Starting phenix.real_space_refine on Sat Jun 28 20:21:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uge_42222/06_2025/8uge_42222.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uge_42222/06_2025/8uge_42222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uge_42222/06_2025/8uge_42222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uge_42222/06_2025/8uge_42222.map" model { file = "/net/cci-nas-00/data/ceres_data/8uge_42222/06_2025/8uge_42222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uge_42222/06_2025/8uge_42222.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 10 7.16 5 P 26 5.49 5 S 169 5.16 5 C 21553 2.51 5 N 5626 2.21 5 O 6150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33534 Number of models: 1 Model: "" Number of chains: 33 Chain: "3A" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3411 Classifications: {'peptide': 440} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 421} Chain breaks: 1 Chain: "3B" Number of atoms: 3138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3138 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "3C" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3025 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 356} Chain: "3D" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1888 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 21, 'TRANS': 215} Chain: "3E" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1518 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain: "3F" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 868 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "3G" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 628 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 6, 'TRANS': 67} Chain: "3H" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 533 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain breaks: 1 Chain: "3I" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 337 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "3J" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 464 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain: "3N" Number of atoms: 3424 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 445, 3415 Classifications: {'peptide': 445} Incomplete info: {'n_c_alpha_c_only': 3} Link IDs: {'PTRANS': 18, 'TRANS': 426} Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Conformer: "B" Number of residues, atoms: 445, 3415 Classifications: {'peptide': 445} Incomplete info: {'n_c_alpha_c_only': 3} Link IDs: {'PTRANS': 18, 'TRANS': 426} Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 bond proxies already assigned to first conformer: 3477 Chain: "3O" Number of atoms: 3124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3124 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 11, 'TRANS': 405} Unresolved chain links: 1 Unresolved chain link angles: 10 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "3P" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3024 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 22, 'TRANS': 356} Chain: "3Q" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1904 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 21, 'TRANS': 217} Chain: "3R" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1518 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain: "3S" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 868 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "3T" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 628 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 6, 'TRANS': 67} Chain: "3U" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 533 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "3V" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 223 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "3W" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 464 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain: "3X" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "3Y" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 421 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "3A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 85 Chain: "3C" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 254 Unusual residues: {'3PE': 2, 'CDL': 1, 'HEM': 2, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 144 Planarities with less than four sites: {'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-4': 2, 'U10:plan-5': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 64 Chain: "3D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'3PE': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'HEC:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "3E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'FES': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "3G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 66 Chain: "3N" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "3P" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 269 Unusual residues: {'3PE': 1, 'CDL': 2, 'HEM': 2, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 179 Planarities with less than four sites: {'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-4': 1, 'U10:plan-5': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 60 Chain: "3Q" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 147 Unusual residues: {'3PE': 1, 'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "3R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'FES': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "3X" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "3Y" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12554 SG CYS3E 217 74.705 44.144 22.435 1.00133.58 S ATOM 12690 SG CYS3E 236 74.898 41.930 19.532 1.00145.70 S ATOM 28378 SG CYS3R 217 86.213 101.198 42.442 1.00143.44 S ATOM 28514 SG CYS3R 236 83.016 101.296 40.513 1.00138.19 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN3N 207 " occ=0.98 ... (16 atoms not shown) pdb=" NE2BGLN3N 207 " occ=0.02 Time building chain proxies: 20.84, per 1000 atoms: 0.62 Number of scatterers: 33534 At special positions: 0 Unit cell: (148.96, 138.32, 170.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 10 26.01 S 169 16.00 P 26 15.00 O 6150 8.00 N 5626 7.00 C 21553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS3E 222 " - pdb=" SG CYS3E 238 " distance=2.03 Simple disulfide: pdb=" SG CYS3H 49 " - pdb=" SG CYS3H 93 " distance=2.03 Simple disulfide: pdb=" SG CYS3H 65 " - pdb=" SG CYS3H 79 " distance=2.03 Simple disulfide: pdb=" SG CYS3R 222 " - pdb=" SG CYS3R 238 " distance=2.03 Simple disulfide: pdb=" SG CYS3U 24 " - pdb=" SG CYS3U 68 " distance=2.03 Simple disulfide: pdb=" SG CYS3U 40 " - pdb=" SG CYS3U 54 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.77 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES3E 301 " pdb="FE1 FES3E 301 " - pdb=" SG CYS3E 217 " pdb="FE1 FES3E 301 " - pdb=" SG CYS3E 236 " pdb="FE2 FES3E 301 " - pdb=" ND1 HIS3E 239 " pdb="FE2 FES3E 301 " - pdb=" ND1 HIS3E 219 " pdb=" FES3R 301 " pdb="FE1 FES3R 301 " - pdb=" SG CYS3R 236 " pdb="FE1 FES3R 301 " - pdb=" SG CYS3R 217 " pdb="FE2 FES3R 301 " - pdb=" N HIS3R 239 " pdb="FE2 FES3R 301 " - pdb=" ND1 HIS3R 219 " Number of angles added : 6 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7688 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 19 sheets defined 56.8% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain '3A' and resid 4 through 10 removed outlier: 3.525A pdb=" N LEU3A 8 " --> pdb=" O TYR3A 4 " (cutoff:3.500A) Processing helix chain '3A' and resid 44 through 48 Processing helix chain '3A' and resid 54 through 64 removed outlier: 4.400A pdb=" N PHE3A 64 " --> pdb=" O GLU3A 60 " (cutoff:3.500A) Processing helix chain '3A' and resid 72 through 82 removed outlier: 3.994A pdb=" N GLU3A 76 " --> pdb=" O GLY3A 72 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL3A 79 " --> pdb=" O LEU3A 75 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET3A 82 " --> pdb=" O GLU3A 78 " (cutoff:3.500A) Processing helix chain '3A' and resid 105 through 118 removed outlier: 3.588A pdb=" N GLU3A 111 " --> pdb=" O PRO3A 107 " (cutoff:3.500A) Processing helix chain '3A' and resid 123 through 142 Processing helix chain '3A' and resid 144 through 158 removed outlier: 3.758A pdb=" N VAL3A 148 " --> pdb=" O SER3A 144 " (cutoff:3.500A) Processing helix chain '3A' and resid 161 through 165 Processing helix chain '3A' and resid 170 through 177 Processing helix chain '3A' and resid 178 through 190 Processing helix chain '3A' and resid 191 through 193 No H-bonds generated for 'chain '3A' and resid 191 through 193' Processing helix chain '3A' and resid 204 through 216 Processing helix chain '3A' and resid 266 through 278 Processing helix chain '3A' and resid 292 through 302 Processing helix chain '3A' and resid 330 through 348 Processing helix chain '3A' and resid 350 through 369 removed outlier: 3.520A pdb=" N LEU3A 369 " --> pdb=" O LEU3A 365 " (cutoff:3.500A) Processing helix chain '3A' and resid 371 through 386 Processing helix chain '3A' and resid 391 through 401 Processing helix chain '3A' and resid 403 through 415 Processing helix chain '3A' and resid 433 through 441 removed outlier: 3.524A pdb=" N MET3A 441 " --> pdb=" O ILE3A 437 " (cutoff:3.500A) Processing helix chain '3B' and resid 64 through 72 Processing helix chain '3B' and resid 81 through 93 removed outlier: 3.745A pdb=" N VAL3B 92 " --> pdb=" O GLY3B 88 " (cutoff:3.500A) Processing helix chain '3B' and resid 115 through 129 removed outlier: 3.792A pdb=" N LEU3B 119 " --> pdb=" O ASP3B 115 " (cutoff:3.500A) Processing helix chain '3B' and resid 133 through 153 removed outlier: 4.470A pdb=" N SER3B 142 " --> pdb=" O ALA3B 138 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN3B 143 " --> pdb=" O ALA3B 139 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU3B 144 " --> pdb=" O LEU3B 140 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG3B 145 " --> pdb=" O GLN3B 141 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE3B 146 " --> pdb=" O SER3B 142 " (cutoff:3.500A) Processing helix chain '3B' and resid 154 through 168 removed outlier: 4.048A pdb=" N GLN3B 158 " --> pdb=" O ASN3B 154 " (cutoff:3.500A) Processing helix chain '3B' and resid 179 through 183 removed outlier: 3.612A pdb=" N ILE3B 183 " --> pdb=" O ASP3B 180 " (cutoff:3.500A) Processing helix chain '3B' and resid 187 through 199 removed outlier: 3.548A pdb=" N LEU3B 191 " --> pdb=" O THR3B 187 " (cutoff:3.500A) Processing helix chain '3B' and resid 200 through 202 No H-bonds generated for 'chain '3B' and resid 200 through 202' Processing helix chain '3B' and resid 212 through 223 Processing helix chain '3B' and resid 266 through 280 Processing helix chain '3B' and resid 293 through 301 Processing helix chain '3B' and resid 332 through 351 removed outlier: 3.753A pdb=" N ASN3B 351 " --> pdb=" O ILE3B 347 " (cutoff:3.500A) Processing helix chain '3B' and resid 353 through 372 Processing helix chain '3B' and resid 374 through 388 Processing helix chain '3B' and resid 394 through 405 Processing helix chain '3B' and resid 406 through 411 removed outlier: 3.526A pdb=" N VAL3B 410 " --> pdb=" O ALA3B 406 " (cutoff:3.500A) Processing helix chain '3B' and resid 413 through 419 Processing helix chain '3C' and resid 8 through 19 Processing helix chain '3C' and resid 28 through 31 Processing helix chain '3C' and resid 32 through 53 Processing helix chain '3C' and resid 61 through 72 Processing helix chain '3C' and resid 75 through 104 removed outlier: 3.693A pdb=" N ILE3C 79 " --> pdb=" O TYR3C 75 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER3C 88 " --> pdb=" O ALA3C 84 " (cutoff:3.500A) Processing helix chain '3C' and resid 105 through 108 removed outlier: 3.537A pdb=" N MET3C 108 " --> pdb=" O GLY3C 105 " (cutoff:3.500A) No H-bonds generated for 'chain '3C' and resid 105 through 108' Processing helix chain '3C' and resid 109 through 133 Processing helix chain '3C' and resid 136 through 148 Processing helix chain '3C' and resid 149 through 153 Processing helix chain '3C' and resid 154 through 155 No H-bonds generated for 'chain '3C' and resid 154 through 155' Processing helix chain '3C' and resid 156 through 166 Processing helix chain '3C' and resid 171 through 202 removed outlier: 3.501A pdb=" N THR3C 176 " --> pdb=" O LYS3C 172 " (cutoff:3.500A) Proline residue: 3C 186 - end of helix Processing helix chain '3C' and resid 220 through 246 removed outlier: 3.570A pdb=" N THR3C 225 " --> pdb=" O HIS3C 221 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE3C 226 " --> pdb=" O PRO3C 222 " (cutoff:3.500A) Processing helix chain '3C' and resid 247 through 250 removed outlier: 4.410A pdb=" N LEU3C 250 " --> pdb=" O PRO3C 247 " (cutoff:3.500A) No H-bonds generated for 'chain '3C' and resid 247 through 250' Processing helix chain '3C' and resid 252 through 257 Processing helix chain '3C' and resid 271 through 284 removed outlier: 4.387A pdb=" N PHE3C 276 " --> pdb=" O TRP3C 272 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ALA3C 277 " --> pdb=" O TYR3C 273 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE3C 280 " --> pdb=" O PHE3C 276 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE3C 284 " --> pdb=" O ILE3C 280 " (cutoff:3.500A) Processing helix chain '3C' and resid 286 through 308 removed outlier: 4.017A pdb=" N ILE3C 298 " --> pdb=" O LEU3C 294 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU3C 301 " --> pdb=" O SER3C 297 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE3C 302 " --> pdb=" O ILE3C 298 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU3C 303 " --> pdb=" O LEU3C 299 " (cutoff:3.500A) Proline residue: 3C 305 - end of helix removed outlier: 3.582A pdb=" N HIS3C 308 " --> pdb=" O MET3C 304 " (cutoff:3.500A) Processing helix chain '3C' and resid 318 through 341 removed outlier: 3.662A pdb=" N GLY3C 340 " --> pdb=" O THR3C 336 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN3C 341 " --> pdb=" O TRP3C 337 " (cutoff:3.500A) Processing helix chain '3C' and resid 346 through 364 removed outlier: 3.581A pdb=" N PHE3C 359 " --> pdb=" O SER3C 355 " (cutoff:3.500A) Processing helix chain '3C' and resid 364 through 376 Processing helix chain '3D' and resid 110 through 124 Processing helix chain '3D' and resid 145 through 156 removed outlier: 3.562A pdb=" N VAL3D 156 " --> pdb=" O LEU3D 152 " (cutoff:3.500A) Processing helix chain '3D' and resid 185 through 193 Processing helix chain '3D' and resid 211 through 220 Processing helix chain '3D' and resid 267 through 284 Processing helix chain '3D' and resid 286 through 321 removed outlier: 4.425A pdb=" N LEU3D 303 " --> pdb=" O MET3D 299 " (cutoff:3.500A) Proline residue: 3D 306 - end of helix removed outlier: 4.519A pdb=" N VAL3D 318 " --> pdb=" O HIS3D 314 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU3D 319 " --> pdb=" O LYS3D 315 " (cutoff:3.500A) Processing helix chain '3E' and resid 79 through 83 removed outlier: 3.511A pdb=" N ILE3E 83 " --> pdb=" O HIS3E 80 " (cutoff:3.500A) Processing helix chain '3E' and resid 103 through 141 removed outlier: 4.323A pdb=" N ASP3E 108 " --> pdb=" O LYS3E 104 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA3E 109 " --> pdb=" O GLU3E 105 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE3E 136 " --> pdb=" O ALA3E 132 " (cutoff:3.500A) Processing helix chain '3E' and resid 180 through 190 Processing helix chain '3E' and resid 200 through 205 Processing helix chain '3F' and resid 25 through 37 removed outlier: 4.078A pdb=" N GLY3F 37 " --> pdb=" O TYR3F 33 " (cutoff:3.500A) Processing helix chain '3F' and resid 45 through 49 Processing helix chain '3F' and resid 52 through 62 Processing helix chain '3F' and resid 63 through 83 Processing helix chain '3F' and resid 88 through 92 removed outlier: 3.530A pdb=" N TRP3F 92 " --> pdb=" O LYS3F 89 " (cutoff:3.500A) Processing helix chain '3F' and resid 101 through 121 removed outlier: 4.652A pdb=" N TYR3F 105 " --> pdb=" O TYR3F 101 " (cutoff:3.500A) Processing helix chain '3G' and resid 34 through 72 removed outlier: 4.635A pdb=" N LEU3G 48 " --> pdb=" O ARG3G 44 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG3G 49 " --> pdb=" O ALA3G 45 " (cutoff:3.500A) Proline residue: 3G 52 - end of helix Processing helix chain '3H' and resid 40 through 51 removed outlier: 3.685A pdb=" N GLU3H 47 " --> pdb=" O THR3H 43 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN3H 48 " --> pdb=" O THR3H 44 " (cutoff:3.500A) Processing helix chain '3H' and resid 52 through 72 removed outlier: 3.659A pdb=" N ARG3H 72 " --> pdb=" O ARG3H 68 " (cutoff:3.500A) Processing helix chain '3H' and resid 79 through 97 removed outlier: 3.902A pdb=" N HIS3H 96 " --> pdb=" O HIS3H 92 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS3H 97 " --> pdb=" O CYS3H 93 " (cutoff:3.500A) Processing helix chain '3H' and resid 98 through 102 removed outlier: 3.701A pdb=" N LEU3H 102 " --> pdb=" O PHE3H 99 " (cutoff:3.500A) Processing helix chain '3I' and resid 51 through 56 Processing helix chain '3J' and resid 6 through 14 Processing helix chain '3J' and resid 17 through 48 removed outlier: 3.887A pdb=" N ARG3J 34 " --> pdb=" O LEU3J 30 " (cutoff:3.500A) Processing helix chain '3J' and resid 56 through 60 Processing helix chain '3N' and resid 44 through 48 Processing helix chain '3N' and resid 54 through 64 removed outlier: 4.528A pdb=" N PHE3N 64 " --> pdb=" O GLU3N 60 " (cutoff:3.500A) Processing helix chain '3N' and resid 72 through 82 removed outlier: 3.873A pdb=" N GLU3N 76 " --> pdb=" O GLY3N 72 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET3N 82 " --> pdb=" O GLU3N 78 " (cutoff:3.500A) Processing helix chain '3N' and resid 107 through 115 WARNING: missing atoms! Processing helix chain '3N' and resid 124 through 132 WARNING: missing atoms! removed outlier: 3.915A pdb=" N ASP3N 132 " --> pdb=" O GLU3N 128 " (cutoff:3.500A) Processing helix chain '3N' and resid 135 through 144 Processing helix chain '3N' and resid 144 through 158 Processing helix chain '3N' and resid 161 through 165 Processing helix chain '3N' and resid 182 through 190 Processing helix chain '3N' and resid 204 through 216 Processing helix chain '3N' and resid 217 through 219 No H-bonds generated for 'chain '3N' and resid 217 through 219' Processing helix chain '3N' and resid 266 through 278 Processing helix chain '3N' and resid 292 through 302 Processing helix chain '3N' and resid 330 through 348 removed outlier: 3.502A pdb=" N GLN3N 339 " --> pdb=" O MET3N 335 " (cutoff:3.500A) Processing helix chain '3N' and resid 350 through 369 Processing helix chain '3N' and resid 371 through 386 removed outlier: 3.547A pdb=" N LEU3N 384 " --> pdb=" O GLY3N 380 " (cutoff:3.500A) Processing helix chain '3N' and resid 391 through 401 Processing helix chain '3N' and resid 403 through 415 Processing helix chain '3N' and resid 433 through 441 Processing helix chain '3O' and resid 64 through 72 Processing helix chain '3O' and resid 81 through 93 removed outlier: 3.568A pdb=" N VAL3O 92 " --> pdb=" O GLY3O 88 " (cutoff:3.500A) Processing helix chain '3O' and resid 115 through 128 removed outlier: 3.941A pdb=" N LEU3O 119 " --> pdb=" O ASP3O 115 " (cutoff:3.500A) Processing helix chain '3O' and resid 133 through 153 removed outlier: 4.473A pdb=" N SER3O 142 " --> pdb=" O ALA3O 138 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN3O 143 " --> pdb=" O ALA3O 139 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG3O 145 " --> pdb=" O GLN3O 141 " (cutoff:3.500A) Processing helix chain '3O' and resid 155 through 168 Processing helix chain '3O' and resid 179 through 183 Processing helix chain '3O' and resid 187 through 199 Processing helix chain '3O' and resid 200 through 202 No H-bonds generated for 'chain '3O' and resid 200 through 202' Processing helix chain '3O' and resid 212 through 224 removed outlier: 3.526A pdb=" N LEU3O 216 " --> pdb=" O SER3O 212 " (cutoff:3.500A) Processing helix chain '3O' and resid 266 through 280 Processing helix chain '3O' and resid 293 through 301 Processing helix chain '3O' and resid 332 through 349 Processing helix chain '3O' and resid 353 through 372 removed outlier: 3.501A pdb=" N VAL3O 372 " --> pdb=" O TYR3O 368 " (cutoff:3.500A) Processing helix chain '3O' and resid 374 through 389 Processing helix chain '3O' and resid 394 through 404 Processing helix chain '3O' and resid 406 through 411 Processing helix chain '3O' and resid 413 through 419 Processing helix chain '3P' and resid 3 through 7 Processing helix chain '3P' and resid 8 through 19 Processing helix chain '3P' and resid 28 through 31 Processing helix chain '3P' and resid 32 through 53 Processing helix chain '3P' and resid 61 through 73 removed outlier: 3.766A pdb=" N VAL3P 73 " --> pdb=" O ILE3P 69 " (cutoff:3.500A) Processing helix chain '3P' and resid 75 through 104 removed outlier: 3.552A pdb=" N ILE3P 79 " --> pdb=" O TYR3P 75 " (cutoff:3.500A) Processing helix chain '3P' and resid 105 through 108 removed outlier: 3.805A pdb=" N MET3P 108 " --> pdb=" O GLY3P 105 " (cutoff:3.500A) No H-bonds generated for 'chain '3P' and resid 105 through 108' Processing helix chain '3P' and resid 109 through 131 Processing helix chain '3P' and resid 136 through 149 Processing helix chain '3P' and resid 150 through 153 Processing helix chain '3P' and resid 156 through 166 Processing helix chain '3P' and resid 171 through 203 Proline residue: 3P 186 - end of helix removed outlier: 3.796A pdb=" N GLU3P 202 " --> pdb=" O LEU3P 198 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR3P 203 " --> pdb=" O PHE3P 199 " (cutoff:3.500A) Processing helix chain '3P' and resid 220 through 246 removed outlier: 3.730A pdb=" N THR3P 225 " --> pdb=" O HIS3P 221 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE3P 226 " --> pdb=" O PRO3P 222 " (cutoff:3.500A) Processing helix chain '3P' and resid 252 through 257 Processing helix chain '3P' and resid 274 through 284 removed outlier: 3.718A pdb=" N ILE3P 280 " --> pdb=" O PHE3P 276 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE3P 284 " --> pdb=" O ILE3P 280 " (cutoff:3.500A) Processing helix chain '3P' and resid 286 through 308 removed outlier: 3.924A pdb=" N ILE3P 298 " --> pdb=" O LEU3P 294 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU3P 301 " --> pdb=" O SER3P 297 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE3P 302 " --> pdb=" O ILE3P 298 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU3P 303 " --> pdb=" O LEU3P 299 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET3P 304 " --> pdb=" O ILE3P 300 " (cutoff:3.500A) Proline residue: 3P 305 - end of helix Processing helix chain '3P' and resid 318 through 341 Processing helix chain '3P' and resid 344 through 364 removed outlier: 4.173A pdb=" N ILE3P 349 " --> pdb=" O HIS3P 345 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE3P 350 " --> pdb=" O PRO3P 346 " (cutoff:3.500A) Processing helix chain '3P' and resid 364 through 377 Processing helix chain '3Q' and resid 22 through 36 Processing helix chain '3Q' and resid 37 through 40 Processing helix chain '3Q' and resid 47 through 52 removed outlier: 4.060A pdb=" N LEU3Q 51 " --> pdb=" O ALA3Q 47 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL3Q 52 " --> pdb=" O TYR3Q 48 " (cutoff:3.500A) No H-bonds generated for 'chain '3Q' and resid 47 through 52' Processing helix chain '3Q' and resid 57 through 67 Processing helix chain '3Q' and resid 97 through 105 Processing helix chain '3Q' and resid 123 through 132 Processing helix chain '3Q' and resid 178 through 195 Processing helix chain '3Q' and resid 197 through 232 Proline residue: 3Q 217 - end of helix removed outlier: 4.634A pdb=" N VAL3Q 229 " --> pdb=" O HIS3Q 225 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU3Q 230 " --> pdb=" O LYS3Q 226 " (cutoff:3.500A) Processing helix chain '3R' and resid 79 through 83 Processing helix chain '3R' and resid 106 through 141 removed outlier: 3.946A pdb=" N GLN3R 135 " --> pdb=" O ASN3R 131 " (cutoff:3.500A) Processing helix chain '3R' and resid 180 through 187 removed outlier: 3.669A pdb=" N ILE3R 184 " --> pdb=" O THR3R 180 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP3R 185 " --> pdb=" O LYS3R 181 " (cutoff:3.500A) Processing helix chain '3R' and resid 188 through 190 No H-bonds generated for 'chain '3R' and resid 188 through 190' Processing helix chain '3R' and resid 200 through 205 Processing helix chain '3S' and resid 13 through 25 removed outlier: 3.892A pdb=" N GLY3S 25 " --> pdb=" O TYR3S 21 " (cutoff:3.500A) Processing helix chain '3S' and resid 32 through 37 Processing helix chain '3S' and resid 40 through 50 Processing helix chain '3S' and resid 51 through 72 Processing helix chain '3S' and resid 82 through 86 removed outlier: 3.651A pdb=" N ASP3S 86 " --> pdb=" O TYR3S 83 " (cutoff:3.500A) Processing helix chain '3S' and resid 90 through 109 Processing helix chain '3T' and resid 32 through 70 removed outlier: 4.617A pdb=" N LEU3T 46 " --> pdb=" O ARG3T 42 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ARG3T 47 " --> pdb=" O ALA3T 43 " (cutoff:3.500A) Proline residue: 3T 50 - end of helix Processing helix chain '3U' and resid 15 through 25 Processing helix chain '3U' and resid 27 through 47 Processing helix chain '3U' and resid 54 through 72 Processing helix chain '3V' and resid 51 through 56 Processing helix chain '3W' and resid 5 through 14 Processing helix chain '3W' and resid 16 through 47 Processing helix chain '3W' and resid 51 through 56 Processing helix chain '3W' and resid 57 through 59 No H-bonds generated for 'chain '3W' and resid 57 through 59' Processing helix chain '3X' and resid 2 through 6 Processing helix chain '3X' and resid 7 through 37 Proline residue: 3X 19 - end of helix Processing helix chain '3X' and resid 38 through 43 Processing helix chain '3X' and resid 47 through 52 Processing helix chain '3Y' and resid 6 through 37 removed outlier: 3.996A pdb=" N TYR3Y 10 " --> pdb=" O LEU3Y 6 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG3Y 11 " --> pdb=" O GLY3Y 7 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU3Y 12 " --> pdb=" O PRO3Y 8 " (cutoff:3.500A) Proline residue: 3Y 19 - end of helix Processing helix chain '3Y' and resid 38 through 43 Processing helix chain '3Y' and resid 47 through 52 Processing sheet with id=AA1, first strand: chain '3A' and resid 15 through 16 removed outlier: 3.608A pdb=" N VAL3A 37 " --> pdb=" O ILE3A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '3A' and resid 280 through 281 removed outlier: 6.234A pdb=" N SER3A 239 " --> pdb=" O VAL3A 422 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N GLY3A 424 " --> pdb=" O SER3A 239 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE3A 241 " --> pdb=" O GLY3A 424 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLY3A 426 " --> pdb=" O ILE3A 241 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N HIS3A 243 " --> pdb=" O GLY3A 426 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU3A 240 " --> pdb=" O SER3G 19 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL3G 15 " --> pdb=" O ARG3A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3B' and resid 25 through 28 removed outlier: 6.514A pdb=" N VAL3B 34 " --> pdb=" O LEU3B 206 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLY3B 208 " --> pdb=" O VAL3B 34 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA3B 36 " --> pdb=" O GLY3B 208 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU3B 96 " --> pdb=" O LEU3I 70 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLY3I 69 " --> pdb=" O PRO3I 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3B' and resid 243 through 246 removed outlier: 3.573A pdb=" N SER3B 328 " --> pdb=" O VAL3B 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3C' and resid 22 through 24 Processing sheet with id=AA6, first strand: chain '3D' and resid 157 through 160 removed outlier: 3.959A pdb=" N PHE3D 169 " --> pdb=" O ASP3D 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '3E' and resid 166 through 169 Processing sheet with id=AA8, first strand: chain '3E' and resid 242 through 243 removed outlier: 6.034A pdb=" N HIS3E 242 " --> pdb=" O ARG3E 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3E' and resid 264 through 267 removed outlier: 7.121A pdb=" N LEU3E 270 " --> pdb=" O THR3E 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3N' and resid 34 through 35 Processing sheet with id=AB2, first strand: chain '3N' and resid 40 through 41 Processing sheet with id=AB3, first strand: chain '3N' and resid 279 through 281 removed outlier: 6.687A pdb=" N VAL3N 325 " --> pdb=" O GLN3N 305 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE3N 307 " --> pdb=" O HIS3N 323 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N HIS3N 323 " --> pdb=" O PHE3N 307 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N THR3N 309 " --> pdb=" O GLY3N 321 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY3N 321 " --> pdb=" O THR3N 309 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN3N 311 " --> pdb=" O LEU3N 319 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU3N 319 " --> pdb=" O ASN3N 311 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N GLY3N 424 " --> pdb=" O SER3N 239 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE3N 241 " --> pdb=" O GLY3N 424 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL3T 13 " --> pdb=" O ARG3N 244 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3O' and resid 26 through 28 removed outlier: 3.855A pdb=" N VAL3O 34 " --> pdb=" O MET3O 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3O' and resid 243 through 245 removed outlier: 4.008A pdb=" N GLY3O 320 " --> pdb=" O SER3O 261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '3P' and resid 22 through 23 Processing sheet with id=AB7, first strand: chain '3Q' and resid 69 through 74 removed outlier: 4.486A pdb=" N PHE3Q 81 " --> pdb=" O ASP3Q 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '3R' and resid 164 through 168 Processing sheet with id=AB9, first strand: chain '3R' and resid 242 through 243 removed outlier: 4.074A pdb=" N LYS3R 251 " --> pdb=" O HIS3R 242 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '3V' and resid 66 through 67 1768 hydrogen bonds defined for protein. 5083 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.32 Time building geometry restraints manager: 11.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 14060 1.41 - 1.62: 19977 1.62 - 1.82: 266 1.82 - 2.03: 8 2.03 - 2.24: 24 Bond restraints: 34335 Sorted by residual: bond pdb=" C8 U103C 504 " pdb=" C9 U103C 504 " ideal model delta sigma weight residual 1.470 1.322 0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" C8 U103P 504 " pdb=" C9 U103P 504 " ideal model delta sigma weight residual 1.470 1.322 0.148 2.00e-02 2.50e+03 5.45e+01 bond pdb=" C8 U103C 503 " pdb=" C9 U103C 503 " ideal model delta sigma weight residual 1.470 1.323 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" C8 U103P 503 " pdb=" C9 U103P 503 " ideal model delta sigma weight residual 1.470 1.324 0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" C3 U103P 503 " pdb=" O3 U103P 503 " ideal model delta sigma weight residual 1.230 1.375 -0.145 2.00e-02 2.50e+03 5.29e+01 ... (remaining 34330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 45961 3.31 - 6.63: 473 6.63 - 9.94: 48 9.94 - 13.26: 12 13.26 - 16.57: 12 Bond angle restraints: 46506 Sorted by residual: angle pdb="FE1 FES3E 301 " pdb=" S2 FES3E 301 " pdb="FE2 FES3E 301 " ideal model delta sigma weight residual 75.66 91.06 -15.40 1.14e+00 7.69e-01 1.82e+02 angle pdb=" S1 FES3E 301 " pdb="FE2 FES3E 301 " pdb=" S2 FES3E 301 " ideal model delta sigma weight residual 104.33 89.15 15.18 1.14e+00 7.69e-01 1.77e+02 angle pdb=" S1 FES3E 301 " pdb="FE1 FES3E 301 " pdb=" S2 FES3E 301 " ideal model delta sigma weight residual 104.33 89.18 15.15 1.20e+00 6.94e-01 1.59e+02 angle pdb="FE1 FES3E 301 " pdb=" S1 FES3E 301 " pdb="FE2 FES3E 301 " ideal model delta sigma weight residual 75.66 90.60 -14.94 1.20e+00 6.94e-01 1.55e+02 angle pdb=" S1 FES3R 301 " pdb="FE2 FES3R 301 " pdb=" S2 FES3R 301 " ideal model delta sigma weight residual 104.33 90.86 13.47 1.14e+00 7.69e-01 1.40e+02 ... (remaining 46501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 19524 35.41 - 70.82: 983 70.82 - 106.24: 80 106.24 - 141.65: 3 141.65 - 177.06: 5 Dihedral angle restraints: 20595 sinusoidal: 8650 harmonic: 11945 Sorted by residual: dihedral pdb=" CB CYS3U 24 " pdb=" SG CYS3U 24 " pdb=" SG CYS3U 68 " pdb=" CB CYS3U 68 " ideal model delta sinusoidal sigma weight residual 93.00 169.05 -76.05 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" C11 U103C 504 " pdb=" C8 U103C 504 " pdb=" C9 U103C 504 " pdb=" C7 U103C 504 " ideal model delta sinusoidal sigma weight residual 180.05 2.99 177.06 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C12 U103C 503 " pdb=" C13 U103C 503 " pdb=" C14 U103C 503 " pdb=" C16 U103C 503 " ideal model delta sinusoidal sigma weight residual 178.80 1.90 176.90 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 20592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4178 0.059 - 0.118: 752 0.118 - 0.177: 66 0.177 - 0.236: 5 0.236 - 0.295: 3 Chirality restraints: 5004 Sorted by residual: chirality pdb=" C2 3PE3C 506 " pdb=" C1 3PE3C 506 " pdb=" C3 3PE3C 506 " pdb=" O21 3PE3C 506 " both_signs ideal model delta sigma weight residual False -2.53 -2.23 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA4 CDL3Q 502 " pdb=" CA3 CDL3Q 502 " pdb=" CA6 CDL3Q 502 " pdb=" OA6 CDL3Q 502 " both_signs ideal model delta sigma weight residual False -2.57 -2.29 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA4 CDL3G 102 " pdb=" CA3 CDL3G 102 " pdb=" CA6 CDL3G 102 " pdb=" OA6 CDL3G 102 " both_signs ideal model delta sigma weight residual False -2.57 -2.30 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 5001 not shown) Planarity restraints: 5834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U103C 503 " -0.003 2.00e-02 2.50e+03 1.08e-01 2.04e+02 pdb=" C1M U103C 503 " 0.099 2.00e-02 2.50e+03 pdb=" C2 U103C 503 " -0.011 2.00e-02 2.50e+03 pdb=" C3 U103C 503 " -0.128 2.00e-02 2.50e+03 pdb=" C4 U103C 503 " 0.182 2.00e-02 2.50e+03 pdb=" C5 U103C 503 " 0.010 2.00e-02 2.50e+03 pdb=" C6 U103C 503 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 U103P 504 " -0.012 2.00e-02 2.50e+03 7.37e-02 9.50e+01 pdb=" C1M U103P 504 " -0.046 2.00e-02 2.50e+03 pdb=" C2 U103P 504 " 0.025 2.00e-02 2.50e+03 pdb=" C3 U103P 504 " 0.080 2.00e-02 2.50e+03 pdb=" C4 U103P 504 " -0.151 2.00e-02 2.50e+03 pdb=" C5 U103P 504 " 0.071 2.00e-02 2.50e+03 pdb=" C6 U103P 504 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL3E 223 " -0.100 5.00e-02 4.00e+02 1.46e-01 3.42e+01 pdb=" N PRO3E 224 " 0.253 5.00e-02 4.00e+02 pdb=" CA PRO3E 224 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO3E 224 " -0.075 5.00e-02 4.00e+02 ... (remaining 5831 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 2 2.00 - 2.72: 2392 2.72 - 3.45: 52220 3.45 - 4.17: 83242 4.17 - 4.90: 152464 Nonbonded interactions: 290320 Sorted by model distance: nonbonded pdb=" CD1 TRP3J 53 " pdb=" CE LYS3J 57 " model vdw 1.270 3.660 nonbonded pdb=" NE1 TRP3J 53 " pdb=" CE LYS3J 57 " model vdw 1.962 3.520 nonbonded pdb=" CD ARG3D 115 " pdb=" OH TYR3J 60 " model vdw 2.022 3.440 nonbonded pdb=" OG1 THR3D 267 " pdb=" OD1 ASP3H 40 " model vdw 2.097 3.040 nonbonded pdb=" NZ LYS3B 95 " pdb=" O ASN3I 71 " model vdw 2.115 3.120 ... (remaining 290315 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 '3A' and (resid 2 or (resid 3 and (name N or name CA or name C or name CB \ or name OG1 or name CG2)) or (resid 4 and (name N or name CA or name C or name \ CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name \ OH )) or resid 5 through 7 or (resid 8 and (name N or name CA or name C or name \ CB or name CG or name CD1 or name CD2)) or (resid 9 and (name N or name CA or n \ ame C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 10 or \ (resid 11 and (name N or name CA or name C or name CB or name CG1 or name CG2)) \ or (resid 12 and (name N or name CA or name C or name CB or name CG or name CD ) \ ) or resid 13 or (resid 14 and (name N or name CA or name C or name CB or name O \ G1 or name CG2)) or resid 15 or (resid 16 and (name N or name CA or name C or na \ me CB or name CG1 or name CG2)) or (resid 17 and (name N or name CA or name C or \ name CB or name OG )) or resid 18 through 22 or (resid 23 and (name N or name C \ A or name C or name CB or name CG or name CD1 or name CD2)) or resid 24 through \ 27 or (resid 28 and (name N or name CA or name C or name CB or name CG or name C \ D or name OE1 or name OE2)) or resid 29 through 35 or (resid 36 and (name N or n \ ame CA or name C or name CB or name OG1 or name CG2)) or (resid 37 and (name N o \ r name CA or name C or name CB or name CG1 or name CG2)) or resid 38 through 42 \ or (resid 43 and (name N or name CA or name C or name CB )) or resid 44 through \ 65 or (resid 66 and (name N or name CA or name C )) or resid 67 through 88 or (r \ esid 89 and (name N or name CA or name C or name CB or name CG or name CD1 or na \ me CD2 or name CE1 or name CE2 or name CZ or name OH )) or resid 90 through 96 o \ r (resid 97 and (name N or name CA or name C or name CB or name CG or name CD1 o \ r name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resid 98 through \ 108 or (resid 109 and (name N or name CA or name C or name CB )) or resid 110 th \ rough 111 or (resid 112 and (name N or name CA or name C or name CB or name CG o \ r name CD1 or name CD2)) or resid 113 through 115 or (resid 116 and (name N or n \ ame CA or name C or name CB or name CG1 or name CG2 or name CD1)) or (resid 117 \ and (name N or name CA or name C or name CB or name CG1 or name CG2)) or resid 1 \ 18 through 120 or (resid 121 and (name N or name CA or name C or name CB or name \ OG )) or resid 122 through 125 or (resid 126 and (name N or name CA or name C o \ r name CB or name CG or name CD or name OE1 or name NE2)) or resid 127 through 1 \ 31 or (resid 132 and (name N or name CA or name C or name CB or name CG or name \ OD1 or name OD2)) or (resid 133 and (name N or name CA or name C or name CB or n \ ame CG1 or name CG2)) or (resid 134 and (name N or name CA or name C or name CB \ or name CG1 or name CG2 or name CD1)) or resid 135 through 168 or (resid 169 and \ (name N or name CA or name C )) or resid 170 through 176 or (resid 177 and (nam \ e N or name CA or name C or name CB or name CG or name CD1 or name CD2)) or resi \ d 178 through 179 or (resid 180 and (name N or name CA or name C or name CB )) o \ r (resid 181 and (name N or name CA or name C or name CB or name CG or name OD1 \ or name OD2)) or resid 182 through 191 or (resid 192 and (name N or name CA or n \ ame C or name CB )) or (resid 193 and (name N or name CA or name C or name CB or \ name CG or name CD )) or resid 194 or (resid 195 and (name N or name CA or name \ C or name CB or name CG or name SD or name CE )) or resid 196 through 197 or (r \ esid 198 and (name N or name CA or name C or name CB )) or resid 199 through 201 \ or (resid 202 and (name N or name CA or name C )) or resid 203 through 206 or r \ esid 208 through 221 or (resid 222 and (name N or name CA or name C or name CB o \ r name OG1 or name CG2)) or resid 228 through 445 or (resid 446 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name \ CE1 or name CE2 or name CZ )) or (resid 502 and (name N or name C1 or name C11 \ or name C12 or name C2 or name C21 or name C22 or name C23 or name C24 or name C \ 25 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or \ name O32 or name P )))) selection = (chain '3N' and (resid 2 through 206 or resid 208 through 222 or resid 228 throu \ gh 446 or resid 502)) } ncs_group { reference = (chain '3B' and (resid 22 through 23 or (resid 24 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2)) or resid 25 through 54 or (re \ sid 55 and (name N or name CA or name C or name CB or name OG )) or resid 56 thr \ ough 124 or (resid 125 and (name N or name CA or name C or name CB or name CG or \ name OD1 or name ND2)) or resid 126 through 127 or (resid 128 and (name N or na \ me CA or name C or name CB )) or resid 129 through 153 or (resid 154 and (name N \ or name CA or name C or name CB or name CG or name OD1 or name ND2)) or resid 1 \ 55 through 171 or (resid 172 and (name N or name CA or name C or name CB or name \ CG or name CD1 or name CD2)) or resid 173 through 182 or (resid 183 and (name N \ or name CA or name C or name CB or name CG1 or name CG2 or name CD1)) or resid \ 184 through 438)) selection = chain '3O' } ncs_group { reference = (chain '3C' and (resid 1 through 378 or (resid 379 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name NE1 or name \ CE2 or name CE3 or name CZ2 or name CZ3 or name CH2)) or resid 501 through 502 o \ r (resid 503 through 504 and (name C1 or name C10 or name C11 or name C12 or nam \ e C13 or name C14 or name C15 or name C16 or name C1M or name C2 or name C3 or n \ ame C3M or name C4 or name C4M or name C5 or name C6 or name C7 or name C8 or na \ me C9 or name O2 or name O3 or name O4 or name O5 )))) selection = (chain '3P' and (resid 1 through 379 or resid 501 through 503 or (resid 504 and \ (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C1M or name C2 or name C3 or name C3M or name C4 or name C4 \ M or name C5 or name C6 or name C7 or name C8 or name C9 or name O2 or name O3 o \ r name O4 or name O5 )))) } ncs_group { reference = (chain '3D' and (resid 92 through 329 or resid 501)) selection = (chain '3Q' and (resid 4 through 240 or (resid 501 and (name NB or name ND or na \ me C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C o \ r name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C \ 4B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or na \ me CBA or name CBB or name CBC or name CBD or name CGA or name CGD or name CHA o \ r name CHB or name CHC or name CHD or name CMA or name CMB or name CMC or name C \ MD or name NA or name NC or name O1A or name O1D or name O2A or name FE )))) } ncs_group { reference = (chain '3E' and (resid 79 through 274 or resid 301 or (resid 302 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C28 or name C29 or name C2A or name C2B or name C3 or name C31 or nam \ e C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name C3A or name C3B or name C3C or name C3D or name C3E or name C3 \ F or name C3G or name O11 or name O12 or name O13 or name O14 or name O21 or nam \ e O22 or name O31 or name O32 or name P )))) selection = chain '3R' } ncs_group { reference = chain '3F' selection = chain '3S' } ncs_group { reference = (chain '3G' and resid 4 through 83) selection = chain '3T' } ncs_group { reference = chain '3H' selection = chain '3U' } ncs_group { reference = chain '3J' selection = chain '3W' } ncs_group { reference = (chain '3X' and resid 2 through 52) selection = (chain '3Y' and resid 2 through 52) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.180 Check model and map are aligned: 0.220 Set scattering table: 0.310 Process input model: 82.700 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 : 0.010 0.582 34354 Z= 0.400 Angle : 0.868 21.634 46524 Z= 0.434 Chirality : 0.045 0.295 5004 Planarity : 0.006 0.146 5834 Dihedral : 19.616 177.060 12889 Min Nonbonded Distance : 1.270 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.96 % Favored : 93.82 % Rotamer: Outliers : 1.15 % Allowed : 29.58 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 4064 helix: 1.13 (0.12), residues: 2040 sheet: -1.25 (0.28), residues: 324 loop : -0.91 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP3R 169 HIS 0.008 0.001 HIS3R 239 PHE 0.028 0.002 PHE3R 265 TYR 0.043 0.002 TYR3F 32 ARG 0.012 0.001 ARG3O 222 Details of bonding type rmsd hydrogen bonds : bond 0.14183 ( 1768) hydrogen bonds : angle 6.33839 ( 5083) metal coordination : bond 0.29248 ( 8) metal coordination : angle 9.16559 ( 6) SS BOND : bond 0.00123 ( 6) SS BOND : angle 2.47131 ( 12) covalent geometry : bond 0.00851 (34335) covalent geometry : angle 0.86081 (46506) Misc. bond : bond 0.32833 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 631 time to evaluate : 3.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU3N 8 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 11 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU3N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU3N 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE3N 116 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP3N 132 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE3N 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP3N 181 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE3O 183 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN3O 412 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 3A 132 ASP cc_start: 0.8062 (m-30) cc_final: 0.7400 (m-30) REVERT: 3A 136 GLN cc_start: 0.8400 (mp10) cc_final: 0.8147 (mp10) REVERT: 3C 288 LEU cc_start: 0.8711 (tt) cc_final: 0.8322 (tt) REVERT: 3C 303 LEU cc_start: 0.8994 (mt) cc_final: 0.8729 (mt) REVERT: 3C 348 ILE cc_start: 0.8956 (mt) cc_final: 0.7783 (pt) REVERT: 3C 352 GLN cc_start: 0.8263 (mt0) cc_final: 0.8044 (mp10) REVERT: 3D 276 CYS cc_start: 0.8271 (m) cc_final: 0.7838 (m) REVERT: 3F 33 TYR cc_start: 0.8694 (t80) cc_final: 0.8178 (t80) REVERT: 3G 26 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7745 (mtm-85) REVERT: 3J 48 ASN cc_start: 0.8563 (m-40) cc_final: 0.8301 (m-40) REVERT: 3O 248 ASN cc_start: 0.7967 (p0) cc_final: 0.7642 (p0) REVERT: 3P 273 TYR cc_start: 0.8698 (p90) cc_final: 0.8158 (p90) REVERT: 3P 304 MET cc_start: 0.8759 (mmm) cc_final: 0.7882 (mmm) REVERT: 3Q 97 ASN cc_start: 0.8587 (p0) cc_final: 0.8272 (p0) REVERT: 3R 199 GLN cc_start: 0.7310 (mt0) cc_final: 0.7056 (mt0) REVERT: 3R 262 THR cc_start: 0.7667 (p) cc_final: 0.6734 (t) REVERT: 3S 102 LYS cc_start: 0.9159 (mmtm) cc_final: 0.8937 (mttm) REVERT: 3U 58 LEU cc_start: 0.9187 (tp) cc_final: 0.8966 (tp) REVERT: 3W 8 ARG cc_start: 0.7225 (mpt180) cc_final: 0.6783 (mpt180) REVERT: 3X 23 MET cc_start: 0.9059 (tmm) cc_final: 0.8795 (tmm) outliers start: 38 outliers final: 23 residues processed: 655 average time/residue: 0.4720 time to fit residues: 497.4663 Evaluate side-chains 514 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 491 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 300 ILE Chi-restraints excluded: chain 3G residue 55 VAL Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3N residue 8 LEU Chi-restraints excluded: chain 3N residue 9 GLN Chi-restraints excluded: chain 3N residue 11 VAL Chi-restraints excluded: chain 3N residue 28 GLU Chi-restraints excluded: chain 3N residue 112 LEU Chi-restraints excluded: chain 3N residue 116 ILE Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 132 ASP Chi-restraints excluded: chain 3N residue 134 ILE Chi-restraints excluded: chain 3N residue 181 ASP Chi-restraints excluded: chain 3N residue 209 LEU Chi-restraints excluded: chain 3N residue 320 LEU Chi-restraints excluded: chain 3O residue 183 ILE Chi-restraints excluded: chain 3Q residue 75 ASN Chi-restraints excluded: chain 3R residue 165 MET Chi-restraints excluded: chain 3R residue 169 TRP Chi-restraints excluded: chain 3T residue 6 HIS Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3X residue 18 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 0.8980 chunk 302 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 203 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 312 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 190 optimal weight: 6.9990 chunk 232 optimal weight: 0.8980 chunk 362 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3A 126 GLN 3B 196 GLN 3B 351 ASN ** 3C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3D 94 HIS 3D 289 HIS 3E 131 ASN 3E 186 GLN ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3H 48 GLN ** 3J 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 9 GLN ** 3N 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3O 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3Q 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3Q 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3U 23 GLN ** 3W 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.089498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.072627 restraints weight = 102565.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.075665 restraints weight = 38966.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.077570 restraints weight = 21110.000| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.527 34354 Z= 0.148 Angle : 0.657 20.566 46524 Z= 0.315 Chirality : 0.042 0.216 5004 Planarity : 0.005 0.087 5834 Dihedral : 14.147 175.353 5360 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.44 % Favored : 94.39 % Rotamer: Outliers : 4.04 % Allowed : 25.97 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.14), residues: 4064 helix: 1.52 (0.11), residues: 2057 sheet: -1.30 (0.28), residues: 315 loop : -0.69 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP3E 169 HIS 0.008 0.001 HIS3D 111 PHE 0.021 0.001 PHE3A 231 TYR 0.033 0.001 TYR3F 32 ARG 0.005 0.001 ARG3N 408 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 1768) hydrogen bonds : angle 4.95012 ( 5083) metal coordination : bond 0.09969 ( 8) metal coordination : angle 15.61041 ( 6) SS BOND : bond 0.00287 ( 6) SS BOND : angle 1.19579 ( 12) covalent geometry : bond 0.00329 (34335) covalent geometry : angle 0.63277 (46506) Misc. bond : bond 0.31059 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 583 time to evaluate : 3.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU3N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU3N 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP3N 132 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE3N 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN3O 412 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 132 ASP cc_start: 0.8462 (m-30) cc_final: 0.7736 (m-30) REVERT: 3A 136 GLN cc_start: 0.8521 (mp10) cc_final: 0.8273 (mp10) REVERT: 3A 176 LYS cc_start: 0.8969 (mptt) cc_final: 0.8761 (mmtm) REVERT: 3B 193 TYR cc_start: 0.8450 (t80) cc_final: 0.8227 (t80) REVERT: 3B 301 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9017 (ttpp) REVERT: 3C 53 MET cc_start: 0.9142 (mtm) cc_final: 0.8738 (mtm) REVERT: 3C 254 ASP cc_start: 0.8482 (m-30) cc_final: 0.8267 (m-30) REVERT: 3D 276 CYS cc_start: 0.8568 (m) cc_final: 0.8116 (m) REVERT: 3E 223 VAL cc_start: 0.3919 (OUTLIER) cc_final: 0.3693 (p) REVERT: 3G 40 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8402 (mp) REVERT: 3H 50 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7498 (tm-30) REVERT: 3H 60 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8070 (pm20) REVERT: 3I 64 LEU cc_start: 0.8592 (tp) cc_final: 0.8339 (tp) REVERT: 3I 67 SER cc_start: 0.8785 (m) cc_final: 0.8500 (t) REVERT: 3J 45 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8107 (mt-10) REVERT: 3N 323 HIS cc_start: 0.9049 (OUTLIER) cc_final: 0.8675 (t-90) REVERT: 3N 335 MET cc_start: 0.9075 (mmp) cc_final: 0.8731 (mmm) REVERT: 3P 11 MET cc_start: 0.8425 (tpp) cc_final: 0.7933 (mpp) REVERT: 3P 273 TYR cc_start: 0.9102 (p90) cc_final: 0.8332 (p90) REVERT: 3P 304 MET cc_start: 0.8847 (mmm) cc_final: 0.7772 (mmm) REVERT: 3Q 37 CYS cc_start: 0.7159 (t) cc_final: 0.6944 (t) REVERT: 3Q 214 LEU cc_start: 0.9100 (tt) cc_final: 0.8372 (mp) REVERT: 3R 175 PHE cc_start: 0.7685 (m-80) cc_final: 0.7296 (m-80) REVERT: 3R 249 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.7097 (pp) REVERT: 3S 47 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8950 (pt) REVERT: 3S 55 TYR cc_start: 0.9004 (t80) cc_final: 0.8662 (t80) REVERT: 3U 23 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8527 (tm-30) REVERT: 3U 58 LEU cc_start: 0.9085 (tp) cc_final: 0.8875 (tp) REVERT: 3W 8 ARG cc_start: 0.7044 (mpt180) cc_final: 0.6708 (mpt180) REVERT: 3W 48 GLN cc_start: 0.8352 (tp40) cc_final: 0.8136 (tp40) REVERT: 3X 12 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8112 (tm-30) REVERT: 3X 16 ASN cc_start: 0.7829 (m-40) cc_final: 0.6983 (m110) REVERT: 3X 23 MET cc_start: 0.9009 (tmm) cc_final: 0.8603 (tmm) REVERT: 3Y 12 GLU cc_start: 0.8297 (mp0) cc_final: 0.7959 (mp0) outliers start: 138 outliers final: 64 residues processed: 676 average time/residue: 0.4537 time to fit residues: 495.5027 Evaluate side-chains 579 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 507 time to evaluate : 3.