Starting phenix.real_space_refine on Tue Aug 26 21:22:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gj1_40082/08_2025/8gj1_40082_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gj1_40082/08_2025/8gj1_40082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gj1_40082/08_2025/8gj1_40082_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gj1_40082/08_2025/8gj1_40082_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gj1_40082/08_2025/8gj1_40082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gj1_40082/08_2025/8gj1_40082.map" } resolution = 3.0 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= 0.001 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: 10 Type Number sf(0) Gaussians Zn 4 6.06 5 Al 3 5.89 5 P 57 5.49 5 Mg 3 5.21 5 S 108 5.16 5 C 13030 2.51 5 N 3744 2.21 5 O 4021 1.98 5 F 12 1.80 5 H 20553 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41535 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 5496 Classifications: {'peptide': 343} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "B" Number of atoms: 5743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5743 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain: "C" Number of atoms: 5747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5747 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain: "D" Number of atoms: 5731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5731 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Chain: "E" Number of atoms: 5190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5190 Classifications: {'peptide': 334} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "F" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 474 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "H" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 5698 Classifications: {'peptide': 366} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 345} Chain: "I" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 5698 Classifications: {'peptide': 366} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 345} Chain: "X" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 732 Classifications: {'DNA': 23} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 22} Chain: "Y" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 923 Classifications: {'DNA': 29} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 28} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6468 SG CYS B 64 87.087 81.901 116.226 1.00154.81 S ATOM 6585 SG CYS B 73 90.536 80.571 116.754 1.00168.20 S ATOM 6618 SG CYS B 76 87.623 78.387 117.751 1.00170.77 S ATOM 6654 SG CYS B 79 88.185 78.878 114.136 1.00162.92 S ATOM 12200 SG CYS C 64 102.993 42.155 93.677 1.00130.29 S ATOM 12317 SG CYS C 73 104.096 38.852 92.307 1.00153.59 S ATOM 12350 SG CYS C 76 100.952 38.937 94.396 1.00146.79 S ATOM 12386 SG CYS C 79 100.776 40.445 91.042 1.00145.85 S ATOM 17958 SG CYS D 64 74.442 17.262 64.038 1.00123.48 S ATOM 18075 SG CYS D 73 72.118 15.198 61.864 1.00142.72 S ATOM 18108 SG CYS D 76 70.873 16.337 65.220 1.00145.21 S ATOM 18144 SG CYS D 79 71.295 18.878 62.544 1.00140.97 S ATOM 23523 SG CYS E 50 31.705 34.856 52.621 1.00131.73 S ATOM 23654 SG CYS E 59 27.992 35.114 53.373 1.00171.77 S ATOM 23687 SG CYS E 62 30.364 35.268 56.239 1.00160.10 S ATOM 23728 SG CYS E 65 30.255 38.166 53.851 1.00149.58 S Time building chain proxies: 6.13, per 1000 atoms: 0.15 Number of scatterers: 41535 At special positions: 0 Unit cell: (121.8, 119.28, 152.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 4 29.99 S 108 16.00 P 57 15.00 Al 3 13.00 Mg 3 11.99 F 12 9.00 O 4021 8.00 N 3744 7.00 C 13030 6.00 H 20553 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 915.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 704 " pdb="ZN ZN B 704 " - pdb=" SG CYS B 76 " pdb="ZN ZN B 704 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 704 " - pdb=" SG CYS B 64 " pdb="ZN ZN B 704 " - pdb=" SG CYS B 79 " pdb=" ZN C 704 " pdb="ZN ZN C 704 " - pdb=" SG CYS C 76 " pdb="ZN ZN C 704 " - pdb=" SG CYS C 79 " pdb="ZN ZN C 704 " - pdb=" SG CYS C 73 " pdb="ZN ZN C 704 " - pdb=" SG CYS C 64 " pdb=" ZN D 704 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 76 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 73 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 79 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 64 " pdb=" ZN E2001 " pdb="ZN ZN E2001 " - pdb=" SG CYS E 59 " pdb="ZN ZN E2001 " - pdb=" SG CYS E 62 " pdb="ZN ZN E2001 " - pdb=" SG CYS E 65 " pdb="ZN ZN E2001 " - pdb=" SG CYS E 50 " Number of angles added : 24 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4774 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 14 sheets defined 54.9% alpha, 14.6% beta 22 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 6.41 Creating SS restraints... Processing helix chain 'A' and resid 5 through 7 No H-bonds generated for 'chain 'A' and resid 5 through 7' Processing helix chain 'A' and resid 8 through 16 removed outlier: 3.917A pdb=" N GLN A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 46 removed outlier: 3.709A pdb=" N LEU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.882A pdb=" N ILE A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 118 through 123 removed outlier: 3.564A pdb=" N ASN A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.866A pdb=" N ASN A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 225 through 240 Processing helix chain 'A' and resid 242 through 264 removed outlier: 3.773A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 268 through 277 Processing helix chain 'A' and resid 279 through 293 removed outlier: 4.379A pdb=" N GLY A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N MET A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 319 through 332 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 50 through 63 removed outlier: 3.555A pdb=" N ASN B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 100 through 110 removed outlier: 3.612A pdb=" N THR B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 128 through 131 Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 163 through 169 removed outlier: 3.585A pdb=" N ARG B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 195 Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.852A pdb=" N GLU B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 261 through 274 Processing helix chain 'B' and resid 277 through 298 Processing helix chain 'B' and resid 299 through 302 removed outlier: 4.072A pdb=" N LEU B 302 " --> pdb=" O PRO B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 299 through 302' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 321 through 339 removed outlier: 3.523A pdb=" N ILE B 325 " --> pdb=" O PRO B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'C' and resid 5 through 10 Processing helix chain 'C' and resid 21 through 35 Processing helix chain 'C' and resid 50 through 63 removed outlier: 3.774A pdb=" N ILE C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 100 through 110 removed outlier: 3.525A pdb=" N THR C 104 " --> pdb=" O LYS C 100 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'C' and resid 132 through 139 removed outlier: 3.505A pdb=" N LEU C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 145 Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 163 through 168 Processing helix chain 'C' and resid 179 through 195 Processing helix chain 'C' and resid 199 through 210 Processing helix chain 'C' and resid 213 through 229 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.971A pdb=" N ALA C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 275 Processing helix chain 'C' and resid 277 through 298 Processing helix chain 'C' and resid 299 through 302 removed outlier: 3.957A pdb=" N LEU C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 299 through 302' Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 306 through 