Starting phenix.real_space_refine on Fri Jun 5 14:35:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyb_71013/06_2026/9oyb_71013.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyb_71013/06_2026/9oyb_71013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oyb_71013/06_2026/9oyb_71013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyb_71013/06_2026/9oyb_71013.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oyb_71013/06_2026/9oyb_71013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyb_71013/06_2026/9oyb_71013.map" } resolution = 3.14 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= 0.017 sd= 0.651 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 68 5.49 5 Mg 3 5.21 5 S 112 5.16 5 C 13057 2.51 5 N 3776 2.21 5 O 4054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21074 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2726 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "B" Number of atoms: 2856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2856 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain: "C" Number of atoms: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2873 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 17, 'TRANS': 351} Chain: "D" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2799 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "E" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2602 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "F" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2835 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 20, 'TRANS': 344} Chain: "G" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2844 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 345} Chain: "H" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "I" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 230 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "M" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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 3209 SG CYS B 64 29.973 83.360 36.019 1.00 65.00 S ATOM 3269 SG CYS B 73 26.387 82.936 36.552 1.00 76.97 S ATOM 3286 SG CYS B 76 28.249 79.741 35.971 1.00 71.73 S ATOM 3308 SG CYS B 79 28.850 81.341 39.117 1.00 74.82 S ATOM 6073 SG CYS C 64 9.698 57.741 68.824 1.00 56.52 S ATOM 6133 SG CYS C 73 8.200 55.499 71.285 1.00 75.52 S ATOM 6150 SG CYS C 76 10.788 53.897 68.842 1.00 62.40 S ATOM 6172 SG CYS C 79 12.089 55.995 71.276 1.00 59.74 S ATOM 8938 SG CYS D 64 34.776 31.360 98.531 1.00 63.49 S ATOM 8998 SG CYS D 73 36.827 29.113 100.485 1.00 68.00 S ATOM 9015 SG CYS D 76 37.701 29.243 96.822 1.00 63.40 S ATOM 9037 SG CYS D 79 38.447 32.249 98.822 1.00 64.64 S ATOM 11661 SG CYS E 50 81.384 33.906 99.412 1.00 68.90 S ATOM 11730 SG CYS E 59 84.716 32.584 98.356 1.00 66.56 S ATOM 11750 SG CYS E 62 82.130 32.518 95.765 1.00 73.26 S ATOM 11771 SG CYS E 65 83.184 35.840 96.753 1.00 65.79 S Time building chain proxies: 5.13, per 1000 atoms: 0.24 Number of scatterers: 21074 At special positions: 0 Unit cell: (123.372, 120.888, 149.868, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 112 16.00 P 68 15.00 Mg 3 11.99 O 4054 8.00 N 3776 7.00 C 13057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 907.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 79 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 76 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 64 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 79 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 73 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 64 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 76 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 73 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 76 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 79 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 64 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 62 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 65 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 59 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 50 " Number of angles added : 24 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 15 sheets defined 55.3% alpha, 15.3% beta 28 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 2.71 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: 3.565A pdb=" N GLN A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.624A pdb=" N ILE A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.595A pdb=" N GLY A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 124 through 130 removed outlier: 3.606A pdb=" N THR A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 130 " --> pdb=" O TRP A 126 " (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 206 removed outlier: 3.553A pdb=" N ALA A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) 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 265 removed outlier: 3.778A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 282 through 293 Processing helix chain 'A' and resid 294 through 315 Processing helix chain 'A' and resid 320 through 332 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 14 through 18 Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 50 through 64 Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 100 through 110 removed outlier: 3.832A pdb=" N ASN B 110 " --> pdb=" O ASP B 106 " (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 145 removed outlier: 4.237A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 removed outlier: 3.660A pdb=" N LYS B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 169 removed outlier: 3.631A pdb=" N LEU B 167 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 169 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.946A 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 244 Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 277 through 298 Processing helix chain 'B' and resid 299 through 302 removed outlier: 4.010A 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 303 through 307 removed outlier: 3.530A pdb=" N ALA B 307 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 321 through 339 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 358 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 Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 100 