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 23 LEU Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 112 LEU Chi-restraints excluded: chain 3A residue 186 VAL Chi-restraints excluded: chain 3A residue 312 ILE Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 285 VAL Chi-restraints excluded: chain 3B residue 301 LYS Chi-restraints excluded: chain 3B residue 411 ILE Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 67 THR Chi-restraints excluded: chain 3C residue 102 LEU Chi-restraints excluded: chain 3C residue 161 VAL Chi-restraints excluded: chain 3C residue 233 LEU Chi-restraints excluded: chain 3C residue 292 LEU Chi-restraints excluded: chain 3C residue 300 ILE Chi-restraints excluded: chain 3D residue 109 LEU Chi-restraints excluded: chain 3D residue 134 VAL Chi-restraints excluded: chain 3D residue 142 VAL Chi-restraints excluded: chain 3D residue 269 SER Chi-restraints excluded: chain 3E residue 214 ILE Chi-restraints excluded: chain 3E residue 223 VAL Chi-restraints excluded: chain 3E residue 239 HIS Chi-restraints excluded: chain 3E residue 272 ILE Chi-restraints excluded: chain 3F residue 66 LEU Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 17 THR Chi-restraints excluded: chain 3G residue 40 LEU Chi-restraints excluded: chain 3G residue 46 CYS Chi-restraints excluded: chain 3H residue 55 CYS Chi-restraints excluded: chain 3H residue 60 GLU Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 70 LEU Chi-restraints excluded: chain 3N residue 9 GLN Chi-restraints excluded: chain 3N residue 28 GLU Chi-restraints excluded: chain 3N residue 41 ILE Chi-restraints excluded: chain 3N residue 58 PHE Chi-restraints excluded: chain 3N residue 112 LEU Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 132 ASP Chi-restraints excluded: chain 3N residue 134 ILE Chi-restraints excluded: chain 3N residue 323 HIS Chi-restraints excluded: chain 3O residue 108 THR Chi-restraints excluded: chain 3O residue 186 VAL Chi-restraints excluded: chain 3O residue 224 LEU Chi-restraints excluded: chain 3O residue 278 VAL Chi-restraints excluded: chain 3P residue 64 SER Chi-restraints excluded: chain 3P residue 102 LEU Chi-restraints excluded: chain 3P residue 268 ILE Chi-restraints excluded: chain 3R residue 200 HIS Chi-restraints excluded: chain 3R residue 209 GLU Chi-restraints excluded: chain 3R residue 225 ILE Chi-restraints excluded: chain 3R residue 249 ILE Chi-restraints excluded: chain 3S residue 37 ILE Chi-restraints excluded: chain 3S residue 47 ILE Chi-restraints excluded: chain 3T residue 70 LYS Chi-restraints excluded: chain 3T residue 73 ASN Chi-restraints excluded: chain 3U residue 23 GLN Chi-restraints excluded: chain 3U residue 37 LEU Chi-restraints excluded: chain 3U residue 39 LEU Chi-restraints excluded: chain 3U residue 42 GLN Chi-restraints excluded: chain 3V residue 51 CYS Chi-restraints excluded: chain 3V residue 56 SER Chi-restraints excluded: chain 3V residue 67 SER Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3V residue 72 VAL Chi-restraints excluded: chain 3X residue 1 MET Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 20 THR Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 18 ILE Chi-restraints excluded: chain 3Y residue 23 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 153 optimal weight: 5.9990 chunk 374 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 347 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 272 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 299 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3B 197 ASN ** 3C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3D 94 HIS ** 3D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3D 270 GLN ** 3D 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3F 91 GLN 3H 48 GLN 3J 58 HIS 3N 9 GLN ** 3N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 435 ASN ** 3P 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3Q 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3Q 200 HIS 3R 131 ASN ** 3R 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3U 23 GLN ** 3W 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.085743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.068949 restraints weight = 100468.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.071835 restraints weight = 38873.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.073625 restraints weight = 21397.358| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.774 34354 Z= 0.257 Angle : 0.726 22.073 46524 Z= 0.343 Chirality : 0.044 0.178 5004 Planarity : 0.005 0.065 5834 Dihedral : 13.522 152.252 5337 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.01 % Favored : 93.84 % Rotamer: Outliers : 5.02 % Allowed : 24.96 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 4064 helix: 1.52 (0.11), residues: 2059 sheet: -1.22 (0.28), residues: 336 loop : -0.62 (0.16), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP3E 169 HIS 0.014 0.001 HIS3R 219 PHE 0.021 0.002 PHE3A 231 TYR 0.020 0.002 TYR3C 81 ARG 0.008 0.001 ARG3H 59 Details of bonding type rmsd hydrogen bonds : bond 0.04736 ( 1768) hydrogen bonds : angle 4.88145 ( 5083) metal coordination : bond 0.08530 ( 8) metal coordination : angle 16.29621 ( 6) SS BOND : bond 0.00529 ( 6) SS BOND : angle 1.11062 ( 12) covalent geometry : bond 0.00604 (34335) covalent geometry : angle 0.70215 (46506) Misc. bond : bond 0.43701 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 502 time to evaluate : 3.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU3N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN3O 412 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 3A 176 LYS cc_start: 0.9104 (mptt) cc_final: 0.8874 (mmtm) REVERT: 3A 209 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8443 (tm) REVERT: 3A 343 MET cc_start: 0.8670 (mmp) cc_final: 0.8299 (mmm) REVERT: 3B 46 ARG cc_start: 0.7725 (ttm170) cc_final: 0.6431 (ttm170) REVERT: 3B 110 GLU cc_start: 0.7400 (tt0) cc_final: 0.7028 (tt0) REVERT: 3B 239 TYR cc_start: 0.8601 (t80) cc_final: 0.8317 (t80) REVERT: 3B 376 GLU cc_start: 0.7735 (tt0) cc_final: 0.7517 (tt0) REVERT: 3C 53 MET cc_start: 0.9049 (mtm) cc_final: 0.8667 (mtm) REVERT: 3C 172 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8210 (tptp) REVERT: 3C 352 GLN cc_start: 0.8920 (mt0) cc_final: 0.8679 (mt0) REVERT: 3C 373 GLU cc_start: 0.8892 (tp30) cc_final: 0.8331 (mm-30) REVERT: 3D 274 ASP cc_start: 0.7692 (m-30) cc_final: 0.7485 (m-30) REVERT: 3E 165 MET cc_start: 0.7354 (tpp) cc_final: 0.6803 (mmm) REVERT: 3F 32 TYR cc_start: 0.9421 (t80) cc_final: 0.8284 (t80) REVERT: 3F 82 MET cc_start: 0.9314 (ttp) cc_final: 0.8960 (ttp) REVERT: 3F 95 TYR cc_start: 0.8768 (t80) cc_final: 0.8472 (t80) REVERT: 3G 40 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8670 (mp) REVERT: 3G 54 PHE cc_start: 0.9357 (m-80) cc_final: 0.9073 (m-80) REVERT: 3H 60 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: 3J 45 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8059 (mt-10) REVERT: 3N 82 MET cc_start: 0.9401 (ptt) cc_final: 0.9104 (ptt) REVERT: 3N 335 MET cc_start: 0.9209 (mmp) cc_final: 0.8840 (mmm) REVERT: 3Q 212 MET cc_start: 0.9070 (mmm) cc_final: 0.8762 (mmm) REVERT: 3R 175 PHE cc_start: 0.8258 (m-80) cc_final: 0.7930 (m-80) REVERT: 3U 23 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: 3U 58 LEU cc_start: 0.9325 (tp) cc_final: 0.8968 (tp) REVERT: 3U 62 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8516 (mt) REVERT: 3W 8 ARG cc_start: 0.7253 (mpt180) cc_final: 0.6757 (mpt180) REVERT: 3W 51 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9194 (mt) REVERT: 3X 11 ARG cc_start: 0.7809 (mtm180) cc_final: 0.6895 (mtm-85) REVERT: 3X 12 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8057 (tm-30) REVERT: 3X 16 ASN cc_start: 0.7937 (m-40) cc_final: 0.7110 (m110) REVERT: 3Y 51 LYS cc_start: 0.9259 (mmmt) cc_final: 0.9052 (mtpp) outliers start: 172 outliers final: 103 residues processed: 624 average time/residue: 0.4413 time to fit residues: 443.9698 Evaluate side-chains 575 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 466 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 14 THR Chi-restraints excluded: chain 3A residue 16 VAL Chi-restraints excluded: chain 3A residue 23 LEU Chi-restraints excluded: chain 3A residue 34 THR Chi-restraints excluded: chain 3A residue 58 PHE Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 112 LEU Chi-restraints excluded: chain 3A residue 186 VAL Chi-restraints excluded: chain 3A residue 209 LEU Chi-restraints excluded: chain 3A residue 290 MET Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 312 ILE Chi-restraints excluded: chain 3B residue 51 ILE Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 275 LEU Chi-restraints excluded: chain 3B residue 285 VAL Chi-restraints excluded: chain 3B residue 410 VAL Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 160 LEU Chi-restraints excluded: chain 3C residue 161 VAL Chi-restraints excluded: chain 3C residue 176 THR Chi-restraints excluded: chain 3C residue 203 THR Chi-restraints excluded: chain 3C residue 209 THR Chi-restraints excluded: chain 3C residue 212 SER Chi-restraints excluded: chain 3C residue 233 LEU Chi-restraints excluded: chain 3C residue 292 LEU Chi-restraints excluded: chain 3C residue 297 SER Chi-restraints excluded: chain 3C residue 300 ILE Chi-restraints excluded: chain 3C residue 343 VAL Chi-restraints excluded: chain 3C residue 371 ILE Chi-restraints excluded: chain 3D residue 125 CYS Chi-restraints excluded: chain 3D residue 134 VAL Chi-restraints excluded: chain 3D residue 142 VAL Chi-restraints excluded: chain 3D residue 269 SER Chi-restraints excluded: chain 3D residue 307 LEU Chi-restraints excluded: chain 3D residue 324 LEU Chi-restraints excluded: chain 3E residue 154 ILE Chi-restraints excluded: chain 3E residue 214 ILE Chi-restraints excluded: chain 3E residue 239 HIS Chi-restraints excluded: chain 3E residue 271 VAL Chi-restraints excluded: chain 3F residue 66 LEU Chi-restraints excluded: chain 3F residue 71 VAL Chi-restraints excluded: chain 3F residue 110 ILE Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 17 THR Chi-restraints excluded: chain 3G residue 34 LYS Chi-restraints excluded: chain 3G residue 40 LEU Chi-restraints excluded: chain 3G residue 48 LEU Chi-restraints excluded: chain 3G residue 55 VAL Chi-restraints excluded: chain 3G residue 60 VAL Chi-restraints excluded: chain 3H residue 55 CYS Chi-restraints excluded: chain 3H residue 60 GLU Chi-restraints excluded: chain 3H residue 87 LEU Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 37 THR Chi-restraints excluded: chain 3I residue 70 LEU Chi-restraints excluded: chain 3J residue 54 LYS Chi-restraints excluded: chain 3J residue 56 ILE Chi-restraints excluded: chain 3N residue 28 GLU Chi-restraints excluded: chain 3N residue 58 PHE Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 209 LEU Chi-restraints excluded: chain 3N residue 407 VAL Chi-restraints excluded: chain 3O residue 47 ILE Chi-restraints excluded: chain 3O residue 108 THR Chi-restraints excluded: chain 3O residue 109 VAL Chi-restraints excluded: chain 3O residue 186 VAL Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 224 LEU Chi-restraints excluded: chain 3O residue 278 VAL Chi-restraints excluded: chain 3O residue 353 SER Chi-restraints excluded: chain 3O residue 355 THR Chi-restraints excluded: chain 3P residue 102 LEU Chi-restraints excluded: chain 3P residue 192 LEU Chi-restraints excluded: chain 3P residue 345 HIS Chi-restraints excluded: chain 3Q residue 3 LEU Chi-restraints excluded: chain 3Q residue 75 ASN Chi-restraints excluded: chain 3Q residue 188 THR Chi-restraints excluded: chain 3R residue 96 VAL Chi-restraints excluded: chain 3R residue 123 VAL Chi-restraints excluded: chain 3R residue 200 HIS Chi-restraints excluded: chain 3R residue 205 VAL Chi-restraints excluded: chain 3R residue 209 GLU Chi-restraints excluded: chain 3R residue 225 ILE Chi-restraints excluded: chain 3R residue 262 THR Chi-restraints excluded: chain 3S residue 37 ILE Chi-restraints excluded: chain 3S residue 75 LEU Chi-restraints excluded: chain 3S residue 98 ILE Chi-restraints excluded: chain 3T residue 34 ILE Chi-restraints excluded: chain 3T residue 46 LEU Chi-restraints excluded: chain 3T residue 53 VAL Chi-restraints excluded: chain 3T residue 73 ASN Chi-restraints excluded: chain 3U residue 23 GLN Chi-restraints excluded: chain 3U residue 37 LEU Chi-restraints excluded: chain 3U residue 39 LEU Chi-restraints excluded: chain 3U residue 42 GLN Chi-restraints excluded: chain 3U residue 62 LEU Chi-restraints excluded: chain 3V residue 50 LEU Chi-restraints excluded: chain 3V residue 51 CYS Chi-restraints excluded: chain 3V residue 67 SER Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3V residue 72 VAL Chi-restraints excluded: chain 3W residue 29 LEU Chi-restraints excluded: chain 3W residue 51 LEU Chi-restraints excluded: chain 3X residue 1 MET Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 18 ILE Chi-restraints excluded: chain 3Y residue 41 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 383 optimal weight: 8.9990 chunk 306 optimal weight: 4.9990 chunk 356 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 395 optimal weight: 9.9990 chunk 328 optimal weight: 0.5980 chunk 362 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 299 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3A 264 ASN ** 3C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3C 201 HIS 3D 94 HIS ** 3D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3D 289 HIS ** 3E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3H 48 GLN 3N 9 GLN 3N 188 GLN ** 3O 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3Q 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3Q 181 GLN ** 3R 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3T 6 HIS ** 3W 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.088135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.071402 restraints weight = 99209.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.074299 restraints weight = 38163.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.076118 restraints weight = 21033.111| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.586 34354 Z= 0.143 Angle : 0.632 19.971 46524 Z= 0.300 Chirality : 0.041 0.188 5004 Planarity : 0.004 0.066 5834 Dihedral : 13.055 136.902 5328 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.44 % Favored : 94.39 % Rotamer: Outliers : 3.46 % Allowed : 26.92 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.14), residues: 4064 helix: 1.71 (0.11), residues: 2062 sheet: -1.23 (0.27), residues: 343 loop : -0.54 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP3R 169 HIS 0.008 0.001 HIS3D 94 PHE 0.021 0.001 PHE3R 265 TYR 0.016 0.001 TYR3P 224 ARG 0.013 0.000 ARG3U 36 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 1768) hydrogen bonds : angle 4.66992 ( 5083) metal coordination : bond 0.07362 ( 8) metal coordination : angle 14.19018 ( 6) SS BOND : bond 0.01113 ( 6) SS BOND : angle 1.97930 ( 12) covalent geometry : bond 0.00335 (34335) covalent geometry : angle 0.61046 (46506) Misc. bond : bond 0.35154 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 529 time to evaluate : 3.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR3N 4 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU3N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN3O 412 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 258 GLU cc_start: 0.8534 (tt0) cc_final: 0.8064 (tt0) REVERT: 3A 343 MET cc_start: 0.8669 (mmp) cc_final: 0.8323 (mmm) REVERT: 3A 378 ASP cc_start: 0.8725 (t0) cc_final: 0.8405 (t0) REVERT: 3B 268 GLU cc_start: 0.7786 (tt0) cc_final: 0.7456 (tt0) REVERT: 3B 376 GLU cc_start: 0.7717 (tt0) cc_final: 0.7503 (tt0) REVERT: 3C 53 MET cc_start: 0.9052 (mtm) cc_final: 0.8789 (mtm) REVERT: 3C 172 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8040 (tptp) REVERT: 3C 216 ASP cc_start: 0.9085 (t0) cc_final: 0.8882 (t0) REVERT: 3C 241 ILE cc_start: 0.9436 (mm) cc_final: 0.9206 (mm) REVERT: 3C 288 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8495 (tt) REVERT: 3C 373 GLU cc_start: 0.8924 (tp30) cc_final: 0.8680 (mm-30) REVERT: 3D 270 GLN cc_start: 0.8770 (tp40) cc_final: 0.8416 (tp40) REVERT: 3D 274 ASP cc_start: 0.7797 (m-30) cc_final: 0.7354 (m-30) REVERT: 3E 147 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8580 (tt) REVERT: 3E 151 LYS cc_start: 0.7939 (pttt) cc_final: 0.7738 (pttm) REVERT: 3E 210 TRP cc_start: 0.9094 (m-90) cc_final: 0.8879 (m-90) REVERT: 3E 223 VAL cc_start: 0.4317 (OUTLIER) cc_final: 0.4074 (p) REVERT: 3F 82 MET cc_start: 0.9243 (ttp) cc_final: 0.8800 (ttp) REVERT: 3F 95 TYR cc_start: 0.8701 (t80) cc_final: 0.8409 (t80) REVERT: 3F 103 GLU cc_start: 0.8441 (tp30) cc_final: 0.8239 (tp30) REVERT: 3F 114 LYS cc_start: 0.9372 (mmtp) cc_final: 0.9145 (mmtm) REVERT: 3G 54 PHE cc_start: 0.9342 (m-80) cc_final: 0.9010 (m-80) REVERT: 3H 40 ASP cc_start: 0.8648 (t70) cc_final: 0.8394 (t70) REVERT: 3H 47 GLU cc_start: 0.7954 (pm20) cc_final: 0.7627 (pm20) REVERT: 3H 60 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7928 (pm20) REVERT: 3J 45 GLU cc_start: 0.8220 (mt-10) cc_final: 0.8014 (mt-10) REVERT: 3N 82 MET cc_start: 0.9354 (ptt) cc_final: 0.9152 (ptt) REVERT: 3O 196 GLN cc_start: 0.8727 (pt0) cc_final: 0.8453 (pm20) REVERT: 3P 236 MET cc_start: 0.9291 (tpp) cc_final: 0.8875 (mmm) REVERT: 3Q 208 MET cc_start: 0.9279 (tmm) cc_final: 0.8922 (tmm) REVERT: 3R 175 PHE cc_start: 0.8139 (m-80) cc_final: 0.7887 (m-80) REVERT: 3U 58 LEU cc_start: 0.9312 (tp) cc_final: 0.8964 (tp) REVERT: 3U 62 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8480 (mt) REVERT: 3W 51 LEU cc_start: 0.9367 (mm) cc_final: 0.9047 (mt) REVERT: 3X 23 MET cc_start: 0.9012 (tmm) cc_final: 0.8606 (tmm) REVERT: 3Y 51 LYS cc_start: 0.9233 (mmmt) cc_final: 0.8996 (mtpp) outliers start: 118 outliers final: 78 residues processed: 611 average time/residue: 0.4676 time to fit residues: 462.3798 Evaluate side-chains 562 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 479 time to evaluate : 3.