318 removed outlier: 4.562A pdb=" N LEU C 311 " --> pdb=" O ALA C 307 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG C 318 " --> pdb=" O ARG C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 339 Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 344 through 359 Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 21 through 35 Processing helix chain 'D' and resid 50 through 63 Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 100 through 109 removed outlier: 3.606A pdb=" N THR D 104 " --> pdb=" O LYS D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 131 Processing helix chain 'D' and resid 132 through 145 removed outlier: 4.107A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 Processing helix chain 'D' and resid 179 through 195 Processing helix chain 'D' and resid 199 through 210 Processing helix chain 'D' and resid 213 through 228 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 247 through 259 Processing helix chain 'D' and resid 260 through 275 Processing helix chain 'D' and resid 277 through 298 Processing helix chain 'D' and resid 299 through 302 removed outlier: 3.954A pdb=" N LEU D 302 " --> pdb=" O PRO D 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 299 through 302' Processing helix chain 'D' and resid 303 through 308 removed outlier: 3.758A pdb=" N MET D 306 " --> pdb=" O GLY D 303 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 307 " --> pdb=" O ASN D 304 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA D 308 " --> pdb=" O ASP D 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 308' Processing helix chain 'D' and resid 309 through 320 removed outlier: 3.516A pdb=" N MET D 313 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 338 Processing helix chain 'D' and resid 344 through 358 removed outlier: 3.549A pdb=" N ALA D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 6 No H-bonds generated for 'chain 'E' and resid 4 through 6' Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.715A pdb=" N ALA E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 89 through 101 removed outlier: 3.768A pdb=" N VAL E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN E 101 " --> pdb=" O THR E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 121 through 134 removed outlier: 3.546A pdb=" N LEU E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS E 130 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 152 through 158 removed outlier: 3.697A pdb=" N ARG E 158 " --> pdb=" O THR E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 199 through 207 Processing helix chain 'E' and resid 208 through 227 Proline residue: E 225 - end of helix Processing helix chain 'E' and resid 228 through 231 removed outlier: 3.694A pdb=" N SER E 231 " --> pdb=" O ASP E 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 228 through 231' Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 240 through 261 Processing helix chain 'E' and resid 270 through 281 Processing helix chain 'E' and resid 282 through 303 Processing helix chain 'E' and resid 307 through 323 removed outlier: 3.527A pdb=" N LEU E 311 " --> pdb=" O ASN E 307 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 323 " --> pdb=" O ILE E 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 13 Processing helix chain 'F' and resid 21 through 25 Processing helix chain 'H' and resid 7 through 18 removed outlier: 4.250A pdb=" N LYS H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Proline residue: H 13 - end of helix Processing helix chain 'H' and resid 27 through 30 Processing helix chain 'H' and resid 72 through 82 removed outlier: 3.528A pdb=" N LEU H 82 " --> pdb=" O ILE H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 116 removed outlier: 3.727A pdb=" N ASP H 115 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 142 removed outlier: 3.539A pdb=" N MET H 135 " --> pdb=" O PRO H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 157 removed outlier: 3.911A pdb=" N ASN H 156 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY H 157 " --> pdb=" O TYR H 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 152 through 157' Processing helix chain 'H' and resid 196 through 207 Processing helix chain 'H' and resid 260 through 274 Processing helix chain 'H' and resid 320 through 331 Processing helix chain 'I' and resid 7 through 11 Processing helix chain 'I' and resid 12 through 19 Processing helix chain 'I' and resid 27 through 31 Processing helix chain 'I' and resid 72 through 82 removed outlier: 3.605A pdb=" N LEU I 82 " --> pdb=" O ILE I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 116 removed outlier: 3.660A pdb=" N ASP I 115 " --> pdb=" O PRO I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 144 removed outlier: 3.797A pdb=" N MET I 135 " --> pdb=" O PRO I 131 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE I 144 " --> pdb=" O GLU I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 155 Processing helix chain 'I' and resid 197 through 207 Processing helix chain 'I' and resid 243 through 248 removed outlier: 4.131A pdb=" N VAL I 247 " --> pdb=" O ASP I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 271 Processing helix chain 'I' and resid 321 through 332 removed outlier: 3.593A pdb=" N LYS I 332 " --> pdb=" O LEU I 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 5.988A pdb=" N ILE A 2 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR A 138 " --> pdb=" O ILE A 2 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A 4 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA A 20 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N VAL A 137 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 22 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N CYS A 139 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 24 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.080A pdb=" N GLU A 161 " --> pdb=" O LEU A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 94 removed outlier: 6.276A pdb=" N LYS B 121 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU B 153 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA B 155 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE B 125 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA B 40 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N PHE B 173 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU B 42 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 360 through 361 Processing sheet with id=AA5, first strand: chain 'C' and resid 90 through 94 removed outlier: 6.321A pdb=" N LYS C 121 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LEU C 153 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA C 155 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE C 125 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR C 41 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 90 through 94 removed outlier: 6.199A pdb=" N LYS D 121 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU D 153 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ALA D 155 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE D 125 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TYR D 41 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N THR D 156 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE D 43 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 77 through 79 removed outlier: 3.982A pdb=" N ALA E 144 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 2 through 6 Processing sheet with id=AA9, first strand: chain 'H' and resid 66 through 71 removed outlier: 6.574A pdb=" N ASN H 32 " --> pdb=" O THR H 47 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N THR H 47 " --> pdb=" O ASN H 32 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASN H 222 " --> pdb=" O GLY H 219 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU H 214 " --> pdb=" O THR H 129 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR H 