi-restraints excluded: chain G residue 220 MET Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 1036 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 305 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 0.0770 chunk 252 optimal weight: 2.9990 overall best weight: 1.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 186 GLN B 189 HIS ** B 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** F 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.228623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.177899 restraints weight = 39331.520| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.91 r_work: 0.3472 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28665 Z= 0.181 Angle : 0.567 8.635 38630 Z= 0.294 Chirality : 0.042 0.211 4310 Planarity : 0.004 0.074 4967 Dihedral : 4.122 33.188 3780 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.76 % Allowed : 11.87 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.14), residues: 3474 helix: 2.36 (0.14), residues: 1326 sheet: -0.24 (0.20), residues: 665 loop : -0.93 (0.15), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 49 TYR 0.018 0.001 TYR B 613 PHE 0.057 0.002 PHE G 495 TRP 0.031 0.002 TRP D 161 HIS 0.007 0.001 HIS B 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (28642) covalent geometry : angle 0.56491 / 0.29 (38613) SS BOND : bond 0.00096 / 0.05 ( 1) SS BOND : angle 1.09186 / 0.73 ( 2) hydrogen bonds : bond 0.03685 / 2.47 ( 1312) hydrogen bonds : angle 4.70494 / 3.42 ( 3855) metal coordination : bond 0.00784 / 0.47 ( 22) metal coordination : angle 2.68204 / 1.78 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 265 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 497 ASN cc_start: 0.7950 (t0) cc_final: 0.7692 (t0) REVERT: B 536 HIS cc_start: 0.6937 (m-70) cc_final: 0.6651 (m-70) REVERT: B 1113 GLN cc_start: 0.7299 (tp40) cc_final: 0.7030 (tp-100) REVERT: D 130 ASN cc_start: 0.6980 (t0) cc_final: 0.6638 (m-40) REVERT: E 197 GLU cc_start: 0.7914 (mp0) cc_final: 0.7639 (mp0) REVERT: F 227 ARG cc_start: 0.5670 (mpt-90) cc_final: 0.5403 (mtm110) REVERT: G 456 ASP cc_start: 0.8437 (t0) cc_final: 0.8120 (t0) REVERT: G 505 MET cc_start: 0.0721 (ttp) cc_final: -0.0045 (tpp) REVERT: G 554 PHE cc_start: 0.6881 (t80) cc_final: 0.6534 (t80) REVERT: G 601 MET cc_start: -0.4541 (mtp) cc_final: -0.4862 (mtp) REVERT: G 745 MET cc_start: 0.5483 (mpp) cc_final: 0.5254 (mpp) REVERT: H 80 HIS cc_start: 0.1564 (m170) cc_final: 0.0778 (m-70) REVERT: H 86 ARG cc_start: 0.1798 (mtt180) cc_final: 0.1067 (mmm160) REVERT: I 230 LYS cc_start: 0.6241 (mmmt) cc_final: 0.5686 (mttm) REVERT: I 896 ARG cc_start: 0.4647 (tpp80) cc_final: 0.2910 (ttp-110) REVERT: I 1066 MET cc_start: 0.1906 (tmm) cc_final: 0.1400 (mmt) outliers start: 55 outliers final: 41 residues processed: 312 average time/residue: 0.1820 time to fit residues: 92.9192 Evaluate side-chains 274 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 944 GLU Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1071 SER Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 212 HIS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 136 ASN Chi-restraints excluded: chain G residue 220 MET Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain G residue 548 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 151 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 145 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 284 optimal weight: 3.9990 chunk 341 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 293 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 267 optimal weight: 9.9990 chunk 254 optimal weight: 4.9990 chunk 295 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS B 186 GLN B 189 HIS ** B 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** F 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.226525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.173894 restraints weight = 38901.574| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.92 r_work: 0.3408 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 28665 Z= 0.245 Angle : 0.621 9.324 38630 Z= 0.320 Chirality : 0.044 0.243 4310 Planarity : 0.004 0.077 4967 Dihedral : 4.370 34.043 3780 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.56 % Allowed : 12.77 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3474 helix: 2.22 (0.14), residues: 1327 