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 14 THR Chi-restraints excluded: chain 3A residue 23 LEU Chi-restraints excluded: chain 3A residue 34 THR Chi-restraints excluded: chain 3A residue 58 PHE Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 112 LEU Chi-restraints excluded: chain 3A residue 149 VAL Chi-restraints excluded: chain 3A residue 257 VAL Chi-restraints excluded: chain 3A residue 294 LEU Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3B residue 51 ILE Chi-restraints excluded: chain 3B residue 285 VAL Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 203 THR Chi-restraints excluded: chain 3C residue 209 THR Chi-restraints excluded: chain 3C residue 283 SER Chi-restraints excluded: chain 3C residue 288 LEU Chi-restraints excluded: chain 3C residue 292 LEU Chi-restraints excluded: chain 3C residue 300 ILE Chi-restraints excluded: chain 3D residue 125 CYS Chi-restraints excluded: chain 3D residue 134 VAL Chi-restraints excluded: chain 3D residue 142 VAL Chi-restraints excluded: chain 3D residue 289 HIS Chi-restraints excluded: chain 3D residue 307 LEU Chi-restraints excluded: chain 3D residue 324 LEU Chi-restraints excluded: chain 3E residue 147 LEU Chi-restraints excluded: chain 3E residue 156 LEU Chi-restraints excluded: chain 3E residue 214 ILE Chi-restraints excluded: chain 3E residue 222 CYS Chi-restraints excluded: chain 3E residue 223 VAL Chi-restraints excluded: chain 3E residue 239 HIS Chi-restraints excluded: chain 3E residue 271 VAL Chi-restraints excluded: chain 3F residue 66 LEU Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 34 LYS Chi-restraints excluded: chain 3G residue 48 LEU Chi-restraints excluded: chain 3G residue 55 VAL Chi-restraints excluded: chain 3H residue 38 LEU Chi-restraints excluded: chain 3H residue 55 CYS Chi-restraints excluded: chain 3H residue 60 GLU Chi-restraints excluded: chain 3H residue 87 LEU Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 76 VAL Chi-restraints excluded: chain 3J residue 54 LYS Chi-restraints excluded: chain 3N residue 28 GLU Chi-restraints excluded: chain 3N residue 58 PHE Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 167 VAL Chi-restraints excluded: chain 3N residue 209 LEU Chi-restraints excluded: chain 3N residue 320 LEU Chi-restraints excluded: chain 3N residue 407 VAL Chi-restraints excluded: chain 3O residue 124 LEU Chi-restraints excluded: chain 3O residue 186 VAL Chi-restraints excluded: chain 3O residue 224 LEU Chi-restraints excluded: chain 3O residue 226 MET Chi-restraints excluded: chain 3O residue 278 VAL Chi-restraints excluded: chain 3P residue 4 ILE Chi-restraints excluded: chain 3P residue 102 LEU Chi-restraints excluded: chain 3P residue 192 LEU Chi-restraints excluded: chain 3P residue 345 HIS Chi-restraints excluded: chain 3Q residue 3 LEU Chi-restraints excluded: chain 3Q residue 68 VAL Chi-restraints excluded: chain 3Q residue 75 ASN Chi-restraints excluded: chain 3R residue 96 VAL Chi-restraints excluded: chain 3R residue 152 ILE Chi-restraints excluded: chain 3R residue 209 GLU Chi-restraints excluded: chain 3R residue 262 THR Chi-restraints excluded: chain 3S residue 37 ILE Chi-restraints excluded: chain 3T residue 44 CYS Chi-restraints excluded: chain 3U residue 37 LEU Chi-restraints excluded: chain 3U residue 39 LEU Chi-restraints excluded: chain 3U residue 42 GLN Chi-restraints excluded: chain 3U residue 62 LEU Chi-restraints excluded: chain 3V residue 51 CYS Chi-restraints excluded: chain 3V residue 67 SER Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3V residue 72 VAL Chi-restraints excluded: chain 3W residue 18 SER Chi-restraints excluded: chain 3W residue 29 LEU Chi-restraints excluded: chain 3X residue 1 MET Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 18 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 139 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 361 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 376 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3A 53 ASN 3B 162 ASN ** 3C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3C 322 GLN 3D 94 HIS ** 3D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3F 91 GLN 3H 48 GLN 3N 9 GLN 3N 188 GLN ** 3O 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3O 284 HIS ** 3P 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3Q 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3R 131 ASN ** 3R 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3W 47 ASN 3X 16 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.081956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.067294 restraints weight = 113267.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.069836 restraints weight = 37874.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.069618 restraints weight = 24812.860| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.962 34354 Z= 0.423 Angle : 0.828 21.951 46524 Z= 0.392 Chirality : 0.048 0.216 5004 Planarity : 0.005 0.059 5834 Dihedral : 13.393 140.510 5328 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.30 % Favored : 93.52 % Rotamer: Outliers : 5.33 % Allowed : 25.40 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 4064 helix: 1.38 (0.11), residues: 2073 sheet: -1.20 (0.28), residues: 333 loop : -0.66 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP3R 169 HIS 0.024 0.002 HIS3D 289 PHE 0.025 0.002 PHE3R 265 TYR 0.024 0.002 TYR3P 81 ARG 0.011 0.001 ARG3U 36 Details of bonding type rmsd hydrogen bonds : bond 0.04959 ( 1768) hydrogen bonds : angle 5.01839 ( 5083) metal coordination : bond 0.07517 ( 8) metal coordination : angle 16.31660 ( 6) SS BOND : bond 0.00398 ( 6) SS BOND : angle 1.49606 ( 12) covalent geometry : bond 0.00990 (34335) covalent geometry : angle 0.80655 (46506) Misc. bond : bond 0.55864 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 459 time to evaluate : 4.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU3N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 3A 100 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8826 (mtpp) REVERT: 3A 136 GLN cc_start: 0.8721 (mp10) cc_final: 0.8397 (mp10) REVERT: 3A 209 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8485 (tm) REVERT: 3A 302 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8895 (mmmt) REVERT: 3A 343 MET cc_start: 0.8822 (mmp) cc_final: 0.8612 (mmm) REVERT: 3A 378 ASP cc_start: 0.8756 (t0) cc_final: 0.8453 (t0) REVERT: 3B 268 GLU cc_start: 0.8144 (tt0) cc_final: 0.7804 (tt0) REVERT: 3B 305 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8804 (tt0) REVERT: 3B 376 GLU cc_start: 0.7904 (tt0) cc_final: 0.7670 (tt0) REVERT: 3C 102 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9154 (tt) REVERT: 3C 172 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8194 (tptp) REVERT: 3C 212 SER cc_start: 0.9207 (OUTLIER) cc_final: 0.8821 (p) REVERT: 3C 352 GLN cc_start: 0.9182 (mt0) cc_final: 0.8877 (mt0) REVERT: 3C 379 TRP cc_start: 0.8447 (p90) cc_final: 0.8146 (p90) REVERT: 3D 274 ASP cc_start: 0.8017 (m-30) cc_final: 0.7704 (m-30) REVERT: 3E 151 LYS cc_start: 0.8060 (pttt) cc_final: 0.7776 (pttm) REVERT: 3E 210 TRP cc_start: 0.9039 (m-90) cc_final: 0.8817 (m-90) REVERT: 3F 82 MET cc_start: 0.9279 (ttp) cc_final: 0.8922 (ttp) REVERT: 3F 95 TYR cc_start: 0.8950 (t80) cc_final: 0.8658 (t80) REVERT: 3F 100 PHE cc_start: 0.8162 (m-10) cc_final: 0.7946 (m-80) REVERT: 3F 114 LYS cc_start: 0.9433 (mmtp) cc_final: 0.9177 (mmtm) REVERT: 3G 54 PHE cc_start: 0.9375 (m-80) cc_final: 0.9123 (m-80) REVERT: 3H 40 ASP cc_start: 0.8804 (t70) cc_final: 0.8496 (t70) REVERT: 3H 47 GLU cc_start: 0.7947 (pm20) cc_final: 0.7743 (pm20) REVERT: 3H 50 GLU cc_start: 0.8012 (pp20) cc_final: 0.7798 (pp20) REVERT: 3H 51 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8504 (mm-40) REVERT: 3H 54 LYS cc_start: 0.8527 (tppt) cc_final: 0.8302 (tppt) REVERT: 3H 60 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7286 (pm20) REVERT: 3H 91 ASP cc_start: 0.8327 (m-30) cc_final: 0.8124 (m-30) REVERT: 3J 45 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8122 (mt-10) REVERT: 3N 58 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8725 (m-80) REVERT: 3N 82 MET cc_start: 0.9402 (ptt) cc_final: 0.9159 (ptt) REVERT: 3N 235 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8488 (ptp90) REVERT: 3O 169 ARG cc_start: 0.9514 (OUTLIER) cc_final: 0.9098 (mtt180) REVERT: 3P 89 MET cc_start: 0.8851 (tpp) cc_final: 0.8575 (tpp) REVERT: 3P 172 LYS cc_start: 0.8490 (tttp) cc_final: 0.8135 (tttt) REVERT: 3P 282 ARG cc_start: 0.8097 (mtm110) cc_final: 0.7787 (mtp180) REVERT: 3Q 215 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9417 (tp) REVERT: 3R 131 ASN cc_start: 0.9119 (OUTLIER) cc_final: 0.8610 (t0) REVERT: 3R 135 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8650 (tp40) REVERT: 3S 47 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9078 (mp) REVERT: 3U 42 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8236 (mp-120) REVERT: 3U 51 GLU cc_start: 0.7535 (pp20) cc_final: 0.7281 (pp20) REVERT: 3U 62 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8645 (mt) REVERT: 3X 23 MET cc_start: 0.8999 (tmm) cc_final: 0.8591 (tmm) REVERT: 3Y 51 LYS cc_start: 0.9229 (mmmt) cc_final: 0.9000 (mtpp) outliers start: 183 outliers final: 122 residues processed: 597 average time/residue: 0.4506 time to fit residues: 435.5477 Evaluate side-chains 567 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 430 time to evaluate : 3.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 14 THR Chi-restraints excluded: chain 3A residue 16 VAL Chi-restraints excluded: chain 3A residue 23 LEU Chi-restraints excluded: chain 3A residue 34 THR Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 100 LYS Chi-restraints excluded: chain 3A residue 112 LEU Chi-restraints excluded: chain 3A residue 127 ILE Chi-restraints excluded: chain 3A residue 187 SER Chi-restraints excluded: chain 3A residue 195 MET Chi-restraints excluded: chain 3A residue 209 LEU Chi-restraints excluded: chain 3A residue 282 SER Chi-restraints excluded: chain 3A residue 290 MET Chi-restraints excluded: chain 3A residue 294 LEU Chi-restraints excluded: chain 3A residue 302 LYS Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3B residue 51 ILE Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 275 LEU Chi-restraints excluded: chain 3B residue 285 VAL Chi-restraints excluded: chain 3B residue 303 VAL Chi-restraints excluded: chain 3B residue 305 GLN Chi-restraints excluded: chain 3B residue 410 VAL Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 102 LEU Chi-restraints excluded: chain 3C residue 160 LEU Chi-restraints excluded: chain 3C residue 161 VAL Chi-restraints excluded: chain 3C residue 203 THR Chi-restraints excluded: chain 3C residue 209 THR Chi-restraints excluded: chain 3C residue 212 SER Chi-restraints excluded: chain 3C residue 233 LEU Chi-restraints excluded: chain 3C residue 283 SER Chi-restraints excluded: chain 3C residue 292 LEU Chi-restraints excluded: chain 3C residue 297 SER Chi-restraints excluded: chain 3C residue 300 ILE Chi-restraints excluded: chain 3C residue 343 VAL Chi-restraints excluded: chain 3D residue 120 VAL Chi-restraints excluded: chain 3D residue 125 CYS Chi-restraints excluded: chain 3D residue 134 VAL Chi-restraints excluded: chain 3D residue 142 VAL Chi-restraints excluded: chain 3D residue 269 SER Chi-restraints excluded: chain 3D residue 307 LEU Chi-restraints excluded: chain 3E residue 83 ILE Chi-restraints excluded: chain 3E residue 90 ASP Chi-restraints excluded: chain 3E residue 139 SER Chi-restraints excluded: chain 3E residue 154 ILE Chi-restraints excluded: chain 3E residue 222 CYS Chi-restraints excluded: chain 3E residue 239 HIS Chi-restraints excluded: chain 3E residue 271 VAL Chi-restraints excluded: chain 3F residue 66 LEU Chi-restraints excluded: chain 3F residue 110 ILE Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 17 THR Chi-restraints excluded: chain 3G residue 34 LYS Chi-restraints excluded: chain 3G residue 40 LEU Chi-restraints excluded: chain 3G residue 48 LEU Chi-restraints excluded: chain 3G residue 55 VAL Chi-restraints excluded: chain 3G residue 60 VAL Chi-restraints excluded: chain 3G residue 72 LYS Chi-restraints excluded: chain 3H residue 38 LEU Chi-restraints excluded: chain 3H residue 52 ILE Chi-restraints excluded: chain 3H residue 55 CYS Chi-restraints excluded: chain 3H residue 60 GLU Chi-restraints excluded: chain 3H residue 87 LEU Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 67 SER Chi-restraints excluded: chain 3I residue 70 LEU Chi-restraints excluded: chain 3J residue 5 THR Chi-restraints excluded: chain 3J residue 54 LYS Chi-restraints excluded: chain 3N residue 28 GLU Chi-restraints excluded: chain 3N residue 58 PHE Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 235 ARG Chi-restraints excluded: chain 3N residue 255 ILE Chi-restraints excluded: chain 3N residue 292 SER Chi-restraints excluded: chain 3N residue 320 LEU Chi-restraints excluded: chain 3N residue 407 VAL Chi-restraints excluded: chain 3O residue 109 VAL Chi-restraints excluded: chain 3O residue 119 LEU Chi-restraints excluded: chain 3O residue 169 ARG Chi-restraints excluded: chain 3O residue 186 VAL Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 226 MET Chi-restraints excluded: chain 3O residue 278 VAL Chi-restraints excluded: chain 3O residue 347 ILE Chi-restraints excluded: chain 3O residue 353 SER Chi-restraints excluded: chain 3O residue 355 THR Chi-restraints excluded: chain 3P residue 4 ILE Chi-restraints excluded: chain 3P residue 102 LEU Chi-restraints excluded: chain 3P residue 156 ILE Chi-restraints excluded: chain 3P residue 192 LEU Chi-restraints excluded: chain 3P residue 316 MET Chi-restraints excluded: chain 3P residue 345 HIS Chi-restraints excluded: chain 3Q residue 3 LEU Chi-restraints excluded: chain 3Q residue 75 ASN Chi-restraints excluded: chain 3Q residue 188 THR Chi-restraints excluded: chain 3Q residue 215 LEU Chi-restraints excluded: chain 3R residue 106 SER Chi-restraints excluded: chain 3R residue 131 ASN Chi-restraints excluded: chain 3R residue 146 VAL Chi-restraints excluded: chain 3R residue 152 ILE Chi-restraints excluded: chain 3R residue 200 HIS Chi-restraints excluded: chain 3R residue 209 GLU Chi-restraints excluded: chain 3R residue 262 THR Chi-restraints excluded: chain 3S residue 37 ILE Chi-restraints excluded: chain 3S residue 47 ILE Chi-restraints excluded: chain 3S residue 59 VAL Chi-restraints excluded: chain 3S residue 79 GLN Chi-restraints excluded: chain 3S residue 98 ILE Chi-restraints excluded: chain 3T residue 17 SER Chi-restraints excluded: chain 3T residue 34 ILE Chi-restraints excluded: chain 3T residue 38 LEU Chi-restraints excluded: chain 3T residue 44 CYS Chi-restraints excluded: chain 3T residue 46 LEU Chi-restraints excluded: chain 3T residue 53 VAL Chi-restraints excluded: chain 3T residue 60 THR Chi-restraints excluded: chain 3T residue 70 LYS Chi-restraints excluded: chain 3T residue 73 ASN Chi-restraints excluded: chain 3U residue 37 LEU Chi-restraints excluded: chain 3U residue 39 LEU Chi-restraints excluded: chain 3U residue 42 GLN Chi-restraints excluded: chain 3U residue 62 LEU Chi-restraints excluded: chain 3V residue 50 LEU Chi-restraints excluded: chain 3V residue 51 CYS Chi-restraints excluded: chain 3V residue 67 SER Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3V residue 70 LEU Chi-restraints excluded: chain 3V residue 72 VAL Chi-restraints excluded: chain 3W residue 18 SER Chi-restraints excluded: chain 3W residue 29 LEU Chi-restraints excluded: chain 3X residue 1 MET Chi-restraints excluded: chain 3X residue 16 ASN Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 18 ILE Chi-restraints excluded: chain 3Y residue 23 MET Chi-restraints excluded: chain 3Y residue 41 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 280 optimal weight: 0.9980 chunk 371 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 225 optimal weight: 0.8980 chunk 390 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 263 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3D 94 HIS 3D 159 GLN ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3G 66 GLN 3H 48 GLN 3N 9 GLN 3N 18 GLN ** 3N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3O 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3O 277 HIS ** 3P 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3Q 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3X 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.085626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.070951 restraints weight = 98231.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.074386 restraints weight = 35150.