129 " --> pdb=" O LEU H 214 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL H 216 " --> pdb=" O GLU H 127 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU H 127 " --> pdb=" O VAL H 216 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE H 218 " --> pdb=" O GLU H 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 309 through 310 removed outlier: 12.424A pdb=" N CYS H 180 " --> pdb=" O THR H 172 " (cutoff:3.500A) removed outlier: 11.363A pdb=" N THR H 172 " --> pdb=" O CYS H 180 " (cutoff:3.500A) removed outlier: 12.490A pdb=" N MET H 182 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 11.299A pdb=" N VAL H 170 " --> pdb=" O MET H 182 " (cutoff:3.500A) removed outlier: 10.573A pdb=" N ILE H 184 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 11.136A pdb=" N ARG H 168 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLN H 186 " --> pdb=" O GLU H 166 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLU H 166 " --> pdb=" O GLN H 186 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY H 164 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER H 190 " --> pdb=" O THR H 162 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR H 162 " --> pdb=" O SER H 190 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER H 192 " --> pdb=" O PHE H 160 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE H 160 " --> pdb=" O SER H 192 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE H 194 " --> pdb=" O MET H 158 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N MET H 158 " --> pdb=" O ILE H 194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 304 through 306 Processing sheet with id=AB3, first strand: chain 'I' and resid 3 through 6 removed outlier: 4.099A pdb=" N ALA I 89 " --> pdb=" O ARG I 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 66 through 71 removed outlier: 7.003A pdb=" N ASN I 32 " --> pdb=" O THR I 47 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N THR I 47 " --> pdb=" O ASN I 32 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 191 through 196 removed outlier: 6.063A pdb=" N GLY I 157 " --> pdb=" O THR I 172 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N THR I 172 " --> pdb=" O GLY I 157 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N SER I 356 " --> pdb=" O SER I 181 " (cutoff:3.500A) removed outlier: 16.004A pdb=" N SER I 354 " --> pdb=" O PRO I 183 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ALA I 357 " --> pdb=" O ASP I 351 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASP I 351 " --> pdb=" O ALA I 357 " (cutoff:3.500A) 1102 hydrogen bonds defined for protein. 3153 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 9.15 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20534 1.03 - 1.23: 43 1.23 - 1.42: 8688 1.42 - 1.62: 12556 1.62 - 1.81: 193 Bond restraints: 42014 Sorted by residual: bond pdb=" F1 ALF B 703 " pdb="AL ALF B 703 " ideal model delta sigma weight residual 1.684 1.801 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" F3 ALF C 703 " pdb="AL ALF C 703 " ideal model delta sigma weight residual 1.685 1.800 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" F1 ALF D 703 " pdb="AL ALF D 703 " ideal model delta sigma weight residual 1.684 1.798 -0.114 2.00e-02 2.50e+03 3.28e+01 bond pdb=" F1 ALF C 703 " pdb="AL ALF C 703 " ideal model delta sigma weight residual 1.684 1.798 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" F2 ALF D 703 " pdb="AL ALF D 703 " ideal model delta sigma weight residual 1.685 1.799 -0.114 2.00e-02 2.50e+03 3.26e+01 ... (remaining 42009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.25: 76134 14.25 - 28.49: 12 28.49 - 42.74: 0 42.74 - 56.99: 0 56.99 - 71.24: 6 Bond angle restraints: 76152 Sorted by residual: angle pdb=" F1 ALF B 703 " pdb="AL ALF B 703 " pdb=" F2 ALF B 703 " ideal model delta sigma weight residual 108.68 179.92 -71.24 3.00e+00 1.11e-01 5.64e+02 angle pdb=" F1 ALF D 703 " pdb="AL ALF D 703 " pdb=" F2 ALF D 703 " ideal model delta sigma weight residual 108.68 179.89 -71.21 3.00e+00 1.11e-01 5.63e+02 angle pdb=" F1 ALF C 703 " pdb="AL ALF C 703 " pdb=" F2 ALF C 703 " ideal model delta sigma weight residual 108.68 179.79 -71.11 3.00e+00 1.11e-01 5.62e+02 angle pdb=" F3 ALF D 703 " pdb="AL ALF D 703 " pdb=" F4 ALF D 703 " ideal model delta sigma weight residual 109.63 179.93 -70.30 3.00e+00 1.11e-01 5.49e+02 angle pdb=" F3 ALF C 703 " pdb="AL ALF C 703 " pdb=" F4 ALF C 703 " ideal model delta sigma weight residual 109.63 179.65 -70.02 3.00e+00 1.11e-01 5.45e+02 ... (remaining 76147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.48: 18674 33.48 - 66.95: 664 66.95 - 100.43: 5 100.43 - 133.91: 2 133.91 - 167.39: 4 Dihedral angle restraints: 19349 sinusoidal: 11161 harmonic: 8188 Sorted by residual: dihedral pdb=" C5' ADP C 701 " pdb=" O5' ADP C 701 " pdb=" PA ADP C 701 " pdb=" O2A ADP C 701 " ideal model delta sinusoidal sigma weight residual -60.00 107.39 -167.39 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O2A ADP D 701 " pdb=" O3A ADP D 701 " pdb=" PA ADP D 701 " pdb=" PB ADP D 701 " ideal model delta sinusoidal sigma weight residual -60.00 102.63 -162.63 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" O2A ADP C 701 " pdb=" O3A ADP C 701 " pdb=" PA ADP C 701 " pdb=" PB ADP C 701 " ideal model delta sinusoidal sigma weight residual -60.00 101.08 -161.07 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 19346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2245 0.029 - 0.057: 780 0.057 - 0.086: 166 0.086 - 0.115: 154 0.115 - 0.143: 40 Chirality restraints: 3385 Sorted by residual: chirality pdb=" CA PRO B 364 " pdb=" N PRO B 364 " pdb=" C PRO B 364 " pdb=" CB PRO B 364 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA PRO H 297 " pdb=" N PRO H 297 " pdb=" C PRO H 297 " pdb=" CB PRO H 297 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE H 292 " pdb=" N ILE H 292 " pdb=" C ILE H 292 " pdb=" CB ILE H 292 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 3382 not shown) Planarity restraints: 6071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 365 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO B 366 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 366 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 366 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 130 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.25e+00 pdb=" N PRO H 131 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO H 131 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO H 131 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 286 " 0.006 2.00e-02 2.50e+03 1.10e-02 1.22e+00 pdb=" C MET A 286 " -0.019 2.00e-02 2.50e+03 pdb=" O MET A 286 " 0.007 2.00e-02 2.50e+03 pdb=" N GLY A 287 " 0.006 2.00e-02 2.50e+03 ... (remaining 6068 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.24: 3182 2.24 - 2.83: 91754 2.83 - 3.42: 104211 3.42 - 4.01: 143505 4.01 - 4.60: 222545 Nonbonded interactions: 565197 Sorted by model distance: nonbonded pdb=" OD2 ASP C 89 " pdb=" H GLY C 118 " model vdw 1.645 2.450 nonbonded pdb=" O GLU A 49 " pdb=" HG1 THR A 79 " model vdw 1.661 2.450 nonbonded pdb=" O CYS D 64 " pdb="HH12 ARG D 119 " model vdw 1.663 2.450 nonbonded pdb=" H1 MET A 1 " pdb=" O ALA A 131 " model vdw 1.667 2.450 nonbonded pdb=" O LEU A 67 " pdb="HE22 GLN A 78 " model vdw 1.670 2.450 ... (remaining 565192 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 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name H \ E2 or name HH )) or resid 4 through 361 or resid 364 through 367 or resid 701 th \ rough 704)) selection = (chain 'C' and (resid 3 through 361 or resid 364 through 367 or resid 701 throug \ h 704)) selection = (chain 'D' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name H \ E2 or name HH )) or resid 4 through 361 or resid 404 through 407 or resid 701 th \ rough 704)) } ncs_group { reference = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 