sheet: -0.51 (0.20), residues: 676 loop : -1.03 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 327 TYR 0.020 0.002 TYR B 613 PHE 0.039 0.002 PHE G 495 TRP 0.013 0.002 TRP B 893 HIS 0.007 0.001 HIS B 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.25 (28642) covalent geometry : angle 0.61889 / 0.32 (38613) SS BOND : bond 0.00133 / 0.07 ( 1) SS BOND : angle 1.53315 / 1.02 ( 2) hydrogen bonds : bond 0.03902 / 2.64 ( 1312) hydrogen bonds : angle 4.77820 / 3.48 ( 3855) metal coordination : bond 0.00655 / 0.44 ( 22) metal coordination : angle 2.64799 / 1.73 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 263 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7306 (mm) REVERT: B 49 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8203 (pp) REVERT: B 497 ASN cc_start: 0.7980 (t0) cc_final: 0.7721 (t0) REVERT: B 1080 ARG cc_start: 0.8613 (mmt-90) cc_final: 0.7377 (ptm160) REVERT: B 1113 GLN cc_start: 0.7520 (tp40) cc_final: 0.7300 (tp-100) REVERT: E 180 MET cc_start: 0.6644 (tmm) cc_final: 0.6376 (tmm) REVERT: E 197 GLU cc_start: 0.7869 (mp0) cc_final: 0.7542 (mp0) REVERT: E 269 LYS cc_start: 0.3820 (pttm) cc_final: 0.3306 (ptmt) REVERT: F 162 LYS cc_start: 0.3924 (mmtm) cc_final: 0.2809 (mttp) REVERT: F 227 ARG cc_start: 0.5661 (mpt-90) cc_final: 0.5321 (mtm110) REVERT: G 456 ASP cc_start: 0.8631 (t0) cc_final: 0.8340 (t0) REVERT: G 505 MET cc_start: 0.0561 (ttp) cc_final: 0.0210 (tpp) REVERT: G 554 PHE cc_start: 0.7073 (t80) cc_final: 0.6667 (t80) REVERT: H 80 HIS cc_start: 0.1709 (m170) cc_final: 0.0815 (m-70) REVERT: H 86 ARG cc_start: 0.1888 (mtt180) cc_final: 0.1131 (mmm160) REVERT: I 230 LYS cc_start: 0.6234 (mmmt) cc_final: 0.5749 (mttm) REVERT: I 896 ARG cc_start: 0.4574 (tpp80) cc_final: 0.2840 (ttp-110) REVERT: I 1066 MET cc_start: 0.1432 (OUTLIER) cc_final: 0.1207 (mmt) outliers start: 80 outliers final: 53 residues processed: 331 average time/residue: 0.1826 time to fit residues: 98.0457 Evaluate side-chains 295 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 239 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 680 CYS Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 944 GLU Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1071 SER Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 212 HIS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 136 ASN Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 1066 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 49 optimal weight: 0.8980 chunk 309 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 84 optimal weight: 0.0670 chunk 292 optimal weight: 0.9990 chunk 205 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 196 optimal weight: 0.0970 chunk 90 optimal weight: 1.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS B 186 GLN B 189 HIS B 743 GLN ** F 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.230224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.174930 restraints weight = 39115.648| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 2.83 r_work: 0.3498 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28665 Z= 0.114 Angle : 0.519 8.735 38630 Z= 0.271 Chirality : 0.040 0.160 4310 Planarity : 0.004 0.074 4967 Dihedral : 4.052 33.951 3780 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.14 % Allowed : 13.76 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3474 helix: 2.36 (0.14), residues: 1326 sheet: -0.38 (0.20), residues: 680 loop : -1.04 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 114 TYR 0.013 0.001 TYR G 277 PHE 0.038 0.001 PHE I 61 TRP 0.014 0.001 TRP B 893 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (28642) covalent geometry : angle 0.51714 / 0.27 (38613) SS BOND : bond 0.00073 / 0.04 ( 1) SS BOND : angle 0.46088 / 0.31 ( 2) hydrogen bonds : bond 0.03274 / 2.19 ( 1312) hydrogen bonds : angle 4.52303 / 3.29 ( 3855) metal coordination : bond 0.00562 / 0.40 ( 22) metal coordination : angle 2.46674 / 1.62 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 262 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7151 (mm) REVERT: A 1023 MET cc_start: 0.7154 (tpt) cc_final: 0.6933 (tpt) REVERT: A 1027 ARG cc_start: 0.8714 (mmm-85) cc_final: 0.8509 (mmt180) REVERT: B 49 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8060 (pp) REVERT: B 497 ASN cc_start: 0.7818 (t0) cc_final: 0.7528 (t0) REVERT: B 672 ASN cc_start: 0.8222 (p0) cc_final: 0.7973 (p0) REVERT: B 743 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.6618 (pp30) REVERT: B 1111 ASN cc_start: 0.7879 (m-40) cc_final: 0.7501 (t0) REVERT: B 1113 GLN cc_start: 0.7464 (tp40) cc_final: 0.7256 (tp-100) REVERT: D 93 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.7505 (tp) REVERT: D 130 ASN cc_start: 0.7013 (t0) cc_final: 0.6782 (m-40) REVERT: E 197 GLU cc_start: 0.7776 (mp0) cc_final: 0.7462 (mp0) REVERT: E 269 LYS cc_start: 0.3785 (pttm) cc_final: 0.3385 (ptmt) REVERT: F 141 MET cc_start: 0.0921 (ttm) cc_final: -0.1408 (mmt) REVERT: F 162 LYS cc_start: 0.4302 (mmtm) cc_final: 0.3035 (mttp) REVERT: F 227 ARG cc_start: 0.5674 (mpt-90) cc_final: 0.5329 (mtm110) REVERT: G 382 LYS cc_start: 0.8044 (mttp) cc_final: 0.7748 (mtmm) REVERT: G 456 ASP cc_start: 0.8651 (t0) cc_final: 0.8339 (t0) REVERT: G 505 MET cc_start: 0.0371 (ttp) cc_final: 0.0020 (tpp) REVERT: G 554 PHE cc_start: 0.7163 (t80) cc_final: 0.6767 (t80) REVERT: G 745 MET cc_start: 0.5738 (mpp) cc_final: 0.5466 (mpp) REVERT: H 80 HIS cc_start: 0.1769 (m170) cc_final: 0.0870 (m-70) REVERT: H 86 ARG cc_start: 0.1875 (mtt180) cc_final: 0.1112 (mmm160) REVERT: I 230 LYS cc_start: 0.6294 (mmmt) cc_final: 0.5861 (mttm) outliers start: 67 outliers final: 40 residues processed: 312 average time/residue: 0.1840 time to fit residues: 93.2491 Evaluate side-chains 283 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 743 GLN Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 944 GLU Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 212 HIS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 136 ASN Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 220 MET Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 151 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 66 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 317 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 152 optimal weight: 0.0270 chunk 203 optimal weight: 7.9990 chunk 252 optimal weight: 0.9980 chunk 292 optimal weight: 8.9990 chunk 126 optimal weight: 0.0000 chunk 5 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 overall best weight: 0.4442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS B 186 GLN B 189 HIS ** F 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 GLN ** G 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.230882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.179698 restraints weight = 39170.332| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 2.72 r_work: 0.3505 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28665 Z= 0.118 Angle : 0.528 9.286 38630 Z= 0.273 Chirality : 0.041 0.181 4310 Planarity : 0.004 0.060 4967 Dihedral : 3.994 33.864 3780 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.02 % Allowed : 14.27 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.14), residues: 3474 helix: 2.38 (0.14), residues: 1326 sheet: -0.31 (0.20), residues: 673 loop : -1.05 (0.15), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 114 TYR 0.012 0.001 TYR G 277 PHE 0.029 0.001 PHE E 127 TRP 0.015 0.001 TRP G 533 HIS 0.004 0.001 HIS B1140 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (28642) covalent geometry : angle 0.52557 / 0.27 (38613) SS BOND : bond 0.00069 / 0.04 ( 1) SS BOND : angle 0.51375 / 0.34 ( 2) hydrogen bonds : bond 0.03249 / 2.17 ( 1312) hydrogen bonds : angle 4.47506 / 3.26 ( 3855) metal coordination : bond 0.00538 / 0.39 ( 22) metal coordination : angle 2.36997 / 1.56 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 255 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8047 (pp) REVERT: B 1080 ARG cc_start: 0.8346 (mmt-90) cc_final: 0.7305 (ptm160) REVERT: B 1113 GLN cc_start: 0.7499 (tp40) cc_final: 0.7290 (tp-100) REVERT: D 130 ASN cc_start: 0.6850 (t0) cc_final: 0.6624 (m-40) REVERT: E 197 GLU cc_start: 0.7807 (mp0) cc_final: 0.7519 (mp0) REVERT: E 269 LYS cc_start: 0.3873 (pttm) cc_final: 0.3515 (ptmt) REVERT: F 141 MET cc_start: 0.1161 (ttm) cc_final: -0.1230 (mmt) REVERT: F 162 LYS cc_start: 0.4001 (mmtm) cc_final: 0.2783 (mttp) REVERT: F 227 ARG cc_start: 0.5545 (mpt-90) cc_final: 0.5287 (mtm110) REVERT: G 382 LYS cc_start: 0.7974 (mttp) cc_final: 0.7711 (mtmm) REVERT: G 456 ASP cc_start: 0.8477 (t0) cc_final: 0.8184 (t0) REVERT: G 505 MET cc_start: 0.0547 (ttp) cc_final: 0.0172 (tpp) REVERT: H 80 HIS cc_start: 