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.074480 restraints weight = 17484.049| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.670 34354 Z= 0.165 Angle : 0.656 21.854 46524 Z= 0.311 Chirality : 0.042 0.179 5004 Planarity : 0.004 0.072 5834 Dihedral : 13.016 137.253 5328 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.39 % Favored : 94.43 % Rotamer: Outliers : 3.98 % Allowed : 26.78 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.14), residues: 4064 helix: 1.63 (0.12), residues: 2066 sheet: -1.08 (0.28), residues: 332 loop : -0.58 (0.16), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP3R 169 HIS 0.006 0.001 HIS3D 94 PHE 0.017 0.001 PHE3A 231 TYR 0.016 0.001 TYR3C 224 ARG 0.009 0.000 ARG3U 36 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 1768) hydrogen bonds : angle 4.74002 ( 5083) metal coordination : bond 0.05388 ( 8) metal coordination : angle 14.22186 ( 6) SS BOND : bond 0.00311 ( 6) SS BOND : angle 1.90597 ( 12) covalent geometry : bond 0.00391 (34335) covalent geometry : angle 0.63527 (46506) Misc. bond : bond 0.41494 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 477 time to evaluate : 3.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR3N 4 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU3N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 100 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8768 (mtpp) REVERT: 3A 136 GLN cc_start: 0.8798 (mp10) cc_final: 0.8534 (mp10) REVERT: 3A 176 LYS cc_start: 0.9170 (mptt) cc_final: 0.8960 (mmtp) REVERT: 3A 209 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8515 (tm) REVERT: 3A 302 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8877 (mmmt) REVERT: 3A 343 MET cc_start: 0.8745 (mmp) cc_final: 0.8513 (mmm) REVERT: 3A 378 ASP cc_start: 0.8702 (t0) cc_final: 0.8361 (t0) REVERT: 3B 239 TYR cc_start: 0.8805 (t80) cc_final: 0.8415 (t80) REVERT: 3B 268 GLU cc_start: 0.7992 (tt0) cc_final: 0.7598 (tt0) REVERT: 3B 305 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8766 (tt0) REVERT: 3B 376 GLU cc_start: 0.7827 (tt0) cc_final: 0.7576 (tt0) REVERT: 3C 172 LYS cc_start: 0.8467 (ttpp) cc_final: 0.8043 (tptp) REVERT: 3C 373 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8672 (mm-30) REVERT: 3D 232 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.6903 (tmm160) REVERT: 3D 270 GLN cc_start: 0.8976 (tp40) cc_final: 0.8609 (tp40) REVERT: 3D 274 ASP cc_start: 0.7941 (m-30) cc_final: 0.7311 (m-30) REVERT: 3E 191 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8011 (pp20) REVERT: 3E 210 TRP cc_start: 0.8998 (m-90) cc_final: 0.8753 (m-90) REVERT: 3F 82 MET cc_start: 0.9240 (ttp) cc_final: 0.8792 (ttp) REVERT: 3F 95 TYR cc_start: 0.8921 (t80) cc_final: 0.8682 (t80) REVERT: 3F 114 LYS cc_start: 0.9428 (mmtp) cc_final: 0.9201 (mmtm) REVERT: 3G 54 PHE cc_start: 0.9331 (m-80) cc_final: 0.9096 (m-80) REVERT: 3H 40 ASP cc_start: 0.8746 (t70) cc_final: 0.8495 (t70) REVERT: 3H 51 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8428 (mm-40) REVERT: 3H 60 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: 3H 91 ASP cc_start: 0.8207 (m-30) cc_final: 0.8000 (m-30) REVERT: 3J 45 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7979 (mt-10) REVERT: 3N 58 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8560 (m-80) REVERT: 3N 335 MET cc_start: 0.9208 (mmp) cc_final: 0.8728 (mmm) REVERT: 3P 89 MET cc_start: 0.8825 (tpp) cc_final: 0.8563 (tpp) REVERT: 3P 172 LYS cc_start: 0.8374 (tttp) cc_final: 0.8001 (tttt) REVERT: 3P 235 MET cc_start: 0.9085 (ttp) cc_final: 0.8260 (tmm) REVERT: 3P 282 ARG cc_start: 0.8001 (mtm110) cc_final: 0.7748 (mtp180) REVERT: 3S 47 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9050 (mp) REVERT: 3U 62 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8600 (mt) REVERT: 3V 53 GLU cc_start: 0.8122 (mp0) cc_final: 0.7794 (mp0) REVERT: 3X 23 MET cc_start: 0.8937 (tmm) cc_final: 0.8466 (tmm) REVERT: 3Y 43 ASP cc_start: 0.9084 (m-30) cc_final: 0.8827 (m-30) REVERT: 3Y 51 LYS cc_start: 0.9222 (mmmt) cc_final: 0.8978 (mtpp) REVERT: 3Y 52 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7518 (m-80) outliers start: 136 outliers final: 86 residues processed: 570 average time/residue: 0.4757 time to fit residues: 437.9147 Evaluate side-chains 552 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 454 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 14 THR Chi-restraints excluded: chain 3A residue 23 LEU Chi-restraints excluded: chain 3A residue 34 THR Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 100 LYS Chi-restraints excluded: chain 3A residue 112 LEU Chi-restraints excluded: chain 3A residue 195 MET Chi-restraints excluded: chain 3A residue 209 LEU Chi-restraints excluded: chain 3A residue 292 SER Chi-restraints excluded: chain 3A residue 294 LEU Chi-restraints excluded: chain 3A residue 302 LYS Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3B residue 51 ILE Chi-restraints excluded: chain 3B residue 227 ARG Chi-restraints excluded: chain 3B residue 275 LEU Chi-restraints excluded: chain 3B residue 285 VAL Chi-restraints excluded: chain 3B residue 305 GLN Chi-restraints excluded: chain 3B residue 410 VAL Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 161 VAL Chi-restraints excluded: chain 3C residue 203 THR Chi-restraints excluded: chain 3C residue 209 THR Chi-restraints excluded: chain 3C residue 233 LEU Chi-restraints excluded: chain 3C residue 292 LEU Chi-restraints excluded: chain 3C residue 300 ILE Chi-restraints excluded: chain 3C residue 343 VAL Chi-restraints excluded: chain 3C residue 373 GLU Chi-restraints excluded: chain 3D residue 125 CYS Chi-restraints excluded: chain 3D residue 134 VAL Chi-restraints excluded: chain 3D residue 232 ARG Chi-restraints excluded: chain 3D residue 269 SER Chi-restraints excluded: chain 3D residue 307 LEU Chi-restraints excluded: chain 3D residue 324 LEU Chi-restraints excluded: chain 3E residue 83 ILE Chi-restraints excluded: chain 3E residue 139 SER Chi-restraints excluded: chain 3E residue 154 ILE Chi-restraints excluded: chain 3E residue 191 GLU Chi-restraints excluded: chain 3E residue 222 CYS Chi-restraints excluded: chain 3E residue 239 HIS Chi-restraints excluded: chain 3E residue 271 VAL Chi-restraints excluded: chain 3F residue 66 LEU Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 40 LEU Chi-restraints excluded: chain 3G residue 46 CYS Chi-restraints excluded: chain 3G residue 48 LEU Chi-restraints excluded: chain 3G residue 55 VAL Chi-restraints excluded: chain 3G residue 72 LYS Chi-restraints excluded: chain 3H residue 55 CYS Chi-restraints excluded: chain 3H residue 60 GLU Chi-restraints excluded: chain 3H residue 87 LEU Chi-restraints excluded: chain 3I residue 70 LEU Chi-restraints excluded: chain 3I residue 76 VAL Chi-restraints excluded: chain 3J residue 5 THR Chi-restraints excluded: chain 3J residue 54 LYS Chi-restraints excluded: chain 3N residue 28 GLU Chi-restraints excluded: chain 3N residue 58 PHE Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 255 ILE Chi-restraints excluded: chain 3N residue 320 LEU Chi-restraints excluded: chain 3N residue 407 VAL Chi-restraints excluded: chain 3O residue 109 VAL Chi-restraints excluded: chain 3O residue 186 VAL Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 278 VAL Chi-restraints excluded: chain 3O residue 347 ILE Chi-restraints excluded: chain 3O residue 353 SER Chi-restraints excluded: chain 3P residue 4 ILE Chi-restraints excluded: chain 3P residue 102 LEU Chi-restraints excluded: chain 3P residue 192 LEU Chi-restraints excluded: chain 3P residue 345 HIS Chi-restraints excluded: chain 3Q residue 3 LEU Chi-restraints excluded: chain 3Q residue 5 LEU Chi-restraints excluded: chain 3Q residue 68 VAL Chi-restraints excluded: chain 3Q residue 75 ASN Chi-restraints excluded: chain 3R residue 106 SER Chi-restraints excluded: chain 3R residue 209 GLU Chi-restraints excluded: chain 3R residue 223 VAL Chi-restraints excluded: chain 3S residue 16 ILE Chi-restraints excluded: chain 3S residue 47 ILE Chi-restraints excluded: chain 3T residue 17 SER Chi-restraints excluded: chain 3T residue 44 CYS Chi-restraints excluded: chain 3T residue 73 ASN Chi-restraints excluded: chain 3U residue 39 LEU Chi-restraints excluded: chain 3U residue 42 GLN Chi-restraints excluded: chain 3U residue 62 LEU Chi-restraints excluded: chain 3V residue 67 SER Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3V residue 72 VAL Chi-restraints excluded: chain 3W residue 4 THR Chi-restraints excluded: chain 3W residue 18 SER Chi-restraints excluded: chain 3W residue 29 LEU Chi-restraints excluded: chain 3X residue 1 MET Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 22 SER Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 18 ILE Chi-restraints excluded: chain 3Y residue 41 ILE Chi-restraints excluded: chain 3Y residue 52 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 120 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 291 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 374 optimal weight: 10.0000 chunk 103 optimal weight: 0.1980 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 267 optimal weight: 7.9990 chunk 225 optimal weight: 5.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3C 44 GLN 3D 94 HIS ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3H 48 GLN 3N 9 GLN ** 3O 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3Q 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3R 135 GLN ** 3R 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3X 16 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 = 0.3243 r_free = 0.3243 target = 0.085756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.069289 restraints weight = 120478.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.072319 restraints weight = 43011.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.074208 restraints weight = 22586.439| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.648 34354 Z= 0.178 Angle : 0.662 22.658 46524 Z= 0.312 Chirality : 0.042 0.181 5004 Planarity : 0.004 0.071 5834 Dihedral : 12.757 137.629 5326 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.71 % Favored : 94.09 % Rotamer: Outliers : 4.09 % Allowed : 27.24 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.14), residues: 4064 helix: 1.69 (0.11), residues: 2062 sheet: -1.13 (0.27), residues: 334 loop : -0.52 (0.17), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.001 TRP3R 169 HIS 0.006 0.001 HIS3R 219 PHE 0.019 0.001 PHE3F 100 TYR 0.023 0.001 TYR3S 20 ARG 0.009 0.001 ARG3U 36 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 1768) hydrogen bonds : angle 4.67983 ( 5083) metal coordination : bond 0.05563 ( 8) metal coordination : angle 14.75953 ( 6) SS BOND : bond 0.00289 ( 6) SS BOND : angle 1.35148 ( 12) covalent geometry : bond 0.00422 (34335) covalent geometry : angle 0.64018 (46506) Misc. bond : bond 0.40541 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 484 time to evaluate : 3.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR3N 4 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU3N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 100 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8775 (mtpp) REVERT: 3A 136 GLN cc_start: 0.8782 (mp10) cc_final: 0.8531 (mp10) REVERT: 3A 176 LYS cc_start: 0.9170 (mptt) cc_final: 0.8904 (mmtp) REVERT: 3A 209 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8523 (tm) REVERT: 3A 378 ASP cc_start: 0.8644 (t0) cc_final: 0.8327 (t0) REVERT: 3B 268 GLU cc_start: 0.8008 (tt0) cc_final: 0.7619 (tt0) REVERT: 3B 305 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8692 (tt0) REVERT: 3B 376 GLU cc_start: 0.7802 (tt0) cc_final: 0.7568 (tt0) REVERT: 3C 102 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9161 (tt) REVERT: 3C 172 LYS cc_start: 0.8460 (ttpp) cc_final: 0.7968 (tptp) REVERT: 3C 254 ASP cc_start: 0.8604 (m-30) cc_final: 0.8395 (m-30) REVERT: 3C 353 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9092 (mm) REVERT: 3C 373 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8708 (mm-30) REVERT: 3D 270 GLN cc_start: 0.8953 (tp40) cc_final: 0.8567 (tp40) REVERT: 3D 274 ASP cc_start: 0.7941 (m-30) cc_final: 0.7290 (m-30) REVERT: 3E 151 LYS cc_start: 0.7988 (pttt) cc_final: 0.7595 (pttm) REVERT: 3E 191 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7859 (pp20) REVERT: 3E 210 TRP cc_start: 0.9058 (m-90) cc_final: 0.8847 (m-90) REVERT: 3F 82 MET cc_start: 0.9213 (ttp) cc_final: 0.8788 (ttp) REVERT: 3F 95 TYR cc_start: 0.8923 (t80) cc_final: 0.8679 (t80) REVERT: 3F 114 LYS cc_start: 0.9428 (mmtp) cc_final: 0.9197 (mmtm) REVERT: 3G 54 PHE cc_start: 0.9333 (m-80) cc_final: 0.9095 (m-80) REVERT: 3G 61 TYR cc_start: 0.9209 (t80) cc_final: 0.8813 (t80) REVERT: 3H 60 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7154 (pm20) REVERT: 3H 91 ASP cc_start: 0.8187 (m-30) cc_final: 0.7978 (m-30) REVERT: 3J 45 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7985 (mt-10) REVERT: 3N 58 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: 3N 335 MET cc_start: 0.9197 (mmp) cc_final: 0.8729 (mmm) REVERT: 3P 89 MET cc_start: 0.8748 (tpp) cc_final: 0.8525 (tpp) REVERT: 3P 172 LYS cc_start: 0.8406 (tttp) cc_final: 0.8045 (tttt) REVERT: 3P 235 MET cc_start: 0.9050 (ttp) cc_final: 0.8397 (tmm) REVERT: 3P 282 ARG cc_start: 0.8043 (mtm110) cc_final: 0.7780 (mtp180) REVERT: 3R 209 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7202 (pm20) REVERT: 3S 47 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9068 (mp) REVERT: 3U 62 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8547 (mt) REVERT: 3V 53 GLU cc_start: 0.8116 (mp0) cc_final: 0.7761 (mp0) REVERT: 3X 5 PHE cc_start: 0.8482 (m-80) cc_final: 0.8133 (m-80) REVERT: 3X 23 MET cc_start: 0.8888 (tmm) cc_final: 0.8464 (tmm) REVERT: 3Y 12 GLU cc_start: 0.8145 (mp0) cc_final: 0.7937 (mp0) REVERT: 3Y 51 LYS cc_start: 0.9121 (mmmt) cc_final: 0.8883 (mtpp) REVERT: 3Y 52 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7685 (m-80) outliers start: 140 outliers final: 104 residues processed: 579 average time/residue: 0.4787 time to fit residues: 448.9346 Evaluate side-chains 575 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 458 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 14 THR Chi-restraints excluded: chain 3A residue 16 VAL Chi-restraints excluded: chain 3A residue 23 LEU Chi-restraints excluded: chain 3A residue 34 THR Chi-restraints excluded: chain 3A residue 58 PHE Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 100 LYS Chi-restraints excluded: chain 3A residue 112 LEU Chi-restraints excluded: chain 3A residue 195 MET Chi-restraints excluded: chain 3A residue 209 LEU Chi-restraints excluded: chain 3A residue 257 VAL Chi-restraints excluded: chain 3A residue 292 SER Chi-restraints excluded: chain 3A residue 294 LEU Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3B residue 51 ILE Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 101 THR Chi-restraints excluded: chain 3B residue 227 ARG Chi-restraints excluded: chain 3B residue 275 LEU Chi-restraints excluded: chain 3B residue 285 VAL Chi-restraints excluded: chain 3B residue 305 GLN Chi-restraints excluded: chain 3B residue 410 VAL Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 21 LEU Chi-restraints excluded: chain 3C residue 102 LEU Chi-restraints excluded: chain 3C residue 161 VAL Chi-restraints excluded: chain 3C residue 203 THR Chi-restraints excluded: chain 3C residue 209 THR Chi-restraints excluded: chain 3C residue 283 SER Chi-restraints excluded: chain 3C residue 292 LEU Chi-restraints excluded: chain 3C residue 300 ILE Chi-restraints excluded: chain 3C residue 343 VAL Chi-restraints excluded: chain 3C residue 353 LEU Chi-restraints excluded: chain 3C residue 373 GLU Chi-restraints excluded: chain 3D residue 125 CYS Chi-restraints excluded: chain 3D residue 128 CYS Chi-restraints excluded: chain 3D residue 134 VAL Chi-restraints excluded: chain 3D residue 159 GLN Chi-restraints excluded: chain 3D residue 269 SER Chi-restraints excluded: chain 3D residue 307 LEU Chi-restraints excluded: chain 3D residue 324 LEU Chi-restraints excluded: chain 3E residue 83 ILE Chi-restraints excluded: chain 3E residue 139 SER Chi-restraints excluded: chain 3E residue 140 MET Chi-restraints excluded: chain 3E residue 191 GLU Chi-restraints excluded: chain 3E residue 222 CYS Chi-restraints excluded: chain 3E residue 239 HIS Chi-restraints excluded: chain 3E residue 271 VAL Chi-restraints excluded: chain 3F residue 25 LEU Chi-restraints excluded: chain 3F residue 66 LEU Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 34 LYS Chi-restraints excluded: chain 3G residue 40 LEU Chi-restraints excluded: chain 3G residue 46 CYS Chi-restraints excluded: chain 3G residue 48 LEU Chi-restraints excluded: chain 3G residue 55 VAL Chi-restraints excluded: chain 3G residue 72 LYS Chi-restraints excluded: chain 3H residue 55 CYS Chi-restraints excluded: chain 3H residue 60 GLU Chi-restraints excluded: chain 3H residue 87 LEU Chi-restraints excluded: chain 3I residue 70 LEU Chi-restraints excluded: chain 3I residue 76 VAL Chi-restraints excluded: chain 3J residue 5 THR Chi-restraints excluded: chain 3J residue 54 LYS Chi-restraints excluded: chain 3N residue 28 GLU Chi-restraints excluded: chain 3N residue 58 PHE Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 166 SER Chi-restraints excluded: chain 3N residue 209 LEU Chi-restraints excluded: chain 3N residue 255 ILE Chi-restraints excluded: chain 3N residue 292 SER Chi-restraints excluded: chain 3N residue 320 LEU Chi-restraints excluded: chain 3N residue 407 VAL Chi-restraints excluded: chain 3O residue 186 VAL Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 226 MET Chi-restraints excluded: chain 3O residue 278 VAL Chi-restraints excluded: chain 3O residue 347 ILE Chi-restraints excluded: chain 3O residue 353 SER Chi-restraints excluded: chain 3P residue 4 ILE Chi-restraints excluded: chain 3P residue 102 LEU Chi-restraints excluded: chain 3P residue 192 LEU Chi-restraints excluded: chain 3P residue 345 HIS Chi-restraints excluded: chain 3Q residue 3 LEU Chi-restraints excluded: chain 3Q residue 5 LEU Chi-restraints excluded: chain 3Q residue 68 VAL Chi-restraints excluded: chain 3Q residue 75 ASN Chi-restraints excluded: chain 3R residue 106 SER Chi-restraints excluded: chain 3R residue 176 VAL Chi-restraints excluded: chain 3R residue 209 GLU Chi-restraints excluded: chain 3R residue 223 VAL Chi-restraints excluded: chain 3R residue 225 ILE Chi-restraints excluded: chain 3S residue 16 ILE Chi-restraints excluded: chain 3S residue 47 ILE Chi-restraints excluded: chain 3S residue 58 ARG Chi-restraints excluded: chain 3S residue 98 ILE Chi-restraints excluded: chain 3T residue 17 SER Chi-restraints excluded: chain 3T residue 44 CYS Chi-restraints excluded: chain 3U residue 37 LEU Chi-restraints excluded: chain 3U residue 39 LEU Chi-restraints excluded: chain 3U residue 42 GLN Chi-restraints excluded: chain 3U residue 62 LEU Chi-restraints excluded: chain 3V residue 50 LEU Chi-restraints excluded: chain 3V residue 67 SER Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3V residue 72 VAL Chi-restraints excluded: chain 3W residue 4 THR Chi-restraints excluded: chain 3W residue 18 SER Chi-restraints excluded: chain 3W residue 29 LEU Chi-restraints excluded: chain 3W residue 58 LYS Chi-restraints excluded: chain 3X residue 1 MET Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 22 SER Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 18 ILE Chi-restraints excluded: chain 3Y residue 41 ILE Chi-restraints excluded: chain 3Y residue 52 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 313 optimal weight: 6.9990 chunk 33 optimal weight: 0.0870 chunk 360 optimal weight: 6.9990 chunk 280 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 267 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 214 optimal weight: 7.9990 overall best weight: 3.