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: 0.160 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 46.200 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 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 : 0.004 0.229 21479 Z= 0.276 Angle : 1.205 71.237 29382 Z= 0.445 Chirality : 0.037 0.143 3385 Planarity : 0.003 0.038 3633 Dihedral : 13.985 167.386 8181 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.02 % Favored : 97.78 % Rotamer: Outliers : 2.45 % Allowed : 4.52 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.07 (0.18), residues: 2521 helix: 3.19 (0.16), residues: 1233 sheet: 1.39 (0.25), residues: 450 loop : 0.65 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 176 TYR 0.005 0.001 TYR D 123 PHE 0.006 0.001 PHE D 120 TRP 0.007 0.001 TRP A 217 HIS 0.003 0.000 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00341 (21461) covalent geometry : angle 1.20347 (29358) hydrogen bonds : bond 0.13359 ( 1152) hydrogen bonds : angle 4.55472 ( 3253) metal coordination : bond 0.00252 ( 16) metal coordination : angle 2.72172 ( 24) Misc. bond : bond 0.22875 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Evaluate side-chains 514 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 462 time to evaluate : 0.943 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8648 (m-40) cc_final: 0.8287 (m110) REVERT: A 68 CYS cc_start: 0.8595 (p) cc_final: 0.8146 (p) REVERT: A 146 GLN cc_start: 0.8950 (mp10) cc_final: 0.8646 (mp10) REVERT: A 157 GLN cc_start: 0.9079 (tt0) cc_final: 0.8826 (tm-30) REVERT: A 288 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8780 (tm-30) REVERT: B 145 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8559 (tm-30) REVERT: B 214 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7797 (tt) REVERT: B 254 GLU cc_start: 0.8814 (tt0) cc_final: 0.8405 (tm-30) REVERT: B 270 GLU cc_start: 0.9020 (tt0) cc_final: 0.8786 (tt0) REVERT: C 81 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8863 (mm-30) REVERT: D 126 ASP cc_start: 0.9166 (m-30) cc_final: 0.8842 (m-30) REVERT: D 277 GLU cc_start: 0.8867 (tp30) cc_final: 0.8462 (tm-30) REVERT: D 306 MET cc_start: 0.8257 (mtt) cc_final: 0.8017 (mtp) REVERT: D 338 GLU cc_start: 0.8693 (pt0) cc_final: 0.8454 (pp20) REVERT: D 351 MET cc_start: 0.8841 (ttm) cc_final: 0.8590 (mtp) REVERT: E 98 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: E 170 GLN cc_start: 0.8767 (tp40) cc_final: 0.8472 (tm-30) REVERT: E 309 GLU cc_start: 0.8606 (tt0) cc_final: 0.8387 (tt0) REVERT: F 18 SER cc_start: 0.9088 (t) cc_final: 0.8730 (p) REVERT: F 26 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8164 (mm-40) REVERT: H 64 GLU cc_start: 0.8649 (tt0) cc_final: 0.8441 (tm-30) REVERT: H 87 GLU cc_start: 0.8326 (tt0) cc_final: 0.8089 (tm-30) REVERT: H 161 GLU cc_start: 0.8496 (tt0) cc_final: 0.8234 (tp30) REVERT: H 162 THR cc_start: 0.9520 (p) cc_final: 0.9126 (t) REVERT: H 307 ASP cc_start: 0.8735 (m-30) cc_final: 0.8283 (t0) REVERT: H 338 MET cc_start: 0.8676 (ttm) cc_final: 0.8421 (tpp) REVERT: I 1 MET cc_start: 0.8250 (mmp) cc_final: 0.7655 (mpt) REVERT: I 36 GLN cc_start: 0.8337 (tt0) cc_final: 0.7505 (tm130) REVERT: I 74 LYS cc_start: 0.9210 (mptm) cc_final: 0.8969 (mmpt) REVERT: I 182 MET cc_start: 0.7764 (mtt) cc_final: 0.7515 (mtt) outliers start: 52 outliers final: 7 residues processed: 501 average time/residue: 1.2782 time to fit residues: 717.6629 Evaluate side-chains 270 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 260 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain H residue 51 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 GLN C 137 ASN C 326 GLN F 8 GLN I 132 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.093618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.065971 restraints weight = 132439.293| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.53 r_work: 0.2862 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21479 Z= 0.198 Angle : 0.832 32.206 29382 Z= 0.353 Chirality : 0.038 0.141 3385 Planarity : 0.004 0.069 3633 Dihedral : 16.705 176.630 3390 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.33 % Favored : 96.51 % Rotamer: Outliers : 2.73 % Allowed : 13.80 % Favored : 83.47 % 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 aren not related in a simple way. whole: 2.61 (0.17), residues: 2521 helix: 2.81 (0.15), residues: 1264 sheet: 1.06 (0.24), residues: 455 loop : 0.40 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 362 TYR 0.013 0.001 TYR E 76 PHE 0.010 0.001 PHE A 127 TRP 0.006 0.001 TRP A 321 HIS 0.020 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00442 (21461) covalent geometry : angle 0.82297 (29358) hydrogen bonds : bond 0.04541 ( 1152) hydrogen bonds : angle 4.08298 ( 3253) metal coordination : bond 0.00651 ( 16) metal coordination : angle 4.39183 ( 24) Misc. bond : bond 0.00960 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Evaluate side-chains 318 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 260 time to evaluate : 0.759 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.9109 (p90) REVERT: A 146 GLN cc_start: 0.9031 (mp10) cc_final: 0.8702 (mp10) REVERT: A 157 GLN cc_start: 0.9038 (tt0) cc_final: 0.8816 (tm-30) REVERT: A 161 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8667 (tm-30) REVERT: A 239 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8544 (tm-30) REVERT: A 323 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8709 (mt-10) REVERT: B 145 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8562 (tm-30) REVERT: B 214 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7768 (tt) REVERT: B 306 MET cc_start: 0.9108 (mtm) cc_final: 0.8803 (mtp) REVERT: C 81 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8927 (mm-30) REVERT: C 179 ASP cc_start: 0.8132 (t0) cc_final: 0.7901 (t70) REVERT: C 310 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8480 (tm-30) REVERT: D 126 ASP cc_start: 0.8955 (m-30) cc_final: 0.8728 (m-30) REVERT: D 277 GLU cc_start: 0.8915 (tp30) cc_final: 0.8345 (tm-30) REVERT: D 338 GLU cc_start: 0.8770 (pt0) cc_final: 0.8402 (pp20) REVERT: D 351 MET cc_start: 0.8742 (ttm) cc_final: 0.8428 (mtp) REVERT: E 72 THR cc_start: 0.9394 (p) cc_final: 0.9014 (t) REVERT: E 98 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8462 (mp0) REVERT: E 277 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8940 (tt) REVERT: E 309 GLU cc_start: 0.8723 (tt0) cc_final: 0.8402 (mp0) REVERT: F 18 SER cc_start: 0.9125 (t) cc_final: 0.8786 (p) REVERT: F 26 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8050 (mm-40) REVERT: H 64 GLU cc_start: 0.8760 (tt0) cc_final: 0.8465 (tm-30) REVERT: H 87 GLU cc_start: 0.8648 (tt0) cc_final: 0.8025 (tm-30) REVERT: H 161 GLU cc_start: 0.8683 (tt0) cc_final: 0.8366 (tp30) REVERT: H 162 THR cc_start: 0.9534 (p) cc_final: 0.9113 (t) REVERT: H 307 ASP cc_start: 0.9101 (m-30) cc_final: 0.8764 (m-30) REVERT: I 1 MET cc_start: 0.8060 (mmp) cc_final: 0.7762 (mmm) REVERT: I 36 GLN cc_start: 0.8228 (tt0) cc_final: 0.7499 (tm130) REVERT: I 74 LYS cc_start: 0.9149 (mptm) cc_final: 0.8948 (mmpt) outliers start: 58 outliers final: 17 residues processed: 297 average time/residue: 1.1031 time to fit residues: 372.8935 Evaluate side-chains 256 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 63 HIS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 311 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 196 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 135 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 206 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 14 ASN A 144 GLN F 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.092451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.064874 restraints weight = 133005.284| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.52 r_work: 0.2840 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21479 Z= 0.173 Angle : 0.800 