0.1702 (m170) cc_final: 0.0797 (m-70) REVERT: H 86 ARG cc_start: 0.1843 (mtt180) cc_final: 0.1146 (mmm160) REVERT: I 126 GLU cc_start: 0.5971 (tp30) cc_final: 0.5193 (tp30) REVERT: I 230 LYS cc_start: 0.6201 (mmmt) cc_final: 0.5789 (mttm) outliers start: 63 outliers final: 47 residues processed: 304 average time/residue: 0.1837 time to fit residues: 90.4730 Evaluate side-chains 289 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 241 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 680 CYS Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 944 GLU Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1071 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 212 HIS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 136 ASN Chi-restraints excluded: chain G residue 220 MET Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 1036 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 285 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 265 optimal weight: 0.8980 chunk 124 optimal weight: 0.0870 chunk 112 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 chunk 301 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 309 optimal weight: 0.0010 chunk 194 optimal weight: 3.9990 overall best weight: 0.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS B 186 GLN B 189 HIS B 743 GLN ** F 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.229620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.172357 restraints weight = 38606.930| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 2.79 r_work: 0.3467 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28665 Z= 0.131 Angle : 0.544 10.609 38630 Z= 0.279 Chirality : 0.041 0.174 4310 Planarity : 0.004 0.060 4967 Dihedral : 3.987 33.523 3780 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.08 % Allowed : 14.66 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3474 helix: 2.37 (0.14), residues: 1326 sheet: -0.33 (0.20), residues: 673 loop : -1.07 (0.15), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 114 TYR 0.016 0.001 TYR G 160 PHE 0.029 0.001 PHE E 127 TRP 0.013 0.001 TRP G 533 HIS 0.012 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (28642) covalent geometry : angle 0.54173 / 0.28 (38613) SS BOND : bond 0.00060 / 0.03 ( 1) SS BOND : angle 0.66182 / 0.44 ( 2) hydrogen bonds : bond 0.03263 / 2.17 ( 1312) hydrogen bonds : angle 4.44751 / 3.24 ( 3855) metal coordination : bond 0.00508 / 0.35 ( 22) metal coordination : angle 2.37729 / 1.57 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 260 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8080 (pp) REVERT: B 536 HIS cc_start: 0.6672 (m-70) cc_final: 0.6404 (m-70) REVERT: B 743 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6687 (pp30) REVERT: B 1080 ARG cc_start: 0.8204 (mmt-90) cc_final: 0.7346 (ptm160) REVERT: D 93 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8273 (mt) REVERT: D 130 ASN cc_start: 0.6825 (t0) cc_final: 0.6561 (m-40) REVERT: D 162 MET cc_start: 0.7953 (ttp) cc_final: 0.7676 (ttm) REVERT: E 197 GLU cc_start: 0.7735 (mp0) cc_final: 0.7440 (mp0) REVERT: E 269 LYS cc_start: 0.3912 (pttm) cc_final: 0.3553 (ptmt) REVERT: F 141 MET cc_start: 0.0946 (ttm) cc_final: -0.1269 (mmt) REVERT: F 162 LYS cc_start: 0.4334 (mmtm) cc_final: 0.3208 (mttp) REVERT: F 227 ARG cc_start: 0.5627 (mpt-90) cc_final: 0.5365 (mtm110) REVERT: G 354 ASN cc_start: 0.7395 (t0) cc_final: 0.7119 (t0) REVERT: G 456 ASP cc_start: 0.8705 (t0) cc_final: 0.8401 (t0) REVERT: G 505 MET cc_start: 0.0189 (ttp) cc_final: -0.0145 (tpp) REVERT: H 80 HIS cc_start: 0.1775 (m170) cc_final: 0.0934 (m-70) REVERT: H 86 ARG cc_start: 0.1916 (mtt180) cc_final: 0.1115 (mmp-170) REVERT: I 126 GLU cc_start: 0.5912 (tp30) cc_final: 0.5156 (tp30) REVERT: I 230 LYS cc_start: 0.6265 (mmmt) cc_final: 0.5873 (mttm) outliers start: 65 outliers final: 54 residues processed: 306 average time/residue: 0.1819 time to fit residues: 91.6250 Evaluate side-chains 298 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 680 CYS Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 743 GLN Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 944 GLU Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1071 SER Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 212 HIS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 136 ASN Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 