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3A 9 GLN 3B 400 GLN 3D 94 HIS ** 3E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 9 GLN 3N 359 ASN ** 3O 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3Q 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3X 16 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 = 0.3192 r_free = 0.3192 target = 0.084323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.067793 restraints weight = 99038.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.070583 restraints weight = 38587.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.072368 restraints weight = 21378.400| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.787 34354 Z= 0.272 Angle : 0.733 22.564 46524 Z= 0.345 Chirality : 0.044 0.243 5004 Planarity : 0.004 0.059 5834 Dihedral : 12.754 140.088 5326 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.06 % Favored : 93.75 % Rotamer: Outliers : 4.61 % Allowed : 27.07 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.14), residues: 4064 helix: 1.57 (0.11), residues: 2073 sheet: -1.11 (0.27), residues: 324 loop : -0.56 (0.17), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP3R 169 HIS 0.007 0.001 HIS3P 97 PHE 0.020 0.002 PHE3E 167 TYR 0.031 0.002 TYR3S 20 ARG 0.011 0.001 ARG3U 36 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 1768) hydrogen bonds : angle 4.80904 ( 5083) metal coordination : bond 0.05521 ( 8) metal coordination : angle 14.80046 ( 6) SS BOND : bond 0.00295 ( 6) SS BOND : angle 1.39062 ( 12) covalent geometry : bond 0.00640 (34335) covalent geometry : angle 0.71357 (46506) Misc. bond : bond 0.48356 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 464 time to evaluate : 3.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR3N 4 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU3N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 100 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8786 (mtpp) REVERT: 3A 136 GLN cc_start: 0.8754 (mp10) cc_final: 0.8480 (mp10) REVERT: 3A 176 LYS cc_start: 0.9170 (mptt) cc_final: 0.8920 (mmtp) REVERT: 3A 209 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8514 (tm) REVERT: 3A 302 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8965 (mmmt) REVERT: 3A 323 HIS cc_start: 0.9501 (OUTLIER) cc_final: 0.9170 (t-90) REVERT: 3A 378 ASP cc_start: 0.8774 (t0) cc_final: 0.8452 (t0) REVERT: 3B 268 GLU cc_start: 0.8107 (tt0) cc_final: 0.7715 (tt0) REVERT: 3B 305 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8799 (tt0) REVERT: 3B 376 GLU cc_start: 0.7840 (tt0) cc_final: 0.7611 (tt0) REVERT: 3C 102 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9187 (tt) REVERT: 3C 172 LYS cc_start: 0.8507 (ttpp) cc_final: 0.8012 (tptp) REVERT: 3C 353 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9119 (mm) REVERT: 3D 232 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7033 (tmm160) REVERT: 3D 270 GLN cc_start: 0.8904 (tp40) cc_final: 0.8292 (tp40) REVERT: 3D 274 ASP cc_start: 0.8018 (m-30) cc_final: 0.7281 (m-30) REVERT: 3E 191 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8032 (pp20) REVERT: 3E 210 TRP cc_start: 0.9101 (m-90) cc_final: 0.8757 (m-90) REVERT: 3F 82 MET cc_start: 0.9221 (ttp) cc_final: 0.8806 (ttp) REVERT: 3F 95 TYR cc_start: 0.8951 (t80) cc_final: 0.8637 (t80) REVERT: 3F 114 LYS cc_start: 0.9447 (mmtp) cc_final: 0.9225 (mmtm) REVERT: 3G 54 PHE cc_start: 0.9349 (m-80) cc_final: 0.9090 (m-80) REVERT: 3H 60 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7187 (pm20) REVERT: 3J 45 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7970 (mt-10) REVERT: 3N 46 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.7948 (ttm170) REVERT: 3N 58 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8592 (m-80) REVERT: 3N 335 MET cc_start: 0.9281 (mmp) cc_final: 0.8777 (mmm) REVERT: 3P 89 MET cc_start: 0.8797 (tpp) cc_final: 0.8497 (tpp) REVERT: 3P 172 LYS cc_start: 0.8468 (tttp) cc_final: 0.8083 (tttt) REVERT: 3P 235 MET cc_start: 0.9077 (ttp) cc_final: 0.8333 (tmm) REVERT: 3P 282 ARG cc_start: 0.8076 (mtm110) cc_final: 0.7817 (mtp180) REVERT: 3Q 80 MET cc_start: 0.8461 (mmp) cc_final: 0.7980 (mmp) REVERT: 3R 209 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7327 (pm20) REVERT: 3S 47 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9072 (mp) REVERT: 3U 62 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8608 (mt) REVERT: 3W 18 SER cc_start: 0.9524 (OUTLIER) cc_final: 0.9236 (p) REVERT: 3W 51 LEU cc_start: 0.9514 (mm) cc_final: 0.9225 (mt) REVERT: 3X 5 PHE cc_start: 0.8495 (m-80) cc_final: 0.8143 (m-80) REVERT: 3X 23 MET cc_start: 0.8909 (tmm) cc_final: 0.8695 (ttm) REVERT: 3Y 51 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8912 (mtpp) REVERT: 3Y 52 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7635 (m-80) outliers start: 158 outliers final: 113 residues processed: 573 average time/residue: 0.4559 time to fit residues: 421.5215 Evaluate side-chains 578 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 448 time to evaluate : 3.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 14 THR Chi-restraints excluded: chain 3A residue 16 VAL Chi-restraints excluded: chain 3A residue 23 LEU Chi-restraints excluded: chain 3A residue 34 THR Chi-restraints excluded: chain 3A residue 51 LYS Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 100 LYS Chi-restraints excluded: chain 3A residue 112 LEU Chi-restraints excluded: chain 3A residue 195 MET Chi-restraints excluded: chain 3A residue 209 LEU Chi-restraints excluded: chain 3A residue 290 MET Chi-restraints excluded: chain 3A residue 292 SER Chi-restraints excluded: chain 3A residue 302 LYS Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 323 HIS Chi-restraints excluded: chain 3A residue 354 VAL Chi-restraints excluded: chain 3B residue 51 ILE Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 101 THR Chi-restraints excluded: chain 3B residue 227 ARG Chi-restraints excluded: chain 3B residue 275 LEU Chi-restraints excluded: chain 3B residue 285 VAL Chi-restraints excluded: chain 3B residue 305 GLN Chi-restraints excluded: chain 3B residue 369 LEU Chi-restraints excluded: chain 3B residue 400 GLN Chi-restraints excluded: chain 3B residue 410 VAL Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 102 LEU Chi-restraints excluded: chain 3C residue 161 VAL Chi-restraints excluded: chain 3C residue 203 THR Chi-restraints excluded: chain 3C residue 233 LEU Chi-restraints excluded: chain 3C residue 283 SER Chi-restraints excluded: chain 3C residue 292 LEU Chi-restraints excluded: chain 3C residue 297 SER Chi-restraints excluded: chain 3C residue 300 ILE Chi-restraints excluded: chain 3C residue 343 VAL Chi-restraints excluded: chain 3C residue 353 LEU Chi-restraints excluded: chain 3C residue 373 GLU Chi-restraints excluded: chain 3D residue 94 HIS Chi-restraints excluded: chain 3D residue 120 VAL Chi-restraints excluded: chain 3D residue 125 CYS Chi-restraints excluded: chain 3D residue 128 CYS Chi-restraints excluded: chain 3D residue 134 VAL Chi-restraints excluded: chain 3D residue 159 GLN Chi-restraints excluded: chain 3D residue 232 ARG Chi-restraints excluded: chain 3D residue 269 SER Chi-restraints excluded: chain 3D residue 307 LEU Chi-restraints excluded: chain 3D residue 324 LEU Chi-restraints excluded: chain 3E residue 83 ILE Chi-restraints excluded: chain 3E residue 139 SER Chi-restraints excluded: chain 3E residue 140 MET Chi-restraints excluded: chain 3E residue 156 LEU Chi-restraints excluded: chain 3E residue 174 LEU Chi-restraints excluded: chain 3E residue 191 GLU Chi-restraints excluded: chain 3E residue 239 HIS Chi-restraints excluded: chain 3E residue 271 VAL Chi-restraints excluded: chain 3F residue 25 LEU Chi-restraints excluded: chain 3F residue 66 LEU Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 17 THR Chi-restraints excluded: chain 3G residue 40 LEU Chi-restraints excluded: chain 3G residue 48 LEU Chi-restraints excluded: chain 3G residue 55 VAL Chi-restraints excluded: chain 3G residue 72 LYS Chi-restraints excluded: chain 3H residue 52 ILE Chi-restraints excluded: chain 3H residue 55 CYS Chi-restraints excluded: chain 3H residue 60 GLU Chi-restraints excluded: chain 3H residue 87 LEU Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 70 LEU Chi-restraints excluded: chain 3J residue 5 THR Chi-restraints excluded: chain 3J residue 54 LYS Chi-restraints excluded: chain 3N residue 28 GLU Chi-restraints excluded: chain 3N residue 46 ARG Chi-restraints excluded: chain 3N residue 58 PHE Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 166 SER Chi-restraints excluded: chain 3N residue 209 LEU Chi-restraints excluded: chain 3N residue 255 ILE Chi-restraints excluded: chain 3N residue 292 SER Chi-restraints excluded: chain 3N residue 320 LEU Chi-restraints excluded: chain 3N residue 407 VAL Chi-restraints excluded: chain 3O residue 186 VAL Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 226 MET Chi-restraints excluded: chain 3O residue 278 VAL Chi-restraints excluded: chain 3O residue 347 ILE Chi-restraints excluded: chain 3O residue 353 SER Chi-restraints excluded: chain 3P residue 4 ILE Chi-restraints excluded: chain 3P residue 102 LEU Chi-restraints excluded: chain 3P residue 112 THR Chi-restraints excluded: chain 3P residue 192 LEU Chi-restraints excluded: chain 3P residue 345 HIS Chi-restraints excluded: chain 3Q residue 3 LEU Chi-restraints excluded: chain 3Q residue 5 LEU Chi-restraints excluded: chain 3Q residue 17 LEU Chi-restraints excluded: chain 3Q residue 68 VAL Chi-restraints excluded: chain 3Q residue 75 ASN Chi-restraints excluded: chain 3R residue 106 SER Chi-restraints excluded: chain 3R residue 200 HIS Chi-restraints excluded: chain 3R residue 209 GLU Chi-restraints excluded: chain 3R residue 223 VAL Chi-restraints excluded: chain 3R residue 225 ILE Chi-restraints excluded: chain 3S residue 16 ILE Chi-restraints excluded: chain 3S residue 47 ILE Chi-restraints excluded: chain 3S residue 58 ARG Chi-restraints excluded: chain 3S residue 98 ILE Chi-restraints excluded: chain 3T residue 17 SER Chi-restraints excluded: chain 3T residue 44 CYS Chi-restraints excluded: chain 3T residue 70 LYS Chi-restraints excluded: chain 3U residue 37 LEU Chi-restraints excluded: chain 3U residue 39 LEU Chi-restraints excluded: chain 3U residue 42 GLN Chi-restraints excluded: chain 3U residue 62 LEU Chi-restraints excluded: chain 3V residue 50 LEU Chi-restraints excluded: chain 3V residue 67 SER Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3V residue 72 VAL Chi-restraints excluded: chain 3W residue 4 THR Chi-restraints excluded: chain 3W residue 18 SER Chi-restraints excluded: chain 3W residue 29 LEU Chi-restraints excluded: chain 3W residue 58 LYS Chi-restraints excluded: chain 3X residue 1 MET Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 22 SER Chi-restraints excluded: chain 3X residue 40 LEU Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 18 ILE Chi-restraints excluded: chain 3Y residue 41 ILE Chi-restraints excluded: chain 3Y residue 52 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 278 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 235 optimal weight: 0.9980 chunk 161 optimal weight: 9.9990 chunk 252 optimal weight: 0.8980 chunk 207 optimal weight: 7.9990 chunk 321 optimal weight: 6.9990 chunk 356 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 234 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 400 GLN 3D 94 HIS ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3H 48 GLN 3N 9 GLN 3O 143 GLN ** 3O 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3Q 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3X 16 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 = 0.3256 r_free = 0.3256 target = 0.087690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.073082 restraints weight = 88040.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.075718 restraints weight = 31861.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.076062 restraints weight = 17308.718| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.550 34354 Z= 0.133 Angle : 0.654 21.997 46524 Z= 0.311 Chirality : 0.041 0.190 5004 Planarity : 0.004 0.089 5834 Dihedral : 12.455 137.313 5326 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.07 % Favored : 94.73 % Rotamer: Outliers : 3.69 % Allowed : 27.93 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.14), residues: 4064 helix: 1.72 (0.12), residues: 2063 sheet: -1.16 (0.27), residues: 345 loop : -0.47 (0.17), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP3R 169 HIS 0.023 0.001 HIS3D 94 PHE 0.016 0.001 PHE3A 231 TYR 0.026 0.001 TYR3S 20 ARG 0.011 0.000 ARG3U 36 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 1768) hydrogen bonds : angle 4.63531 ( 5083) metal coordination : bond 0.05921 ( 8) metal coordination : angle 14.11576 ( 6) SS BOND : bond 0.00299 ( 6) SS BOND : angle 1.13880 ( 12) covalent geometry : bond 0.00309 (34335) covalent geometry : angle 0.63344 (46506) Misc. bond : bond 0.35850 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 509 time to evaluate : 3.