30.344 29382 Z= 0.337 Chirality : 0.038 0.139 3385 Planarity : 0.004 0.046 3633 Dihedral : 15.521 171.338 3383 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.01 % Favored : 96.79 % Rotamer: Outliers : 2.68 % Allowed : 14.32 % Favored : 83.00 % 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 aren not related in a simple way. whole: 2.46 (0.17), residues: 2521 helix: 2.75 (0.15), residues: 1259 sheet: 0.97 (0.24), residues: 460 loop : 0.24 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 3 TYR 0.016 0.001 TYR E 230 PHE 0.030 0.001 PHE A 127 TRP 0.013 0.001 TRP B 10 HIS 0.007 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00388 (21461) covalent geometry : angle 0.78916 (29358) hydrogen bonds : bond 0.03983 ( 1152) hydrogen bonds : angle 3.96070 ( 3253) metal coordination : bond 0.00523 ( 16) metal coordination : angle 4.62159 ( 24) Misc. bond : bond 0.00112 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Evaluate side-chains 298 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 0.902 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.9075 (p90) REVERT: A 157 GLN cc_start: 0.8989 (tt0) cc_final: 0.8781 (tm-30) REVERT: A 161 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8666 (tm-30) REVERT: B 145 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8603 (tm-30) REVERT: B 214 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7763 (tt) REVERT: B 306 MET cc_start: 0.9114 (mtm) cc_final: 0.8792 (mtp) REVERT: C 81 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8880 (mm-30) REVERT: C 179 ASP cc_start: 0.8201 (t0) cc_final: 0.7950 (t0) REVERT: C 310 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8555 (pp20) REVERT: D 126 ASP cc_start: 0.8978 (m-30) cc_final: 0.8723 (m-30) REVERT: D 277 GLU cc_start: 0.8912 (tp30) cc_final: 0.8322 (tm-30) REVERT: D 284 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8346 (mp0) REVERT: D 338 GLU cc_start: 0.8749 (pt0) cc_final: 0.8362 (pp20) REVERT: E 72 THR cc_start: 0.9420 (p) cc_final: 0.9060 (t) REVERT: E 98 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8437 (mp0) REVERT: E 277 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8932 (tt) REVERT: E 309 GLU cc_start: 0.8752 (tt0) cc_final: 0.8406 (mp0) REVERT: F 18 SER cc_start: 0.9131 (t) cc_final: 0.8809 (p) REVERT: F 26 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8054 (mm-40) REVERT: H 51 MET cc_start: 0.7483 (mtm) cc_final: 0.7128 (ptp) REVERT: H 64 GLU cc_start: 0.8718 (tt0) cc_final: 0.8429 (tm-30) REVERT: H 87 GLU cc_start: 0.8654 (tt0) cc_final: 0.8033 (tm-30) REVERT: H 162 THR cc_start: 0.9543 (p) cc_final: 0.9291 (t) REVERT: H 204 MET cc_start: 0.9126 (tpp) cc_final: 0.8904 (tpp) REVERT: H 307 ASP cc_start: 0.9117 (m-30) cc_final: 0.8789 (m-30) REVERT: I 1 MET cc_start: 0.8180 (mmp) cc_final: 0.7915 (mpt) REVERT: I 36 GLN cc_start: 0.8250 (tt0) cc_final: 0.7463 (tm130) REVERT: I 74 LYS cc_start: 0.9200 (mptm) cc_final: 0.8962 (mmpt) REVERT: I 97 MET cc_start: 0.8566 (ttm) cc_final: 0.8285 (ttp) REVERT: I 176 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.6838 (ppt-90) outliers start: 57 outliers final: 27 residues processed: 281 average time/residue: 1.1339 time to fit residues: 361.3847 Evaluate side-chains 258 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 63 HIS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 176 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 157 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 237 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN B 182 GLN F 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.091825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.064582 restraints weight = 133039.437| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.47 r_work: 0.2838 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21479 Z= 0.167 Angle : 0.799 30.439 29382 Z= 0.336 Chirality : 0.037 0.133 3385 Planarity : 0.004 0.101 3633 Dihedral : 15.317 175.907 3383 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.49 % Favored : 96.35 % Rotamer: Outliers : 2.31 % Allowed : 14.74 % Favored : 82.95 % 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 aren not related in a simple way. whole: 2.45 (0.17), residues: 2521 helix: 2.75 (0.15), residues: 1257 sheet: 1.18 (0.24), residues: 434 loop : 0.11 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 362 TYR 0.015 0.001 TYR E 230 PHE 0.008 0.001 PHE A 127 TRP 0.008 0.001 TRP B 10 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00377 (21461) covalent geometry : angle 0.78847 (29358) hydrogen bonds : bond 0.03754 ( 1152) hydrogen bonds : angle 3.91082 ( 3253) metal coordination : bond 0.00476 ( 16) metal coordination : angle 4.64452 ( 24) Misc. bond : bond 0.00081 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 234 time to evaluate : 1.317 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: 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: A 7 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7764 (pm20) REVERT: A 157 GLN cc_start: 0.9026 (tt0) cc_final: 0.8816 (tm-30) REVERT: A 161 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8671 (tm-30) REVERT: B 145 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8596 (tm-30) REVERT: B 214 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7752 (tt) REVERT: B 306 MET cc_start: 0.9121 (mtm) cc_final: 0.8887 (mtp) REVERT: C 81 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8863 (mm-30) REVERT: C 179 ASP cc_start: 0.8236 (t0) cc_final: 0.7971 (t0) REVERT: C 310 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8548 (pp20) REVERT: D 126 ASP cc_start: 0.8963 (m-30) cc_final: 0.8732 (m-30) REVERT: D 277 GLU cc_start: 0.8888 (tp30) cc_final: 0.8281 (tm-30) REVERT: D 284 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8360 (mp0) REVERT: D 338 GLU cc_start: 0.8731 (pt0) cc_final: 0.8330 (pp20) REVERT: E 8 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7452 (tpp-160) REVERT: E 72 THR cc_start: 0.9422 (p) cc_final: 0.9044 (t) REVERT: E 98 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8414 (mp0) REVERT: E 277 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8905 (tt) REVERT: E 309 GLU cc_start: 0.8756 (tt0) cc_final: 0.8404 (mp0) REVERT: F 18 SER cc_start: 0.9153 (t) cc_final: 0.8852 (p) REVERT: F 26 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8062 (mm-40) REVERT: H 64 GLU cc_start: 0.8696 (tt0) cc_final: 0.8413 (tm-30) REVERT: H 87 GLU cc_start: 0.8642 (tt0) cc_final: 0.8035 (tm-30) REVERT: H 204 MET cc_start: 0.9117 (tpp) cc_final: 0.8889 (tpp) REVERT: H 307 ASP cc_start: 0.9103 (m-30) cc_final: 0.8760 (m-30) REVERT: H 364 MET cc_start: 0.8147 (ptp) cc_final: 0.7906 (pmt) REVERT: I 1 MET cc_start: 0.8216 (mmp) cc_final: 0.7921 (mpt) REVERT: I 36 GLN cc_start: 0.8228 (tt0) cc_final: 0.7480 (tm130) REVERT: I 53 MET cc_start: 0.7982 (tpt) cc_final: 0.6925 (tpt) REVERT: I 74 LYS cc_start: 0.9221 (mptm) cc_final: 0.8979 (mmpt) REVERT: I 97 MET cc_start: 0.8542 (ttm) cc_final: 0.8266 (ttp) REVERT: I 176 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.6893 (ppt-90) outliers start: 49 outliers final: 22 residues processed: 267 average time/residue: 1.5284 time to fit residues: 465.8215 Evaluate side-chains 257 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 63 HIS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 176 ARG Chi-restraints excluded: chain I residue 311 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 65 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 249 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 155 optimal weight: 0.0970 chunk 123 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.091678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.064421 restraints weight = 132659.849| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.46 r_work: 0.2829 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21479 Z= 0.157 Angle : 0.794 30.444 29382 