through 110 removed outlier: 4.358A 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 145 removed outlier: 4.764A pdb=" N LYS C 141 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 removed outlier: 3.577A pdb=" N LYS C 161 " --> pdb=" O ASP C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 170 removed outlier: 3.683A pdb=" N ARG C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS C 170 " --> pdb=" O ILE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 195 Processing helix chain 'C' and resid 199 through 211 removed outlier: 4.063A pdb=" N GLU C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) 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: 3.568A pdb=" N ALA C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 274 Processing helix chain 'C' and resid 277 through 298 removed outlier: 3.699A pdb=" N LEU C 282 " --> pdb=" O TRP C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 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 34 Processing helix chain 'D' and resid 50 through 63 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 128 through 131 Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 163 through 170 removed outlier: 3.541A pdb=" N ARG D 169 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 195 Processing helix chain 'D' and resid 199 through 211 removed outlier: 3.853A pdb=" N GLU D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 228 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.754A pdb=" N ALA D 249 " --> pdb=" O ASP D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 274 Processing helix chain 'D' and resid 277 through 298 Processing helix chain 'D' and resid 299 through 302 removed outlier: 3.915A 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 307 removed outlier: 3.563A pdb=" N MET D 306 " --> pdb=" O GLY D 303 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 307 " --> pdb=" O ASN D 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 307' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 321 through 339 Processing helix chain 'D' and resid 344 through 357 Processing helix chain 'E' and resid 6 through 20 removed outlier: 4.705A pdb=" N ASP E 10 " --> pdb=" O TRP E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 49 Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 89 through 101 removed outlier: 3.538A 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: 3.549A pdb=" N LEU E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS E 130 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 4.731A 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 159 removed outlier: 3.611A pdb=" N ARG E 158 " --> pdb=" O THR E 154 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS E 159 " --> pdb=" O LEU E 155 " (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 197 through 206 removed outlier: 3.535A pdb=" N PHE E 205 " --> pdb=" O ALA E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 227 Proline residue: E 225 - end of helix Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 231 through 237 removed outlier: 4.537A pdb=" N ALA E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) 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 324 Processing helix chain 'F' and resid 7 through 18 removed outlier: 4.209A pdb=" N LYS F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) Proline residue: F 13 - end of helix Processing helix chain 'F' and resid 72 through 82 Processing helix chain 'F' and resid 114 through 116 No H-bonds generated for 'chain 'F' and resid 114 through 116' Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.636A pdb=" N THR F 142 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 157 removed outlier: 3.915A pdb=" N GLY F 157 " --> pdb=" O TYR F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 207 Processing helix chain 'F' and resid 259 through 273 removed outlier: 3.739A pdb=" N LEU F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 332 removed outlier: 3.615A pdb=" N LYS F 332 " --> pdb=" O LEU F 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 18 removed outlier: 4.310A pdb=" N LYS G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) Proline residue: G 13 - end of helix removed outlier: 3.768A pdb=" N GLN G 16 " --> pdb=" O LYS G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 30 Processing helix chain 'G' and resid 72 through 82 Processing helix chain 'G' and resid 131 through 141 Processing helix chain 'G' and resid 142 through 146 Processing helix chain 'G' and resid 152 through 155 Processing helix chain 'G' and resid 197 through 207 Processing helix chain 'G' and resid 243 through 248 removed outlier: 3.601A pdb=" N VAL G 247 " --> pdb=" O ASP G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 271 Processing helix chain 'G' and resid 321 through 332 removed outlier: 3.762A pdb=" N LYS G 332 " --> pdb=" O LEU G 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 13 Processing helix chain 'J' and resid 21 through 25 removed outlier: 3.509A pdb=" N LEU J 25 " --> pdb=" O PRO J 22 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 6.942A pdb=" N GLN A 78 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE A 111 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU A 80 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ARG A 113 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 82 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG A 77 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 49 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 162 removed outlier: 5.957A 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 90 through 94 removed outlier: 6.356A pdb=" N ILE B 91 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASP B 126 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE B 93 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LYS B 121 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU B 153 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N TYR B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA B 155 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE B 125 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR B 41 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR B 156 " --> pdb=" O TYR B 41 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE B 