220 MET Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 1036 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 240 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 chunk 324 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 chunk 314 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 44 optimal weight: 0.0020 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS B 186 GLN B 189 HIS ** F 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.230535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.175540 restraints weight = 39112.611| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.84 r_work: 0.3447 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28665 Z= 0.142 Angle : 0.553 11.494 38630 Z= 0.283 Chirality : 0.041 0.183 4310 Planarity : 0.004 0.062 4967 Dihedral : 4.021 34.034 3780 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.14 % Allowed : 14.88 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.14), residues: 3474 helix: 2.34 (0.14), residues: 1327 sheet: -0.38 (0.20), residues: 684 loop : -1.09 (0.15), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 114 TYR 0.025 0.001 TYR G 160 PHE 0.029 0.001 PHE E 127 TRP 0.010 0.001 TRP B 893 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (28642) covalent geometry : angle 0.55100 / 0.28 (38613) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 0.74449 / 0.50 ( 2) hydrogen bonds : bond 0.03287 / 2.19 ( 1312) hydrogen bonds : angle 4.45263 / 3.24 ( 3855) metal coordination : bond 0.00498 / 0.34 ( 22) metal coordination : angle 2.38576 / 1.57 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 247 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8107 (pp) REVERT: B 536 HIS cc_start: 0.6944 (m-70) cc_final: 0.6606 (m-70) REVERT: B 672 ASN cc_start: 0.8390 (p0) cc_final: 0.8160 (p0) REVERT: B 1080 ARG cc_start: 0.8520 (mmt-90) cc_final: 0.7350 (ptm160) REVERT: D 93 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8311 (mt) REVERT: D 130 ASN cc_start: 0.6941 (t0) cc_final: 0.6607 (m-40) REVERT: E 197 GLU cc_start: 0.7830 (mp0) cc_final: 0.7539 (mp0) REVERT: E 269 LYS cc_start: 0.4045 (pttm) cc_final: 0.3716 (ptmt) REVERT: F 11 MET cc_start: 0.1251 (ptm) cc_final: 0.0935 (ptm) REVERT: F 141 MET cc_start: 0.0880 (ttm) cc_final: -0.1306 (mmt) REVERT: F 162 LYS cc_start: 0.4505 (mmtm) cc_final: 0.2925 (mttp) REVERT: F 227 ARG cc_start: 0.5671 (mpt-90) cc_final: 0.5386 (mtm110) REVERT: G 126 LEU cc_start: 0.3719 (OUTLIER) cc_final: 0.3363 (mt) REVERT: G 251 MET cc_start: 0.6655 (mmm) cc_final: 0.6309 (mmm) REVERT: G 354 ASN cc_start: 0.7387 (t0) cc_final: 0.7095 (t0) REVERT: G 456 ASP cc_start: 0.8741 (t0) cc_final: 0.8425 (t0) REVERT: G 505 MET cc_start: 0.0138 (ttp) cc_final: -0.0189 (tpp) REVERT: H 80 HIS cc_start: 0.1669 (m170) cc_final: 0.0764 (m-70) REVERT: H 86 ARG cc_start: 0.1898 (mtt180) cc_final: 0.1106 (mmp-170) REVERT: I 126 GLU cc_start: 0.5877 (tp30) cc_final: 0.5159 (tp30) REVERT: I 230 LYS cc_start: 0.6350 (mmmt) cc_final: 0.5938 (mttm) outliers start: 67 outliers final: 57 residues processed: 295 average time/residue: 0.1724 time to fit residues: 84.0664 Evaluate side-chains 303 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 243 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 680 CYS Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 944 GLU Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1071 SER Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 212 HIS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 136 ASN Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 220 MET Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 1036 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 193 optimal weight: 20.0000 chunk 326 optimal weight: 7.9990 chunk 299 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 217 optimal weight: 6.9990 chunk 256 optimal weight: 4.9990 chunk 205 optimal weight: 0.7980 chunk 265 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 200 optimal weight: 9.9990 chunk 236 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS B 156 ASN B 186 GLN B 189 HIS B 743 GLN ** F 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.225340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.165317 restraints weight = 38601.196| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 3.21 r_work: 0.3344 