Z= 0.333 Chirality : 0.037 0.134 3385 Planarity : 0.003 0.041 3633 Dihedral : 15.172 179.964 3383 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.41 % Favored : 96.47 % Rotamer: Outliers : 2.26 % Allowed : 15.12 % Favored : 82.62 % 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 aren not related in a simple way. whole: 2.47 (0.17), residues: 2521 helix: 2.80 (0.15), residues: 1251 sheet: 1.24 (0.25), residues: 431 loop : 0.04 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 246 TYR 0.017 0.001 TYR E 230 PHE 0.027 0.001 PHE A 127 TRP 0.008 0.001 TRP B 10 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00355 (21461) covalent geometry : angle 0.78275 (29358) hydrogen bonds : bond 0.03599 ( 1152) hydrogen bonds : angle 3.86555 ( 3253) metal coordination : bond 0.00433 ( 16) metal coordination : angle 4.63358 ( 24) Misc. bond : bond 0.00088 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 0.947 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8609 (tm-30) REVERT: B 214 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7739 (tt) REVERT: B 306 MET cc_start: 0.9158 (mtm) cc_final: 0.8870 (mtp) REVERT: C 81 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8836 (mm-30) REVERT: C 213 SER cc_start: 0.9033 (OUTLIER) cc_final: 0.8789 (p) REVERT: D 126 ASP cc_start: 0.8959 (m-30) cc_final: 0.8727 (m-30) REVERT: D 277 GLU cc_start: 0.8899 (tp30) cc_final: 0.8289 (tm-30) REVERT: D 284 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8342 (mp0) REVERT: D 338 GLU cc_start: 0.8722 (pt0) cc_final: 0.8306 (pp20) REVERT: D 351 MET cc_start: 0.8758 (ttm) cc_final: 0.8379 (mtp) REVERT: E 72 THR cc_start: 0.9423 (p) cc_final: 0.9030 (t) REVERT: E 98 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8448 (mp0) REVERT: E 277 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8916 (tt) REVERT: E 309 GLU cc_start: 0.8762 (tt0) cc_final: 0.8405 (mp0) REVERT: F 18 SER cc_start: 0.9154 (t) cc_final: 0.8860 (p) REVERT: F 26 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8027 (mm-40) REVERT: H 64 GLU cc_start: 0.8694 (tt0) cc_final: 0.8402 (tm-30) REVERT: H 87 GLU cc_start: 0.8655 (tt0) cc_final: 0.8043 (tm-30) REVERT: H 204 MET cc_start: 0.9131 (tpp) cc_final: 0.8901 (tpp) REVERT: H 307 ASP cc_start: 0.9129 (m-30) cc_final: 0.8782 (m-30) REVERT: H 364 MET cc_start: 0.8113 (ptp) cc_final: 0.7862 (pmt) REVERT: I 1 MET cc_start: 0.8232 (mmp) cc_final: 0.7940 (mpt) REVERT: I 36 GLN cc_start: 0.8235 (tt0) cc_final: 0.7477 (tm130) REVERT: I 74 LYS cc_start: 0.9216 (mptm) cc_final: 0.8978 (mmpt) REVERT: I 97 MET cc_start: 0.8532 (ttm) cc_final: 0.8250 (ttp) REVERT: I 176 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.6959 (ppt-90) REVERT: I 277 LYS cc_start: 0.9275 (tppt) cc_final: 0.9030 (mmmm) outliers start: 48 outliers final: 24 residues processed: 261 average time/residue: 1.1216 time to fit residues: 335.7607 Evaluate side-chains 251 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 63 HIS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 176 ARG Chi-restraints excluded: chain I residue 311 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 146 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.0670 chunk 170 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 GLN F 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.090929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.063724 restraints weight = 133066.619| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.45 r_work: 0.2820 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21479 Z= 0.180 Angle : 0.800 30.640 29382 Z= 0.338 Chirality : 0.037 0.133 3385 Planarity : 0.003 0.038 3633 Dihedral : 15.106 179.592 3383 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.81 % Favored : 96.07 % Rotamer: Outliers : 2.12 % Allowed : 15.97 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.17), residues: 2521 helix: 2.76 (0.15), residues: 1252 sheet: 1.19 (0.25), residues: 431 loop : -0.06 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 246 TYR 0.018 0.001 TYR E 230 PHE 0.009 0.001 PHE A 127 TRP 0.007 0.001 TRP B 10 HIS 0.005 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00406 (21461) covalent geometry : angle 0.78962 (29358) hydrogen bonds : bond 0.03663 ( 1152) hydrogen bonds : angle 3.88932 ( 3253) metal coordination : bond 0.00504 ( 16) metal coordination : angle 4.62517 ( 24) Misc. bond : bond 0.00107 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 1.170 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: 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: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.9116 (p90) REVERT: B 145 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8612 (tm-30) REVERT: B 214 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7760 (tt) REVERT: B 306 MET cc_start: 0.9158 (mtm) cc_final: 0.8864 (mtp) REVERT: C 81 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8824 (mm-30) REVERT: C 213 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8822 (p) REVERT: C 310 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8561 (pp20) REVERT: D 126 ASP cc_start: 0.8986 (m-30) cc_final: 0.8751 (m-30) REVERT: D 277 GLU cc_start: 0.8899 (tp30) cc_final: 0.8324 (tm-30) REVERT: D 284 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8354 (mp0) REVERT: D 338 GLU cc_start: 0.8723 (pt0) cc_final: 0.8316 (pp20) REVERT: D 351 MET cc_start: 0.8766 (ttm) cc_final: 0.8378 (mtp) REVERT: E 72 THR cc_start: 0.9425 (p) cc_final: 0.9028 (t) REVERT: E 98 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: E 122 ASP cc_start: 0.8279 (t0) cc_final: 0.8074 (t0) REVERT: E 277 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8927 (tt) REVERT: E 309 GLU cc_start: 0.8761 (tt0) cc_final: 0.8396 (mp0) REVERT: F 18 SER cc_start: 0.9194 (t) cc_final: 0.8893 (p) REVERT: F 26 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8048 (mm-40) REVERT: H 64 GLU cc_start: 0.8696 (tt0) cc_final: 0.8401 (tm-30) REVERT: H 87 GLU cc_start: 0.8656 (tt0) cc_final: 0.8032 (tm-30) REVERT: H 204 MET cc_start: 0.9146 (tpp) cc_final: 0.8882 (tpp) REVERT: H 307 ASP cc_start: 0.9140 (m-30) cc_final: 0.8795 (m-30) REVERT: I 1 MET cc_start: 0.8270 (mmp) cc_final: 0.7977 (mpt) REVERT: I 36 GLN cc_start: 0.8239 (tt0) cc_final: 0.7474 (tm130) REVERT: I 74 LYS cc_start: 0.9215 (mptm) cc_final: 0.8971 (mmpt) REVERT: I 97 MET cc_start: 0.8527 (ttm) cc_final: 0.8245 (ttp) REVERT: I 176 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.6962 (ppt-90) REVERT: I 277 LYS cc_start: 0.9274 (tppt) cc_final: 0.9029 (mmmm) outliers start: 45 outliers final: 22 residues processed: 252 average time/residue: 1.4529 time to fit residues: 419.9725 Evaluate side-chains 248 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 63 HIS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 176 ARG Chi-restraints excluded: chain I residue 311 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 237 optimal weight: 0.8980 chunk 203 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN F 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.092498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.066729 restraints weight = 131393.869| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.48 r_work: 0.2858 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21479 Z= 0.107 Angle : 0.793 30.118 29382 Z= 0.330 Chirality : 0.037 0.141 3385 Planarity : 0.003 0.039 3633 Dihedral : 14.908 171.885 3383 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.09 % Favored : 96.79 % Rotamer: Outliers : 1.74 % Allowed : 16.67 % Favored : 81.58 % 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 aren not related in a simple way. whole: 2.63 (0.17), residues: 2521 helix: 2.99 (0.15), residues: 1251 sheet: 1.29 (0.25), residues: 430 loop : 0.04 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 246 TYR 0.018 0.001 TYR E 230 PHE 0.036 0.001 PHE A 127 TRP 0.009 0.001 TRP B 10 HIS 