43 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N PHE B 173 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU B 42 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU B 175 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER B 44 " --> pdb=" O LEU B 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 197 through 198 removed outlier: 6.601A pdb=" N ALA B 197 " --> pdb=" O VAL B 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 359 through 361 Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 94 removed outlier: 6.142A pdb=" N LYS C 121 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU C 153 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA C 155 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE C 125 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N TYR C 41 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR C 156 " --> pdb=" O TYR C 41 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE C 43 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA C 40 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N PHE C 173 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU C 42 " --> pdb=" O PHE C 173 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 90 through 94 removed outlier: 6.431A pdb=" N ILE D 91 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ASP D 126 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE D 93 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LYS D 121 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU D 153 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ALA D 155 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE D 125 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 76 through 79 removed outlier: 6.417A pdb=" N LYS E 110 " --> pdb=" O TRP E 140 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE E 142 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL E 112 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ALA E 144 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL E 114 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU E 27 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N THR E 145 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ILE E 29 " --> pdb=" O THR E 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.666A pdb=" N ASN G 295 " --> pdb=" O GLY G 280 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY G 280 " --> pdb=" O ASN G 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 111 through 112 removed outlier: 3.741A pdb=" N GLY F 66 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN F 32 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR F 47 " --> pdb=" O ASN F 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 309 through 310 removed outlier: 4.310A pdb=" N ASP F 351 " --> pdb=" O ALA F 357 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA F 357 " --> pdb=" O ASP F 351 " (cutoff:3.500A) removed outlier: 16.017A pdb=" N SER F 181 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 16.053A pdb=" N THR F 172 " --> pdb=" O SER F 181 " (cutoff:3.500A) removed outlier: 14.975A pdb=" N VAL F 170 " --> pdb=" O PRO F 183 " (cutoff:3.500A) removed outlier: 14.221A pdb=" N GLY F 185 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 13.472A pdb=" N ARG F 168 " --> pdb=" O GLY F 185 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N SER F 187 " --> pdb=" O GLU F 166 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N GLU F 166 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLY F 164 " --> pdb=" O PRO F 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 304 through 306 removed outlier: 3.508A pdb=" N GLU F 304 " --> pdb=" O ILE F 292 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 2 through 6 Processing sheet with id=AB5, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.941A pdb=" N ASN G 32 " --> pdb=" O THR G 47 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N THR G 47 " --> pdb=" O ASN G 32 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 254 through 259 removed outlier: 4.596A pdb=" N ASP G 351 " --> pdb=" O ALA G 357 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA G 357 " --> pdb=" O ASP G 351 " (cutoff:3.500A) removed outlier: 16.088A pdb=" N SER G 181 " --> pdb=" O THR G 172 " (cutoff:3.500A) removed outlier: 16.235A pdb=" N THR G 172 " --> pdb=" O SER G 181 " (cutoff:3.500A) removed outlier: 14.976A pdb=" N VAL G 170 " --> pdb=" O PRO G 183 " (cutoff:3.500A) removed outlier: 13.851A pdb=" N GLY G 185 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 13.854A pdb=" N ARG G 168 " --> pdb=" O GLY G 185 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N SER G 187 " --> pdb=" O GLU G 166 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N GLU G 166 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLY G 164 " --> pdb=" O PRO G 189 " (cutoff:3.500A) 1096 hydrogen bonds defined for protein. 3141 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7198 1.36 - 1.51: 6103 1.51 - 1.65: 8087 1.65 - 1.80: 158 1.80 - 1.95: 28 Bond restraints: 21574 Sorted by residual: bond pdb=" CB ASP C 222 " pdb=" CG ASP C 222 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.19e+00 bond pdb=" C3' DT M 7 " pdb=" O3' DT M 7 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.60e+00 bond pdb=" SD MET B 294 " pdb=" CE MET B 294 " ideal model delta sigma weight residual 1.791 1.762 0.029 2.50e-02 1.60e+03 1.31e+00 bond pdb=" CG LEU C 252 " pdb=" CD1 LEU C 252 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CG LEU D 333 " pdb=" CD2 LEU D 333 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 ... (remaining 21569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 29031 2.09 - 4.19: 451 4.19 - 6.28: 53 6.28 - 8.37: 2 8.37 - 10.47: 1 Bond angle restraints: 29538 Sorted by residual: angle pdb=" N GLY D 20 " pdb=" CA GLY D 20 " pdb=" C GLY D 20 " ideal model delta sigma weight residual 115.08 120.88 -5.80 1.19e+00 7.06e-01 2.38e+01 angle pdb=" C ASP F 120 " pdb=" N ASP F 121 " pdb=" CA ASP F 121 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.78e+00 angle pdb=" CA LEU C 139 " pdb=" CB LEU C 139 " pdb=" CG LEU C 139 " ideal model delta sigma weight residual 116.30 126.77 -10.47 3.50e+00 8.16e-02 8.94e+00 angle pdb=" C CYS F 333 " pdb=" N GLU F 334 " pdb=" CA GLU F 334 " ideal model delta sigma weight residual 121.54 127.06 -5.52 1.91e+00 2.74e-01 8.36e+00 angle pdb=" N SER C 2 " pdb=" CA SER C 2 " pdb=" C SER C 2 " ideal model delta sigma weight residual 110.80 104.77 6.03 2.13e+00 2.20e-01 8.02e+00 ... (remaining 29533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 12436 34.06 - 68.13: 538 68.13 - 102.19: 33 102.19 - 136.26: 3 136.26 - 170.32: 2 Dihedral angle restraints: 13012 sinusoidal: 5677 harmonic: 7335 Sorted by residual: dihedral pdb=" CA GLN G 16 " pdb=" C GLN G 16 " pdb=" N VAL G 17 " pdb=" CA VAL G 17 " ideal model delta harmonic sigma weight residual 180.00 156.78 23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA SER C 2 " pdb=" C SER C 2 " pdb=" N TYR C 3 " pdb=" CA TYR C 3 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA VAL D 19 " pdb=" C VAL D 19 " pdb=" N GLY D 20 " pdb=" CA GLY D 20 " ideal model delta harmonic sigma weight residual 180.00 158.72 21.28 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 13009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2195 0.035 - 0.071: 906 0.071 - 0.106: 239 0.106 - 0.141: 61 0.141 - 0.177: 6 Chirality restraints: 3407 Sorted by residual: chirality pdb=" CB THR B 71 " pdb=" CA THR B 71 " pdb=" OG1 THR B 71 " pdb=" CG2 THR B 71 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CG LEU A 73 " pdb=" CB LEU A 73 " pdb=" CD1 LEU A 73 " pdb=" CD2 LEU A 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA ASP F 121 " pdb=" N ASP F 121 " pdb=" C ASP F 121 " pdb=" CB ASP F 121 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 3404 not shown) Planarity restraints: 3630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE G 241 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO G 242 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO G 242 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 242 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 1 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.26e+00 pdb=" C MET C 1 " 0.031 2.00e-02 2.50e+03 pdb=" O MET C 1 " -0.012 2.00e-02 2.50e+03 pdb=" N SER C 2 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 35 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" CD GLN A 35 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLN A 35 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 GLN A 35 " -0.010 2.00e-02 2.50e+03 ... (remaining 3627 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 6 2.44 - 3.06: 13187 3.06 - 3.67: 31759 3.67 - 4.29: 47412 4.29 - 4.90: 79299 Nonbonded interactions: 171663 Sorted by model distance: nonbonded pdb=" OG1 THR C 52 " pdb="MG MG C 703 " model vdw 1.829 2.170 nonbonded pdb=" OG1 THR D 52 " pdb="MG MG D 703 " model vdw 1.892 2.170 nonbonded pdb=" OG1 THR B 52 " pdb="MG MG B 703 " model vdw 1.895 2.170 nonbonded pdb=" O2G AGS B 702 " pdb="MG MG B 703 " model vdw 1.972 2.170 nonbonded pdb=" O2G AGS D 702 " pdb="MG MG D 703 " model vdw 2.026 2.170 ... (remaining 171658 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 2 through 361 or resid 701 through 703)) selection = (chain 'C' and (resid 2 through 361 or resid 701 through 703)) selection = chain 'D' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 365) } 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.070 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 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 : 0.005 0.045 21590 Z= 0.225 Angle : 0.664 13.180 29562 Z= 0.334 Chirality : 0.042 0.177 3407 Planarity : 0.004 0.046 3630 Dihedral : 17.383 170.321 8252 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.17), residues: 2516 helix: 1.52 (0.14), residues: 1281 sheet: 1.04 (0.24), residues: 437 loop : 0.02 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 47 TYR 0.016 0.002 TYR F 154 PHE 0.022 0.002 PHE C 87 TRP 0.019 0.002 TRP C 10 HIS 0.009 0.002 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (21574) covalent geometry : angle 0.63960 / 0.33 (29538) hydrogen bonds : bond 0.13721 / 8.89 ( 1167) hydrogen bonds : angle 5.12871 / 3.74 ( 3283) metal coordination : bond 0.00841 / 0.43 ( 16) metal coordination : angle 6.28577 / 3.80 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8074 (mp0) cc_final: 0.7819 (mp0) REVERT: A 277 ARG cc_start: 0.9202 (mtp85) cc_final: 0.8430 (mtp85) REVERT: B 71 THR cc_start: 0.9243 (t) cc_final: 0.9042 (p) REVERT: B 265 MET cc_start: 0.8689 (mmp) cc_final: 0.8433 (mmp) REVERT: C 1 MET cc_start: 0.6045 (ptm) cc_final: 0.5794 (ptm) REVERT: C 248 GLN cc_start: 0.8427 (tt0) cc_final: 0.8126 (tt0) REVERT: C 294 MET cc_start: 0.8899 (mmp) cc_final: 0.8581 (mmp) REVERT: D 137 ASN cc_start: 0.8703 (m-40) cc_final: 0.8470 (m-40) REVERT: D 244 LEU cc_start: 0.8744 (mt) cc_final: 0.8392 (mt) REVERT: D 284 GLU cc_start: 0.7994 (tp30) cc_final: 0.7696 (mm-30) REVERT: E 314 ASP cc_start: 0.8436 (t0) cc_final: 0.8217 (t0) REVERT: F 288 ASN cc_start: 0.7865 (m-40) cc_final: 0.7574 (m-40) REVERT: G 8 GLU cc_start: 0.8353 (pp20) cc_final: 0.8035 (pp20) REVERT: G 12 LYS cc_start: 0.8601 (tppt) cc_final: 0.8358 (tppt) REVERT: G 165 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7513 (mm-30) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.2053 time to fit residues: 100.8824 Evaluate side-chains 300 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 269 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS G 275 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.049407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2255 r_free = 0.2255 target = 0.038700 restraints weight = 48089.074| |-----------------------------------------------------------------------------| r_work (start): 0.2251 rms_B_bonded: 1.45 r_work: 0.2154 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2053 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21590 Z= 0.176 Angle : 0.628 11.678 29562 Z= 0.313 Chirality : 0.040 0.168 3407 Planarity : 0.004 0.044 3630 Dihedral : 16.541 171.106 3452 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.71 % Allowed : 6.99 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.17), residues: 2516 helix: 1.82 (0.15), residues: 1293 sheet: 1.12 (0.24), residues: 437 loop : 0.17 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 80 TYR 0.025 0.002 TYR F 310 PHE 0.017 0.002 PHE F 3 TRP 0.018 0.001 TRP C 10 HIS 0.009 