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 28665 Z= 0.291 Angle : 0.682 11.375 38630 Z= 0.349 Chirality : 0.046 0.256 4310 Planarity : 0.005 0.066 4967 Dihedral : 4.506 34.036 3780 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.24 % Allowed : 15.04 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.14), residues: 3474 helix: 2.11 (0.14), residues: 1334 sheet: -0.71 (0.19), residues: 687 loop : -1.14 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 188 TYR 0.024 0.002 TYR B 613 PHE 0.034 0.002 PHE B1030 TRP 0.019 0.002 TRP H 27 HIS 0.023 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.29 (28642) covalent geometry : angle 0.68000 / 0.35 (38613) SS BOND : bond 0.00106 / 0.06 ( 1) SS BOND : angle 1.90966 / 1.27 ( 2) hydrogen bonds : bond 0.04003 / 2.70 ( 1312) hydrogen bonds : angle 4.74524 / 3.46 ( 3855) metal coordination : bond 0.00552 / 0.33 ( 22) metal coordination : angle 2.65779 / 1.75 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 246 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8207 (pp) REVERT: B 743 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6764 (pp30) REVERT: B 1080 ARG cc_start: 0.8504 (mmt-90) cc_final: 0.7501 (mtp-110) REVERT: D 93 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8127 (mt) REVERT: D 111 MET cc_start: 0.4544 (pmm) cc_final: 0.3550 (tpp) REVERT: D 130 ASN cc_start: 0.7156 (t0) cc_final: 0.6756 (m-40) REVERT: E 197 GLU cc_start: 0.7774 (mp0) cc_final: 0.7415 (mp0) REVERT: F 11 MET cc_start: 0.1211 (ptm) cc_final: 0.0936 (ptm) REVERT: F 141 MET cc_start: 0.0680 (ttm) cc_final: -0.1342 (mmt) REVERT: F 227 ARG cc_start: 0.5752 (mpt-90) cc_final: 0.5370 (mtm110) REVERT: G 456 ASP cc_start: 0.8870 (t0) cc_final: 0.8606 (t0) REVERT: G 505 MET cc_start: 0.0188 (ttp) cc_final: -0.0170 (tpp) REVERT: I 126 GLU cc_start: 0.5928 (tp30) cc_final: 0.5168 (tp30) REVERT: I 230 LYS cc_start: 0.6323 (mmmt) cc_final: 0.5952 (mttm) outliers start: 70 outliers final: 55 residues processed: 302 average time/residue: 0.1801 time to fit residues: 88.5225 Evaluate side-chains 296 residues out of total 3125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 238 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 680 CYS Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 743 GLN Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 944 GLU Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1071 SER Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 212 HIS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 136 ASN Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 498 MET Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 1036 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 334 optimal weight: 20.0000 chunk 134 optimal weight: 0.0980 chunk 189 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 0.1980 chunk 336 optimal weight: 4.9990 chunk 301 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 309 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS B 156 ASN B 743 GLN ** F 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 GLN ** G 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.225128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.164741 restraints weight = 38181.771| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 3.04 r_work: 0.3365 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.276 28665 Z= 0.297 Angle : 0.845 59.195 38630 Z= 0.474 Chirality : 0.045 0.594 4310 Planarity : 0.005 0.151 4967 Dihedral : 4.508 34.030 3780 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.98 % Allowed : 15.46 % Favored : 82.56 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3474 helix: 2.11 (0.14), residues: 1334 sheet: -0.74 (0.19), residues: 685 loop : -1.15 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 243 TYR 0.022 0.002 TYR B 613 PHE 0.030 0.002 PHE B1030 TRP 0.016 0.002 TRP H 27 HIS 0.158 0.002 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.30 (28642) covalent geometry : angle 0.84384 / 0.47 (38613) SS BOND : bond 0.00158 / 0.08 ( 1) SS BOND : angle 1.47596 / 0.98 ( 2) hydrogen bonds : bond 0.03935 / 2.64 ( 1312) hydrogen bonds : angle 4.74350 / 3.46 ( 3855) metal coordination : bond 0.00516 / 0.31 ( 22) metal coordination : angle 2.67844 / 1.76 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9081.54 seconds wall clock time: 155 minutes 42.79 seconds (9342.79 seconds total)