0.004 0.000 HIS C 23 Details of bonding type rmsd covalent geometry : bond 0.00247 (21461) covalent geometry : angle 0.78277 (29358) hydrogen bonds : bond 0.03136 ( 1152) hydrogen bonds : angle 3.64913 ( 3253) metal coordination : bond 0.00185 ( 16) metal coordination : angle 4.51984 ( 24) Misc. bond : bond 0.00065 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9185 (mtt) cc_final: 0.8935 (mmt) REVERT: B 145 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8604 (tm-30) REVERT: B 214 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7627 (tt) REVERT: B 306 MET cc_start: 0.9123 (mtm) cc_final: 0.8839 (mtp) REVERT: C 81 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8822 (mm-30) REVERT: C 213 SER cc_start: 0.9017 (OUTLIER) cc_final: 0.8780 (p) REVERT: D 126 ASP cc_start: 0.8931 (m-30) cc_final: 0.8712 (m-30) REVERT: D 277 GLU cc_start: 0.8856 (tp30) cc_final: 0.8225 (tm-30) REVERT: D 284 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8362 (mp0) REVERT: D 338 GLU cc_start: 0.8603 (pt0) cc_final: 0.8207 (pp20) REVERT: D 351 MET cc_start: 0.8729 (ttm) cc_final: 0.8334 (mtp) REVERT: E 72 THR cc_start: 0.9411 (p) cc_final: 0.9016 (t) REVERT: E 86 ASN cc_start: 0.8489 (p0) cc_final: 0.7996 (p0) REVERT: E 98 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: E 239 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8397 (tm-30) REVERT: E 277 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8913 (tt) REVERT: F 18 SER cc_start: 0.9193 (t) cc_final: 0.8902 (p) REVERT: F 26 GLN cc_start: 0.8397 (mm-40) cc_final: 0.7999 (mm-40) REVERT: H 64 GLU cc_start: 0.8677 (tt0) cc_final: 0.8394 (tm-30) REVERT: H 87 GLU cc_start: 0.8637 (tt0) cc_final: 0.8019 (tm-30) REVERT: H 204 MET cc_start: 0.9151 (tpp) cc_final: 0.8890 (tpp) REVERT: H 307 ASP cc_start: 0.9133 (m-30) cc_final: 0.8789 (m-30) REVERT: H 364 MET cc_start: 0.8162 (ptp) cc_final: 0.7911 (pmt) REVERT: I 1 MET cc_start: 0.8232 (mmp) cc_final: 0.7956 (mpt) REVERT: I 36 GLN cc_start: 0.8223 (tt0) cc_final: 0.7422 (tm-30) REVERT: I 74 LYS cc_start: 0.9211 (mptm) cc_final: 0.8965 (mmpt) REVERT: I 97 MET cc_start: 0.8527 (ttm) cc_final: 0.8256 (ttp) REVERT: I 176 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.6797 (ppt-90) REVERT: I 277 LYS cc_start: 0.9248 (tppt) cc_final: 0.8995 (mmmm) outliers start: 37 outliers final: 17 residues processed: 252 average time/residue: 1.2539 time to fit residues: 363.2607 Evaluate side-chains 245 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 360 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 176 ARG Chi-restraints excluded: chain I residue 311 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 114 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 209 optimal weight: 7.9990 chunk 250 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 GLN F 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.091239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.063984 restraints weight = 131813.003| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.44 r_work: 0.2830 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21479 Z= 0.154 Angle : 0.794 30.300 29382 Z= 0.334 Chirality : 0.037 0.137 3385 Planarity : 0.003 0.036 3633 Dihedral : 14.765 168.000 3383 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.73 % Favored : 96.15 % Rotamer: Outliers : 1.84 % Allowed : 17.15 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.55 (0.17), residues: 2521 helix: 2.95 (0.15), residues: 1252 sheet: 1.19 (0.24), residues: 440 loop : -0.02 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 246 TYR 0.019 0.001 TYR E 230 PHE 0.008 0.001 PHE A 127 TRP 0.007 0.001 TRP B 10 HIS 0.003 0.001 HIS C 23 Details of bonding type rmsd covalent geometry : bond 0.00351 (21461) covalent geometry : angle 0.78390 (29358) hydrogen bonds : bond 0.03301 ( 1152) hydrogen bonds : angle 3.73876 ( 3253) metal coordination : bond 0.00437 ( 16) metal coordination : angle 4.46790 ( 24) Misc. bond : bond 0.00071 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 1.234 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: 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: A 74 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.9108 (p90) REVERT: B 145 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8620 (tm-30) REVERT: B 214 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7735 (tt) REVERT: B 306 MET cc_start: 0.9129 (mtm) cc_final: 0.8840 (mtp) REVERT: C 81 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8835 (mm-30) REVERT: C 213 SER cc_start: 0.9038 (OUTLIER) cc_final: 0.8783 (p) REVERT: D 126 ASP cc_start: 0.8973 (m-30) cc_final: 0.8744 (m-30) REVERT: D 277 GLU cc_start: 0.8872 (tp30) cc_final: 0.8239 (tm-30) REVERT: D 284 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8313 (mp0) REVERT: D 338 GLU cc_start: 0.8616 (pt0) cc_final: 0.8218 (pp20) REVERT: D 351 MET cc_start: 0.8757 (ttm) cc_final: 0.8361 (mtp) REVERT: E 72 THR cc_start: 0.9423 (p) cc_final: 0.9021 (t) REVERT: E 86 ASN cc_start: 0.8514 (p0) cc_final: 0.8009 (p0) REVERT: E 98 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: E 277 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8917 (tt) REVERT: F 18 SER cc_start: 0.9190 (t) cc_final: 0.8905 (p) REVERT: F 26 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8039 (mm-40) REVERT: H 64 GLU cc_start: 0.8692 (tt0) cc_final: 0.8404 (tm-30) REVERT: H 87 GLU cc_start: 0.8667 (tt0) cc_final: 0.8054 (tm-30) REVERT: H 204 MET cc_start: 0.9140 (tpp) cc_final: 0.8877 (tpp) REVERT: H 307 ASP cc_start: 0.9133 (m-30) cc_final: 0.8785 (m-30) REVERT: I 1 MET cc_start: 0.8301 (mmp) cc_final: 0.7954 (mmm) REVERT: I 36 GLN cc_start: 0.8222 (tt0) cc_final: 0.7486 (tm130) REVERT: I 74 LYS cc_start: 0.9210 (mptm) cc_final: 0.8959 (mmpt) REVERT: I 97 MET cc_start: 0.8522 (ttm) cc_final: 0.8263 (ttp) REVERT: I 176 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.6973 (ppt-90) REVERT: I 277 LYS cc_start: 0.9254 (tppt) cc_final: 0.8998 (mmmm) outliers start: 39 outliers final: 20 residues processed: 246 average time/residue: 1.5186 time to fit residues: 429.1913 Evaluate side-chains 242 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 360 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 63 HIS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 176 ARG Chi-restraints excluded: chain I residue 311 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 189 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 234 optimal weight: 0.6980 chunk 187 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.091376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.064254 restraints weight = 132046.606| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.44 r_work: 0.2835 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21479 Z= 0.140 Angle : 0.806 30.376 29382 Z= 0.339 Chirality : 0.037 0.155 3385 Planarity : 0.003 0.040 3633 Dihedral : 14.620 164.819 3381 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.73 % Favored : 96.15 % Rotamer: Outliers : 1.74 % Allowed : 17.38 % Favored : 80.88 % 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 aren not related in a simple way. whole: 2.55 (0.17), residues: 2521 helix: 2.95 (0.15), residues: 1252 sheet: 1.28 (0.25), residues: 429 loop : -0.06 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 246 TYR 0.019 0.001 TYR E 230 PHE 0.014 0.001 PHE A 127 TRP 0.007 0.001 TRP B 10 HIS 0.004 0.001 HIS C 23 Details of bonding type rmsd covalent geometry : bond 0.00323 (21461) covalent geometry : angle 0.79621 (29358) hydrogen bonds : bond 0.03279 ( 1152) hydrogen bonds : angle 3.70800 ( 3253) metal coordination : bond 0.00307 ( 16) metal coordination : angle 4.44906 ( 24) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Evaluate side-chains 253 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 1.223 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: 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: A 74 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.9099 (p90) REVERT: B 145 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8640 (tm-30) REVERT: B 214 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7722 (tt) REVERT: B 306 MET cc_start: 0.9127 (mtm) cc_final: 0.8845 (mtp) REVERT: C 81 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8829 (mm-30) REVERT: C 213 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8796 (p) REVERT: D 126 ASP cc_start: 0.8970 (m-30) cc_final: 0.8741 (m-30) REVERT: D 277 GLU cc_start: 0.8864 (tp30) cc_final: 0.8236 (tm-30) REVERT: D 284 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: D 338 GLU cc_start: 0.8587 (pt0) cc_final: 0.8202 (pp20) REVERT: E 72 THR cc_start: 0.9426 (p) cc_final: 0.9026 (t) REVERT: E 86 ASN cc_start: 0.8520 (p0) cc_final: 0.8009 (p0) REVERT: E 98 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8400 (mp0) REVERT: E 122 ASP cc_start: 0.8214 (t0) cc_final: 0.8010 (t0) REVERT: E 239 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8434 (tm-30) REVERT: E 277 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8920 (tt) REVERT: F 18 SER cc_start: 0.9171 (t) cc_final: 0.8875 (p) REVERT: F 26 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8006 (mm-40) REVERT: H 64 GLU cc_start: 0.8682 (tt0) cc_final: 0.8396 (tm-30) REVERT: H 87 GLU cc_start: 0.8649 (tt0) cc_final: 0.8024 (tm-30) REVERT: H 204 MET cc_start: 0.9139 (tpp) cc_final: 0.8874 (tpp) REVERT: H 307 ASP cc_start: 0.9132 (m-30) cc_final: 0.8787 (m-30) REVERT: I 1 MET cc_start: 0.8358 (mmp) cc_final: 0.8063 (mmm) REVERT: I 36 GLN cc_start: 0.8241 (tt0) cc_final: 0.7456 (tm-30) REVERT: I 53 MET cc_start: 0.7997 (tpt) cc_final: 0.6958 (tpt) REVERT: I 74 LYS cc_start: 0.9220 (mptm) cc_final: 0.8965 (mmpt) REVERT: I 97 MET cc_start: 0.8521 (ttm) cc_final: 0.8253 (ttp) REVERT: I 176 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.6962 (ppt-90) REVERT: I 277 LYS cc_start: 0.9248 (tppt) cc_final: 0.8989 (mmmm) outliers start: 37 outliers final: 22 residues processed: 244 average time/residue: 1.4985 time to fit residues: 419.3285 Evaluate side-chains 245 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 360 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 63 HIS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 176 ARG Chi-restraints excluded: chain I residue 311 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 176 optimal weight: 4.9990 chunk 179 optimal weight: 0.0170 chunk 109 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 130 optimal weight: 0.0980 chunk 123 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.2224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.091774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.064580 restraints weight = 131449.253| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.43 r_work: 0.2842 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21479 Z= 0.122 Angle : 0.799 30.233 29382 Z= 0.335 Chirality : 0.037 0.173 3385 Planarity : 0.003 0.039 3633 Dihedral : 14.556 162.295 3381 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.57 % Favored : 96.31 % Rotamer: Outliers : 1.84 % Allowed : 17.33 % Favored : 80.83 % 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 aren not related in a simple way. whole: 2.59 (0.17), residues: 2521 helix: 2.98 (0.15), residues: 1251 sheet: 1.34 (0.25), residues: 421 loop : -0.04 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 246 TYR 0.018 0.001 TYR E 230 PHE 0.027 0.001 PHE A 127 TRP 0.007 0.001 TRP B 10 HIS 0.004 0.001 HIS C 23 Details of bonding type rmsd covalent geometry : bond 0.00283 (21461) covalent geometry : angle 0.78927 (29358) hydrogen bonds : bond 0.03186 ( 1152) hydrogen bonds : angle 3.68439 ( 3253) metal coordination : bond 0.00340 ( 16) metal coordination : angle 4.36692 ( 24) Misc. bond : bond 0.00014 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 1.101 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: 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 145 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8630 (tm-30) REVERT: B 214 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7705 (tt) REVERT: B 306 MET cc_start: 0.9122 (mtm) cc_final: 0.8846 (mtp) REVERT: C 81 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8835 (mm-30) REVERT: C 213 SER cc_start: 0.9013 (OUTLIER) cc_final: 0.8776 (p) REVERT: D 126 ASP cc_start: 0.8954 (m-30) cc_final: 0.8739 (m-30) REVERT: D 277 GLU cc_start: 0.8855 (tp30) cc_final: 0.8223 (tm-30) REVERT: D 284 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8317 (mp0) REVERT: D 338 GLU cc_start: 0.8557 (pt0) cc_final: 0.8180 (pp20) REVERT: E 72 THR cc_start: 0.9422 (p) cc_final: 0.9020 (t) REVERT: E 86 ASN cc_start: 0.8524 (p0) cc_final: 0.8017 (p0) REVERT: E 98 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: E 239 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8424 (tm-30) REVERT: E 277 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8912 (tt) REVERT: F 8 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8441 (mp10) REVERT: F 18 SER cc_start: 0.9172 (t) cc_final: 0.8881 (p) REVERT: F 26 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8003 (mm-40) REVERT: H 64 GLU cc_start: 0.8691 (tt0) cc_final: 0.8411 (tm-30) REVERT: H 87 GLU cc_start: 0.8654 (tt0) cc_final: 0.8024 (tm-30) REVERT: H 204 MET cc_start: 0.9138 (tpp) cc_final: 0.8877 (tpp) REVERT: H 307 ASP cc_start: 0.9124 (m-30) cc_final: 0.8775 (m-30) REVERT: I 1 MET cc_start: 0.8431 (mmp) cc_final: 0.8057 (mmm) REVERT: I 36 GLN cc_start: 0.8231 (tt0) cc_final: 0.7405 (tm-30) REVERT: I 53 MET cc_start: 0.7947 (tpt) cc_final: 0.6928 (tpt) REVERT: I 74 LYS cc_start: 0.9219 (mptm) cc_final: 0.8965 (mmpt) REVERT: I 97 MET cc_start: 0.8516 (ttm) cc_final: 0.8248 (ttp) REVERT: I 176 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.6968 (ppt-90) REVERT: I 277 LYS cc_start: 0.9246 (tppt) cc_final: 0.8985 (mmmm) outliers start: 39 outliers final: 18 residues processed: 245 average time/residue: 1.3761 time to fit residues: 387.4217 Evaluate side-chains 240 residues out of total 2123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain D residue 360 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 103 HIS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 63 HIS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 176 ARG Chi-restraints excluded: chain I residue 311 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 53 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 247 optimal weight: 0.9980 chunk 213 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.090477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.063451 restraints weight = 131183.897| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.36 r_work: 0.2861 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21479 Z= 0.111 Angle : 0.802 30.186 29382 Z= 0.336 Chirality : 0.037 0.155 3385 Planarity : 0.003 0.040 3633 Dihedral : 14.405 154.416 3381 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.49 % Favored : 96.39 % Rotamer: Outliers : 1.46 % Allowed : 17.48 % Favored : 81.06 % 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 aren not related in a simple way. whole: 2.68 (0.17), residues: 2521 helix: 3.05 (0.15), residues: 1251 sheet: 1.34 (0.25), residues: 424 loop : 0.01 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 246 TYR 0.018 0.001 TYR E 230 PHE 0.029 0.001 PHE I 3 TRP 0.008 0.001 TRP B 10 HIS 0.005 0.000 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00263 (21461) covalent geometry : angle 0.79276 (29358) hydrogen bonds : bond 0.02976 ( 1152) hydrogen bonds : angle 3.58110 ( 3253) metal coordination : bond 0.00257 ( 16) metal coordination : angle 4.25335 ( 24) Misc. bond : bond 0.00028 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12508.27 seconds wall clock time: 212 minutes 0.19 seconds (12720.19 seconds total)