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (21574) covalent geometry : angle 0.60421 / 0.31 (29538) hydrogen bonds : bond 0.04619 / 3.07 ( 1167) hydrogen bonds : angle 4.19645 / 3.08 ( 3283) metal coordination : bond 0.00597 / 0.30 ( 16) metal coordination : angle 6.02020 / 3.67 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 321 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 265 MET cc_start: 0.8695 (mmp) cc_final: 0.8459 (mmp) REVERT: C 1 MET cc_start: 0.6194 (ptm) cc_final: 0.5887 (ptm) REVERT: C 294 MET cc_start: 0.8909 (mmp) cc_final: 0.8649 (mmp) REVERT: D 137 ASN cc_start: 0.8702 (m-40) cc_final: 0.8482 (m-40) REVERT: D 244 LEU cc_start: 0.8785 (mt) cc_final: 0.8448 (mt) REVERT: D 284 GLU cc_start: 0.8024 (tp30) cc_final: 0.7755 (mm-30) REVERT: E 85 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8680 (mtmm) REVERT: F 154 TYR cc_start: 0.9203 (p90) cc_final: 0.8881 (p90) REVERT: F 206 MET cc_start: 0.9004 (ttp) cc_final: 0.8751 (ttm) REVERT: F 278 PHE cc_start: 0.8738 (m-80) cc_final: 0.8525 (m-80) REVERT: F 288 ASN cc_start: 0.7835 (m-40) cc_final: 0.7533 (m-40) REVERT: G 8 GLU cc_start: 0.8340 (pp20) cc_final: 0.7941 (pp20) REVERT: G 165 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7549 (mm-30) outliers start: 15 outliers final: 8 residues processed: 328 average time/residue: 0.1985 time to fit residues: 91.8881 Evaluate side-chains 308 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 299 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 172 optimal weight: 0.4980 chunk 194 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 208 optimal weight: 2.9990 chunk 229 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 182 GLN C 269 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 GLN G 15 GLN G 61 GLN ** G 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.050271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2280 r_free = 0.2280 target = 0.039509 restraints weight = 47876.351| |-----------------------------------------------------------------------------| r_work (start): 0.2275 rms_B_bonded: 1.46 r_work: 0.2178 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2077 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21590 Z= 0.136 Angle : 0.568 11.639 29562 Z= 0.285 Chirality : 0.038 0.163 3407 Planarity : 0.004 0.044 3630 Dihedral : 16.483 171.305 3452 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.95 % Allowed : 8.60 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.17), residues: 2516 helix: 2.02 (0.15), residues: 1292 sheet: 1.20 (0.24), residues: 434 loop : 0.27 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 80 TYR 0.010 0.001 TYR F 310 PHE 0.011 0.001 PHE G 3 TRP 0.017 0.001 TRP C 10 HIS 0.008 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (21574) covalent geometry : angle 0.54692 / 0.28 (29538) hydrogen bonds : bond 0.04009 / 2.67 ( 1167) hydrogen bonds : angle 3.93748 / 2.90 ( 3283) metal coordination : bond 0.00384 / 0.19 ( 16) metal coordination : angle 5.45256 / 3.33 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 316 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: A 277 ARG cc_start: 0.9203 (mtt-85) cc_final: 0.8592 (mtp85) REVERT: B 98 ARG cc_start: 0.8866 (mmt90) cc_final: 0.8625 (mmt-90) REVERT: B 265 MET cc_start: 0.8680 (mmp) cc_final: 0.8429 (mmp) REVERT: C 1 MET cc_start: 0.6189 (ptm) cc_final: 0.5898 (ptm) REVERT: D 137 ASN cc_start: 0.8676 (m-40) cc_final: 0.8454 (m-40) REVERT: D 244 LEU cc_start: 0.8764 (mt) cc_final: 0.8516 (mt) REVERT: D 284 GLU cc_start: 0.8082 (tp30) cc_final: 0.7779 (mm-30) REVERT: F 154 TYR cc_start: 0.9193 (p90) cc_final: 0.8906 (p90) REVERT: F 206 MET cc_start: 0.9061 (ttp) cc_final: 0.8819 (ttm) REVERT: F 278 PHE cc_start: 0.8716 (m-80) cc_final: 0.8447 (m-80) REVERT: F 288 ASN cc_start: 0.7835 (m-40) cc_final: 0.7591 (m-40) REVERT: G 8 GLU cc_start: 0.8418 (pp20) cc_final: 0.8029 (pp20) REVERT: G 56 ARG cc_start: 0.8943 (mtt90) cc_final: 0.8693 (mtt90) REVERT: G 165 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7478 (tp30) outliers start: 20 outliers final: 11 residues processed: 329 average time/residue: 0.1946 time to fit residues: 90.8172 Evaluate side-chains 313 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 301 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 281 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 191 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 179 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 269 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.050093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2273 r_free = 0.2273 target = 0.039319 restraints weight = 47926.168| |-----------------------------------------------------------------------------| r_work (start): 0.2268 rms_B_bonded: 1.46 r_work: 0.2171 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2070 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21590 Z= 0.144 Angle : 0.567 11.813 29562 Z= 0.285 Chirality : 0.038 0.210 3407 Planarity : 0.004 0.044 3630 Dihedral : 16.471 171.306 3452 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.32 % Allowed : 9.69 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.17), residues: 2516 helix: 2.09 (0.15), residues: 1293 sheet: 1.23 (0.24), residues: 430 loop : 0.28 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 80 TYR 0.016 0.001 TYR F 310 PHE 0.012 0.001 PHE F 3 TRP 0.016 0.001 TRP C 10 HIS 0.007 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (21574) covalent geometry : angle 0.54768 / 0.28 (29538) hydrogen bonds : bond 0.03903 / 2.61 ( 1167) hydrogen bonds : angle 3.86737 / 2.85 ( 3283) metal coordination : bond 0.00397 / 0.21 ( 16) metal coordination : angle 5.18972 / 3.17 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 302 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: A 277 ARG cc_start: 0.9199 (mtt-85) cc_final: 0.8590 (mtp85) REVERT: B 98 ARG cc_start: 0.8854 (mmt90) cc_final: 0.8638 (mmt-90) REVERT: B 265 MET cc_start: 0.8670 (mmp) cc_final: 0.8444 (mmp) REVERT: C 1 MET cc_start: 0.6288 (ptm) cc_final: 0.6031 (ptm) REVERT: C 117 ARG cc_start: 0.8715 (mtp85) cc_final: 0.8354 (ttp-110) REVERT: D 137 ASN cc_start: 0.8696 (m-40) cc_final: 0.8482 (m-40) REVERT: D 171 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8687 (mp) REVERT: D 244 LEU cc_start: 0.8746 (mt) cc_final: 0.8487 (mt) REVERT: D 284 GLU cc_start: 0.8122 (tp30) cc_final: 0.7813 (mm-30) REVERT: E 85 LYS cc_start: 0.8853 (mtmm) cc_final: 0.8572 (mtmm) REVERT: F 154 TYR cc_start: 0.9207 (p90) cc_final: 0.8913 (p90) REVERT: F 173 ASP cc_start: 0.8402 (t0) cc_final: 0.8095 (t0) REVERT: F 206 MET cc_start: 0.9067 (ttp) cc_final: 0.8822 (ttm) REVERT: F 278 PHE cc_start: 0.8781 (m-80) cc_final: 0.8478 (m-80) REVERT: F 288 ASN cc_start: 0.7915 (m-40) cc_final: 0.7673 (m-40) REVERT: G 8 GLU cc_start: 0.8440 (pp20) cc_final: 0.8069 (pp20) REVERT: G 56 ARG cc_start: 0.8935 (mtt90) cc_final: 0.8649 (mtt90) REVERT: G 165 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7517 (tp30) outliers start: 28 outliers final: 16 residues processed: 323 average time/residue: 0.2003 time to fit residues: 92.1137 Evaluate side-chains 313 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 295 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 70 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 0.0770 chunk 174 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 210 optimal weight: 0.7980 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN C 269 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS G 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.049522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2257 r_free = 0.2257 target = 0.038779 restraints weight = 47879.107| |-----------------------------------------------------------------------------| r_work (start): 0.2253 rms_B_bonded: 1.45 r_work: 0.2155 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2054 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21590 Z= 0.169 Angle : 0.583 11.336 29562 Z= 0.293 Chirality : 0.039 0.173 3407 Planarity : 0.004 0.043 3630 Dihedral : 16.509 171.531 3452 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.70 % Allowed : 10.87 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.17), residues: 2516 helix: 2.08 (0.15), residues: 1291 sheet: 1.18 (0.24), residues: 438 loop : 0.28 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 263 TYR 0.018 0.001 TYR F 310 PHE 0.013 0.001 PHE G 3 TRP 0.015 0.001 TRP C 10 HIS 0.007 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (21574) covalent geometry : angle 0.56367 / 0.29 (29538) hydrogen bonds : bond 0.04084 / 2.73 ( 1167) hydrogen bonds : angle 3.86789 / 2.85 ( 3283) metal coordination : bond 0.00489 / 0.27 ( 16) metal coordination : angle 5.28986 / 3.23 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 301 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: A 277 ARG cc_start: 0.9196 (mtt-85) cc_final: 0.8563 (mtp85) REVERT: B 265 MET cc_start: 0.8679 (mmp) cc_final: 0.8465 (mmp) REVERT: C 1 MET cc_start: 0.6358 (ptm) cc_final: 0.6095 (ptm) REVERT: D 137 ASN cc_start: 0.8718 (m-40) cc_final: 0.8496 (m-40) REVERT: D 171 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8706 (mp) REVERT: D 244 LEU cc_start: 0.8783 (mt) cc_final: 0.8539 (mt) REVERT: D 284 GLU cc_start: 0.8126 (tp30) cc_final: 0.7866 (mm-30) REVERT: E 204 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8501 (mp) REVERT: F 154 TYR cc_start: 0.9211 (p90) cc_final: 0.8918 (p90) REVERT: F 173 ASP cc_start: 0.8413 (t0) cc_final: 0.8099 (t0) REVERT: F 206 MET cc_start: 0.9071 (ttp) cc_final: 0.8690 (ttm) REVERT: F 278 PHE cc_start: 0.8823 (m-80) cc_final: 0.8532 (m-80) REVERT: F 288 ASN cc_start: 0.7919 (m-40) cc_final: 0.7677 (m-40) REVERT: G 8 GLU cc_start: 0.8461 (pp20) cc_final: 0.8103 (pp20) REVERT: G 56 ARG cc_start: 0.8920 (mtt90) cc_final: 0.8624 (mtt90) REVERT: G 130 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8556 (pp) REVERT: G 165 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7548 (tp30) REVERT: G 206 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8140 (ttm) outliers start: 36 outliers final: 18 residues processed: 327 average time/residue: 0.1925 time to fit residues: 90.4132 Evaluate side-chains 310 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 287 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 204 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 219 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 269 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.049077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2243 r_free = 0.2243 target = 0.038349 restraints weight = 47939.965| |-----------------------------------------------------------------------------| r_work (start): 0.2239 rms_B_bonded: 1.45 r_work: 0.2141 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2040 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21590 Z= 0.188 Angle : 0.600 10.945 29562 Z= 0.301 Chirality : 0.039 0.242 3407 Planarity : 0.004 0.043 3630 Dihedral : 16.561 171.756 3452 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.65 % Allowed : 12.24 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.17), residues: 2516 helix: 2.02 (0.15), residues: 1292 sheet: 1.09 (0.24), residues: 439 loop : 0.28 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 263 TYR 0.027 0.002 TYR F 310 PHE 0.012 0.001 PHE F 3 TRP 0.017 0.002 TRP C 10 HIS 0.007 0.001 HIS E 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (21574) covalent geometry : angle 0.58054 / 0.30 (29538) hydrogen bonds : bond 0.04248 / 2.85 ( 1167) hydrogen bonds : angle 3.90413 / 2.87 ( 3283) metal coordination : bond 0.00539 / 0.31 ( 16) metal coordination : angle 5.38852 / 3.30 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 301 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: A 277 ARG cc_start: 0.9195 (mtt-85) cc_final: 0.8548 (mtp85) REVERT: B 265 MET cc_start: 0.8676 (mmp) cc_final: 0.8450 (mmp) REVERT: C 1 MET cc_start: 0.6492 (ptm) cc_final: 0.6279 (ptm) REVERT: D 137 ASN cc_start: 0.8736 (m-40) cc_final: 0.8516 (m-40) REVERT: D 171 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8723 (mp) REVERT: D 244 LEU cc_start: 0.8795 (mt) cc_final: 0.8565 (mt) REVERT: D 284 GLU cc_start: 0.8139 (tp30) cc_final: 0.7864 (mm-30) REVERT: E 204 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8534 (mp) REVERT: F 154 TYR cc_start: 0.9214 (p90) cc_final: 0.8911 (p90) REVERT: F 206 MET cc_start: 0.9061 (ttp) cc_final: 0.8755 (ttm) REVERT: F 288 ASN cc_start: 0.7978 (m-40) cc_final: 0.7647 (m110) REVERT: G 8 