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR3N 4 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU3N 28 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 100 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8789 (mtpp) REVERT: 3A 136 GLN cc_start: 0.8808 (mp10) cc_final: 0.8561 (mp10) REVERT: 3A 176 LYS cc_start: 0.9157 (mptt) cc_final: 0.8870 (mmtp) REVERT: 3A 209 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8523 (tm) REVERT: 3A 334 MET cc_start: 0.9018 (tpp) cc_final: 0.8758 (tpp) REVERT: 3A 378 ASP cc_start: 0.8629 (t0) cc_final: 0.8311 (t0) REVERT: 3B 110 GLU cc_start: 0.7801 (tt0) cc_final: 0.7297 (tt0) REVERT: 3B 268 GLU cc_start: 0.7998 (tt0) cc_final: 0.7570 (tt0) REVERT: 3B 305 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8757 (tt0) REVERT: 3B 376 GLU cc_start: 0.7786 (tt0) cc_final: 0.7552 (tt0) REVERT: 3C 102 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9167 (tt) REVERT: 3C 172 LYS cc_start: 0.8362 (ttpp) cc_final: 0.7860 (tptp) REVERT: 3C 254 ASP cc_start: 0.8596 (m-30) cc_final: 0.8373 (m-30) REVERT: 3C 353 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9098 (mm) REVERT: 3D 270 GLN cc_start: 0.8907 (tp40) cc_final: 0.8548 (tp40) REVERT: 3D 274 ASP cc_start: 0.7899 (m-30) cc_final: 0.7295 (m-30) REVERT: 3E 191 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8230 (pp20) REVERT: 3F 95 TYR cc_start: 0.8885 (t80) cc_final: 0.8655 (t80) REVERT: 3F 114 LYS cc_start: 0.9423 (mmtp) cc_final: 0.9210 (mmtm) REVERT: 3G 54 PHE cc_start: 0.9273 (m-80) cc_final: 0.9033 (m-80) REVERT: 3G 61 TYR cc_start: 0.9171 (t80) cc_final: 0.8801 (t80) REVERT: 3H 60 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: 3J 45 GLU cc_start: 0.8240 (mt-10) cc_final: 0.8000 (mt-10) REVERT: 3N 58 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8412 (m-80) REVERT: 3N 335 MET cc_start: 0.9090 (mmp) cc_final: 0.8667 (mmm) REVERT: 3P 89 MET cc_start: 0.8712 (tpp) cc_final: 0.8435 (tpp) REVERT: 3P 172 LYS cc_start: 0.8337 (tttp) cc_final: 0.8003 (tttt) REVERT: 3P 282 ARG cc_start: 0.8011 (mtm110) cc_final: 0.7600 (mtm-85) REVERT: 3Q 80 MET cc_start: 0.8497 (mmp) cc_final: 0.8082 (mmp) REVERT: 3R 199 GLN cc_start: 0.7042 (mt0) cc_final: 0.6809 (mt0) REVERT: 3R 209 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7259 (pm20) REVERT: 3S 47 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9072 (mp) REVERT: 3U 62 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8610 (mt) REVERT: 3V 53 GLU cc_start: 0.8287 (mp0) cc_final: 0.7872 (mp0) REVERT: 3V 55 LEU cc_start: 0.8744 (tp) cc_final: 0.8525 (tp) REVERT: 3W 43 TYR cc_start: 0.9369 (t80) cc_final: 0.8985 (t80) REVERT: 3X 5 PHE cc_start: 0.8436 (m-80) cc_final: 0.8071 (m-80) REVERT: 3X 23 MET cc_start: 0.8896 (tmm) cc_final: 0.8444 (tmm) REVERT: 3Y 51 LYS cc_start: 0.9137 (mmmt) cc_final: 0.8911 (mtpp) REVERT: 3Y 52 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7683 (m-80) outliers start: 126 outliers final: 104 residues processed: 588 average time/residue: 0.4759 time to fit residues: 453.6980 Evaluate side-chains 601 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 485 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 14 THR Chi-restraints excluded: chain 3A residue 16 VAL Chi-restraints excluded: chain 3A residue 23 LEU Chi-restraints excluded: chain 3A residue 34 THR Chi-restraints excluded: chain 3A residue 51 LYS Chi-restraints excluded: chain 3A residue 58 PHE Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 100 LYS Chi-restraints excluded: chain 3A residue 112 LEU Chi-restraints excluded: chain 3A residue 187 SER Chi-restraints excluded: chain 3A residue 195 MET Chi-restraints excluded: chain 3A residue 209 LEU Chi-restraints excluded: chain 3A residue 304 CYS Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 354 VAL Chi-restraints excluded: chain 3B residue 51 ILE Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 101 THR Chi-restraints excluded: chain 3B residue 227 ARG Chi-restraints excluded: chain 3B residue 275 LEU Chi-restraints excluded: chain 3B residue 285 VAL Chi-restraints excluded: chain 3B residue 305 GLN Chi-restraints excluded: chain 3B residue 400 GLN Chi-restraints excluded: chain 3B residue 410 VAL Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 102 LEU Chi-restraints excluded: chain 3C residue 161 VAL Chi-restraints excluded: chain 3C residue 203 THR Chi-restraints excluded: chain 3C residue 233 LEU Chi-restraints excluded: chain 3C residue 292 LEU Chi-restraints excluded: chain 3C residue 300 ILE Chi-restraints excluded: chain 3C residue 343 VAL Chi-restraints excluded: chain 3C residue 353 LEU Chi-restraints excluded: chain 3C residue 362 ILE Chi-restraints excluded: chain 3C residue 373 GLU Chi-restraints excluded: chain 3D residue 109 LEU Chi-restraints excluded: chain 3D residue 120 VAL Chi-restraints excluded: chain 3D residue 125 CYS Chi-restraints excluded: chain 3D residue 128 CYS Chi-restraints excluded: chain 3D residue 134 VAL Chi-restraints excluded: chain 3D residue 142 VAL Chi-restraints excluded: chain 3D residue 159 GLN Chi-restraints excluded: chain 3D residue 324 LEU Chi-restraints excluded: chain 3E residue 83 ILE Chi-restraints excluded: chain 3E residue 139 SER Chi-restraints excluded: chain 3E residue 140 MET Chi-restraints excluded: chain 3E residue 191 GLU Chi-restraints excluded: chain 3E residue 222 CYS Chi-restraints excluded: chain 3E residue 239 HIS Chi-restraints excluded: chain 3E residue 271 VAL Chi-restraints excluded: chain 3F residue 25 LEU Chi-restraints excluded: chain 3F residue 66 LEU Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 40 LEU Chi-restraints excluded: chain 3G residue 55 VAL Chi-restraints excluded: chain 3G residue 72 LYS Chi-restraints excluded: chain 3H residue 55 CYS Chi-restraints excluded: chain 3H residue 60 GLU Chi-restraints excluded: chain 3H residue 87 LEU Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 70 LEU Chi-restraints excluded: chain 3I residue 76 VAL Chi-restraints excluded: chain 3J residue 5 THR Chi-restraints excluded: chain 3J residue 54 LYS Chi-restraints excluded: chain 3N residue 28 GLU Chi-restraints excluded: chain 3N residue 58 PHE Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 166 SER Chi-restraints excluded: chain 3N residue 209 LEU Chi-restraints excluded: chain 3N residue 292 SER Chi-restraints excluded: chain 3N residue 320 LEU Chi-restraints excluded: chain 3O residue 33 LEU Chi-restraints excluded: chain 3O residue 110 GLU Chi-restraints excluded: chain 3O residue 186 VAL Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 226 MET Chi-restraints excluded: chain 3O residue 278 VAL Chi-restraints excluded: chain 3O residue 347 ILE Chi-restraints excluded: chain 3P residue 4 ILE Chi-restraints excluded: chain 3P residue 102 LEU Chi-restraints excluded: chain 3P residue 112 THR Chi-restraints excluded: chain 3P residue 192 LEU Chi-restraints excluded: chain 3P residue 345 HIS Chi-restraints excluded: chain 3Q residue 3 LEU Chi-restraints excluded: chain 3Q residue 5 LEU Chi-restraints excluded: chain 3Q residue 17 LEU Chi-restraints excluded: chain 3Q residue 68 VAL Chi-restraints excluded: chain 3Q residue 75 ASN Chi-restraints excluded: chain 3R residue 106 SER Chi-restraints excluded: chain 3R residue 209 GLU Chi-restraints excluded: chain 3R residue 223 VAL Chi-restraints excluded: chain 3R residue 225 ILE Chi-restraints excluded: chain 3S residue 16 ILE Chi-restraints excluded: chain 3S residue 47 ILE Chi-restraints excluded: chain 3S residue 58 ARG Chi-restraints excluded: chain 3T residue 17 SER Chi-restraints excluded: chain 3T residue 44 CYS Chi-restraints excluded: chain 3U residue 37 LEU Chi-restraints excluded: chain 3U residue 39 LEU Chi-restraints excluded: chain 3U residue 42 GLN Chi-restraints excluded: chain 3U residue 62 LEU Chi-restraints excluded: chain 3V residue 50 LEU Chi-restraints excluded: chain 3V residue 68 VAL Chi-restraints excluded: chain 3V residue 72 VAL Chi-restraints excluded: chain 3W residue 4 THR Chi-restraints excluded: chain 3W residue 18 SER Chi-restraints excluded: chain 3W residue 29 LEU Chi-restraints excluded: chain 3W residue 58 LYS Chi-restraints excluded: chain 3X residue 1 MET Chi-restraints excluded: chain 3X residue 13 LEU Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 22 SER Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 18 ILE Chi-restraints excluded: chain 3Y residue 41 ILE Chi-restraints excluded: chain 3Y residue 52 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 5 optimal weight: 0.0370 chunk 298 optimal weight: 0.1980 chunk 52 optimal weight: 10.0000 chunk 318 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 350 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 340 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3D 94 HIS 3E 186 GLN ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3H 48 GLN 3N 9 GLN ** 3O 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3P 312 GLN ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3Q 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.072374 restraints weight = 95276.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.075248 restraints weight = 37428.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.077053 restraints weight = 20710.663| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.478 34354 Z= 0.128 Angle : 0.650 20.629 46524 Z= 0.309 Chirality : 0.042 0.252 5004 Planarity : 0.004 0.089 5834 Dihedral : 12.159 136.666 5326 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.97 % Favored : 94.83 % Rotamer: Outliers : 3.37 % Allowed : 28.39 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 4064 helix: 1.77 (0.12), residues: 2064 sheet: -1.18 (0.26), residues: 353 loop : -0.38 (0.17), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP3R 169 HIS 0.007 0.001 HIS3D 94 PHE 0.014 0.001 PHE3C 91 TYR 0.024 0.001 TYR3S 20 ARG 0.013 0.000 ARG3U 36 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 1768) hydrogen bonds : angle 4.55793 ( 5083) metal coordination : bond 0.05791 ( 8) metal coordination : angle 13.95328 ( 6) SS BOND : bond 0.00310 ( 6) SS BOND : angle 1.12510 ( 12) covalent geometry : bond 0.00297 (34335) covalent geometry : angle 0.62991 (46506) Misc. bond : bond 0.32331 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8128 Ramachandran restraints generated. 4064 Oldfield, 0 Emsley, 4064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 510 time to evaluate : 5.456 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR3N 4 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN3N 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 136 GLN cc_start: 0.8830 (mp10) cc_final: 0.8491 (mp10) REVERT: 3A 176 LYS cc_start: 0.9154 (mptt) cc_final: 0.8867 (mmtp) REVERT: 3A 209 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8506 (tm) REVERT: 3A 343 MET cc_start: 0.8682 (mmm) cc_final: 0.8443 (mmm) REVERT: 3A 353 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7783 (mt-10) REVERT: 3A 378 ASP cc_start: 0.8653 (t0) cc_final: 0.8346 (t0) REVERT: 3B 110 GLU cc_start: 0.7799 (tt0) cc_final: 0.7247 (tt0) REVERT: 3B 268 GLU cc_start: 0.8010 (tt0) cc_final: 0.7634 (tt0) REVERT: 3B 305 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8714 (tt0) REVERT: 3B 376 GLU cc_start: 0.7837 (tt0) cc_final: 0.7609 (tt0) REVERT: 3C 172 LYS cc_start: 0.8368 (ttpp) cc_final: 0.7867 (tptp) REVERT: 3C 254 ASP cc_start: 0.8605 (m-30) cc_final: 0.8370 (m-30) REVERT: 3C 353 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9035 (mm) REVERT: 3C 373 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8589 (mm-30) REVERT: 3D 270 GLN cc_start: 0.8832 (tp40) cc_final: 0.8479 (tp40) REVERT: 3D 274 ASP cc_start: 0.7931 (m-30) cc_final: 0.7312 (m-30) REVERT: 3E 130 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8266 (tttt) REVERT: 3E 151 LYS cc_start: 0.7829 (pttt) cc_final: 0.7542 (pttm) REVERT: 3E 191 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8044 (pp20) REVERT: 3F 95 TYR cc_start: 0.8837 (t80) cc_final: 0.8542 (t80) REVERT: 3F 114 LYS cc_start: 0.9438 (mmtp) cc_final: 0.9221 (mmtm) REVERT: 3G 54 PHE cc_start: 0.9268 (m-80) cc_final: 0.9044 (m-80) REVERT: 3H 60 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7172 (pm20) REVERT: 3J 45 GLU cc_start: 0.8217 (mt-10) cc_final: 0.8014 (mt-10) REVERT: 3N 58 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8355 (m-80) REVERT: 3N 335 MET cc_start: 0.8954 (mmp) cc_final: 0.8650 (mmm) REVERT: 3P 89 MET cc_start: 0.8653 (tpp) cc_final: 0.8383 (tpp) REVERT: 3P 172 LYS cc_start: 0.8335 (tttp) cc_final: 0.8006 (tttt) REVERT: 3P 235 MET cc_start: 0.9352 (tmm) cc_final: 0.8603 (tmm) REVERT: 3Q 80 MET cc_start: 0.8354 (mmp) cc_final: 0.7984 (mmp) REVERT: 3Q 185 ASP cc_start: 0.8607 (m-30) cc_final: 0.8267 (m-30) REVERT: 3R 209 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7312 (pm20) REVERT: 3S 47 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.9078 (mp) REVERT: 3U 62 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8611 (mt) REVERT: 3V 53 GLU cc_start: 0.8194 (mp0) cc_final: 0.7976 (mp0) REVERT: 3V 55 LEU cc_start: 0.8841 (tp) cc_final: 0.8630 (tp) REVERT: 3X 5 PHE cc_start: 0.8477 (m-80) cc_final: 0.8127 (m-80) REVERT: 3X 23 MET cc_start: 0.8902 (tmm) cc_final: 0.8469 (tmm) REVERT: 3Y 52 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7635 (m-80) outliers start: 115 outliers final: 86 residues processed: 580 average time/residue: 0.5692 time to fit residues: 539.5263 Evaluate side-chains 591 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 493 time to evaluate : 4.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 14 THR Chi-restraints excluded: chain 3A residue 16 VAL Chi-restraints excluded: chain 3A residue 34 THR Chi-restraints excluded: chain 3A residue 58 PHE Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 112 LEU Chi-restraints excluded: chain 3A residue 187 SER Chi-restraints excluded: chain 3A residue 209 LEU Chi-restraints excluded: chain 3A residue 304 CYS Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 354 VAL Chi-restraints excluded: chain 3B residue 51 ILE Chi-restraints excluded: chain 3B residue 101 THR Chi-restraints excluded: chain 3B residue 275 LEU Chi-restraints excluded: chain 3B residue 285 VAL Chi-restraints excluded: chain 3B residue 305 GLN Chi-restraints excluded: chain 3B residue 410 VAL Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 203 THR Chi-restraints excluded: chain 3C residue 233 LEU Chi-restraints excluded: chain 3C residue 283 SER Chi-restraints excluded: chain 3C residue 292 LEU Chi-restraints excluded: chain 3C residue 300 ILE Chi-restraints excluded: chain 3C residue 343 VAL Chi-restraints excluded: chain 3C residue 353 LEU Chi-restraints excluded: chain 3C residue 362 ILE Chi-restraints excluded: chain 3C residue 373 GLU Chi-restraints excluded: chain 3D residue 109 LEU Chi-restraints excluded: chain 3D residue 125 CYS Chi-restraints excluded: chain 3D residue 128 CYS Chi-restraints excluded: chain 3D residue 134 VAL Chi-restraints excluded: chain 3D residue 142 VAL Chi-restraints excluded: chain 3D residue 159 GLN Chi-restraints excluded: chain 3D residue 324 LEU Chi-restraints excluded: chain 3E residue 83 ILE Chi-restraints excluded: chain 3E residue 130 LYS Chi-restraints excluded: chain 3E residue 139 SER Chi-restraints excluded: chain 3E residue 191 GLU Chi-restraints excluded: chain 3E residue 239 HIS Chi-restraints excluded: chain 3E residue 271 VAL Chi-restraints excluded: chain 3F residue 66 LEU Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 40 LEU Chi-restraints excluded: chain 3G residue 46 CYS Chi-restraints excluded: chain 3G residue 55 VAL Chi-restraints excluded: chain 3G residue 72 LYS Chi-restraints excluded: chain 3H residue 55 CYS Chi-restraints excluded: chain 3H residue 60 GLU Chi-restraints excluded: chain 3H residue 87 LEU Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3J residue 5 THR Chi-restraints excluded: chain 3J residue 54 LYS Chi-restraints excluded: chain 3N residue 58 PHE Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 209 LEU Chi-restraints excluded: chain 3N residue 292 SER Chi-restraints excluded: chain 3O residue 110 GLU Chi-restraints excluded: chain 3O residue 186 VAL Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 226 MET Chi-restraints excluded: chain 3O residue 278 VAL Chi-restraints excluded: chain 3O residue 347 ILE Chi-restraints excluded: chain 3P residue 4 ILE Chi-restraints excluded: chain 3P residue 102 LEU Chi-restraints excluded: chain 3P residue 112 THR Chi-restraints excluded: chain 3P residue 192 LEU Chi-restraints excluded: chain 3P residue 345 HIS Chi-restraints excluded: chain 3Q residue 3 LEU Chi-restraints excluded: chain 3Q residue 5 LEU Chi-restraints excluded: chain 3Q residue 17 LEU Chi-restraints excluded: chain 3Q residue 68 VAL Chi-restraints excluded: chain 3Q residue 75 ASN Chi-restraints excluded: chain 3R residue 106 SER Chi-restraints excluded: chain 3R residue 209 GLU Chi-restraints excluded: chain 3R residue 223 VAL Chi-restraints excluded: chain 3R residue 225 ILE Chi-restraints excluded: chain 3S residue 16 ILE Chi-restraints excluded: chain 3S residue 47 ILE Chi-restraints excluded: chain 3S residue 58 ARG Chi-restraints excluded: chain 3T residue 17 SER Chi-restraints excluded: chain 3T residue 44 CYS Chi-restraints excluded: chain 3U residue 37 LEU Chi-restraints excluded: chain 3U residue 39 LEU Chi-restraints excluded: chain 3U residue 42 GLN Chi-restraints excluded: chain 3U residue 62 LEU Chi-restraints excluded: chain 3V residue 50 LEU Chi-restraints excluded: chain 3V residue 72 VAL Chi-restraints excluded: chain 3W residue 4 THR Chi-restraints excluded: chain 3W residue 18 SER Chi-restraints excluded: chain 3W residue 29 LEU Chi-restraints excluded: chain 3W residue 58 LYS Chi-restraints excluded: chain 3X residue 1 MET Chi-restraints excluded: chain 3X residue 13 LEU Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 18 ILE Chi-restraints excluded: chain 3Y residue 41 ILE Chi-restraints excluded: chain 3Y residue 52 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 41 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 263 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 298 optimal weight: 0.0470 chunk 130 optimal weight: 0.5980 chunk 253 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 319 optimal weight: 5.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 400 GLN 3D 94 HIS 3D 123 GLN ** 3E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3H 48 GLN 3N 9 GLN ** 3O 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3Q 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.089717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.075188 restraints weight = 83892.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.078042 restraints weight = 31258.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.078415 restraints weight = 16553.429| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.344 34354 Z= 0.126 Angle : 0.649 20.035 46524 Z= 0.307 Chirality : 0.041 0.244 5004 Planarity : 0.004 0.088 5834 Dihedral : 11.949 135.948 5322 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.83 % Favored : 94.95 % Rotamer: Outliers : 3.08 % Allowed : 28.71 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.14), residues: 4064 helix: 1.85 (0.12), residues: 2061 sheet: -1.04 (0.27), residues: 345 loop : -0.38 (0.17), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP3R 169 HIS 0.009 0.001 HIS3D 94 PHE 0.015 0.001 PHE3R 175 TYR 0.022 0.001 TYR3S 20 ARG 0.012 0.000 ARG3U 36 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 1768) hydrogen bonds : angle 4.50529 ( 5083) metal coordination : bond 0.05775 ( 8) metal coordination : angle 13.80556 ( 6) SS BOND : bond 0.00315 ( 6) SS BOND : angle 1.12909 ( 12) covalent geometry : bond 0.00294 (34335) covalent geometry : angle 0.62948 (46506) Misc. bond : bond 0.28131 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13238.48 seconds wall clock time: 234 minutes 39.28 seconds (14079.28 seconds total)