GLU cc_start: 0.8499 (pp20) cc_final: 0.8191 (pp20) REVERT: G 56 ARG cc_start: 0.8929 (mtt90) cc_final: 0.8632 (mtt90) REVERT: G 105 ARG cc_start: 0.8406 (ttm110) cc_final: 0.8119 (ttm110) REVERT: G 130 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8568 (pp) REVERT: G 165 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7562 (tp30) REVERT: G 206 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8104 (ttm) outliers start: 35 outliers final: 21 residues processed: 327 average time/residue: 0.1914 time to fit residues: 88.9942 Evaluate side-chains 320 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 294 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 170 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 168 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 chunk 211 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 269 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.051000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2297 r_free = 0.2297 target = 0.040185 restraints weight = 47775.687| |-----------------------------------------------------------------------------| r_work (start): 0.2292 rms_B_bonded: 1.47 r_work: 0.2196 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2096 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21590 Z= 0.115 Angle : 0.545 11.284 29562 Z= 0.275 Chirality : 0.037 0.164 3407 Planarity : 0.004 0.045 3630 Dihedral : 16.489 170.828 3452 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.51 % Allowed : 12.52 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.17), residues: 2516 helix: 2.20 (0.15), residues: 1293 sheet: 1.08 (0.24), residues: 448 loop : 0.39 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 263 TYR 0.019 0.001 TYR F 310 PHE 0.014 0.001 PHE G 3 TRP 0.018 0.001 TRP C 10 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (21574) covalent geometry : angle 0.52775 / 0.27 (29538) hydrogen bonds : bond 0.03448 / 2.30 ( 1167) hydrogen bonds : angle 3.71863 / 2.73 ( 3283) metal coordination : bond 0.00290 / 0.16 ( 16) metal coordination : angle 4.81679 / 2.97 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 313 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: A 277 ARG cc_start: 0.9164 (mtt-85) cc_final: 0.8513 (mtp85) REVERT: C 1 MET cc_start: 0.6362 (ptm) cc_final: 0.6088 (ptm) REVERT: D 137 ASN cc_start: 0.8699 (m-40) cc_final: 0.8484 (m-40) REVERT: D 171 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8623 (mt) REVERT: E 57 LYS cc_start: 0.8893 (ttpp) cc_final: 0.8693 (ptmm) REVERT: E 204 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8361 (mp) REVERT: F 154 TYR cc_start: 0.9210 (p90) cc_final: 0.8953 (p90) REVERT: F 206 MET cc_start: 0.9026 (ttp) cc_final: 0.8759 (ttm) REVERT: F 288 ASN cc_start: 0.7918 (m-40) cc_final: 0.7594 (m110) REVERT: F 315 MET cc_start: 0.7542 (ttm) cc_final: 0.7297 (ttm) REVERT: G 8 GLU cc_start: 0.8499 (pp20) cc_final: 0.8229 (pp20) REVERT: G 56 ARG cc_start: 0.8897 (mtt90) cc_final: 0.8590 (mtt90) REVERT: G 130 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8540 (pp) outliers start: 32 outliers final: 18 residues processed: 334 average time/residue: 0.1952 time to fit residues: 93.1084 Evaluate side-chains 315 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 293 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 217 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN C 269 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.050466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2283 r_free = 0.2283 target = 0.039666 restraints weight = 47328.857| |-----------------------------------------------------------------------------| r_work (start): 0.2278 rms_B_bonded: 1.46 r_work: 0.2181 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2080 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21590 Z= 0.138 Angle : 0.574 10.991 29562 Z= 0.289 Chirality : 0.038 0.144 3407 Planarity : 0.004 0.066 3630 Dihedral : 16.447 171.037 3452 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.32 % Allowed : 13.23 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.17), residues: 2516 helix: 2.23 (0.15), residues: 1293 sheet: 1.06 (0.24), residues: 449 loop : 0.41 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 279 TYR 0.018 0.001 TYR F 310 PHE 0.012 0.001 PHE F 3 TRP 0.014 0.001 TRP C 10 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (21574) covalent geometry : angle 0.55678 / 0.29 (29538) hydrogen bonds : bond 0.03660 / 2.45 ( 1167) hydrogen bonds : angle 3.71651 / 2.73 ( 3283) metal coordination : bond 0.00340 / 0.19 ( 16) metal coordination : angle 4.87420 / 2.98 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 294 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: C 1 MET cc_start: 0.6409 (ptm) cc_final: 0.6181 (ptm) REVERT: D 137 ASN cc_start: 0.8712 (m-40) cc_final: 0.8476 (m-40) REVERT: D 171 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8701 (mp) REVERT: E 204 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8394 (mp) REVERT: F 154 TYR cc_start: 0.9212 (p90) cc_final: 0.8961 (p90) REVERT: F 206 MET cc_start: 0.9027 (ttp) cc_final: 0.8807 (ttm) REVERT: F 288 ASN cc_start: 0.7945 (m-40) cc_final: 0.7629 (m110) REVERT: G 8 GLU cc_start: 0.8509 (pp20) cc_final: 0.8248 (pp20) REVERT: G 56 ARG cc_start: 0.8898 (mtt90) cc_final: 0.8586 (mtt90) REVERT: G 130 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8545 (pp) outliers start: 28 outliers final: 18 residues processed: 314 average time/residue: 0.1952 time to fit residues: 87.5218 Evaluate side-chains 315 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 293 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 9 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 229 optimal weight: 0.0970 chunk 203 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 269 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.050468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2283 r_free = 0.2283 target = 0.039633 restraints weight = 47662.043| |-----------------------------------------------------------------------------| r_work (start): 0.2279 rms_B_bonded: 1.46 r_work: 0.2182 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2081 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21590 Z= 0.138 Angle : 0.574 11.110 29562 Z= 0.290 Chirality : 0.038 0.142 3407 Planarity : 0.004 0.043 3630 Dihedral : 16.450 171.155 3452 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.18 % Allowed : 13.33 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.17), residues: 2516 helix: 2.24 (0.15), residues: 1292 sheet: 1.04 (0.23), residues: 449 loop : 0.41 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 263 TYR 0.017 0.001 TYR F 310 PHE 0.012 0.001 PHE G 3 TRP 0.015 0.001 TRP C 10 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (21574) covalent geometry : angle 0.55713 / 0.29 (29538) hydrogen bonds : bond 0.03649 / 2.45 ( 1167) hydrogen bonds : angle 3.70013 / 2.72 ( 3283) metal coordination : bond 0.00337 / 0.19 ( 16) metal coordination : angle 4.87200 / 2.98 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 302 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: A 277 ARG cc_start: 0.9171 (mtt-85) cc_final: 0.8547 (mtp85) REVERT: C 1 MET cc_start: 0.6416 (ptm) cc_final: 0.6185 (ptm) REVERT: D 137 ASN cc_start: 0.8720 (m-40) cc_final: 0.8487 (m-40) REVERT: D 171 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8705 (mp) REVERT: E 204 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8390 (mp) REVERT: F 154 TYR cc_start: 0.9217 (p90) cc_final: 0.8970 (p90) REVERT: F 206 MET cc_start: 0.9031 (ttp) cc_final: 0.8828 (ttm) REVERT: F 288 ASN cc_start: 0.8008 (m-40) cc_final: 0.7695 (m110) REVERT: G 8 GLU cc_start: 0.8502 (pp20) cc_final: 0.8260 (pp20) REVERT: G 56 ARG cc_start: 0.8896 (mtt90) cc_final: 0.8577 (mtt90) REVERT: G 130 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8544 (pp) outliers start: 25 outliers final: 15 residues processed: 319 average time/residue: 0.1922 time to fit residues: 88.4242 Evaluate side-chains 312 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 293 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 69 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 152 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 237 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 269 ASN E 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.051066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2299 r_free = 0.2299 target = 0.040221 restraints weight = 47656.870| |-----------------------------------------------------------------------------| r_work (start): 0.2294 rms_B_bonded: 1.46 r_work: 0.2198 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2098 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21590 Z= 0.124 Angle : 0.563 10.950 29562 Z= 0.286 Chirality : 0.037 0.163 3407 Planarity : 0.004 0.044 3630 Dihedral : 16.428 171.124 3452 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.09 % Allowed : 13.66 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.17), residues: 2516 helix: 2.29 (0.15), residues: 1291 sheet: 1.04 (0.24), residues: 443 loop : 0.41 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 263 TYR 0.017 0.001 TYR F 310 PHE 0.012 0.001 PHE G 3 TRP 0.016 0.001 TRP C 10 HIS 0.008 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (21574) covalent geometry : angle 0.54701 / 0.28 (29538) hydrogen bonds : bond 0.03468 / 2.32 ( 1167) hydrogen bonds : angle 3.64972 / 2.68 ( 3283) metal coordination : bond 0.00278 / 0.16 ( 16) metal coordination : angle 4.70871 / 2.90 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 303 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: A 277 ARG cc_start: 0.9174 (mtt-85) cc_final: 0.8542 (mtp85) REVERT: C 1 MET cc_start: 0.6400 (ptm) cc_final: 0.6131 (ptm) REVERT: C 117 ARG cc_start: 0.8791 (mtp85) cc_final: 0.8273 (ttp-110) REVERT: D 137 ASN cc_start: 0.8709 (m-40) cc_final: 0.8479 (m-40) REVERT: D 171 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8608 (mt) REVERT: E 204 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8385 (mp) REVERT: F 154 TYR cc_start: 0.9209 (p90) cc_final: 0.8978 (p90) REVERT: F 288 ASN cc_start: 0.8015 (m-40) cc_final: 0.7731 (m110) REVERT: G 8 GLU cc_start: 0.8497 (pp20) cc_final: 0.8226 (pp20) REVERT: G 56 ARG cc_start: 0.8894 (mtt90) cc_final: 0.8586 (mtt90) REVERT: G 96 ARG cc_start: 0.8262 (tpp-160) cc_final: 0.7851 (mmt-90) REVERT: G 100 ARG cc_start: 0.8819 (mmm-85) cc_final: 0.8430 (mmm-85) REVERT: G 105 ARG cc_start: 0.8383 (ttm110) cc_final: 0.7923 (ttm110) REVERT: G 130 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8541 (pp) REVERT: G 206 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8169 (ttm) outliers start: 23 outliers final: 16 residues processed: 318 average time/residue: 0.1993 time to fit residues: 90.4199 Evaluate side-chains 319 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 298 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 242 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 chunk 141 optimal weight: 0.0370 chunk 58 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 199 optimal weight: 0.0070 chunk 138 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 241 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.051634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2326 r_free = 0.2326 target = 0.041093 restraints weight = 47651.283| |-----------------------------------------------------------------------------| r_work (start): 0.2322 rms_B_bonded: 1.31 r_work: 0.2233 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2137 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21590 Z= 0.117 Angle : 0.559 10.789 29562 Z= 0.284 Chirality : 0.037 0.162 3407 Planarity : 0.004 0.045 3630 Dihedral : 16.403 171.143 3452 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.09 % Allowed : 13.56 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.17), residues: 2516 helix: 2.35 (0.15), residues: 1289 sheet: 1.04 (0.24), residues: 443 loop : 0.44 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 263 TYR 0.016 0.001 TYR F 310 PHE 0.011 0.001 PHE G 3 TRP 0.016 0.001 TRP C 10 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (21574) covalent geometry : angle 0.54346 / 0.28 (29538) hydrogen bonds : bond 0.03339 / 2.23 ( 1167) hydrogen bonds : angle 3.60884 / 2.65 ( 3283) metal coordination : bond 0.00235 / 0.13 ( 16) metal coordination : angle 4.59706 / 2.83 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5100.33 seconds wall clock time: 87 minutes 59.95 seconds (5279.95 seconds total)