Starting phenix.real_space_refine on Fri May 30 11:36:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ugd_42221/05_2025/8ugd_42221.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ugd_42221/05_2025/8ugd_42221.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/8ugd_42221/05_2025/8ugd_42221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ugd_42221/05_2025/8ugd_42221.map" model { file = "/net/cci-nas-00/data/ceres_data/8ugd_42221/05_2025/8ugd_42221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ugd_42221/05_2025/8ugd_42221.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= 0.003 sd= 0.018 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 21562 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 20 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 33543 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 breaks: 1 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: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 229 Unusual residues: {'3PE': 1, 'CDL': 1, 'HEM': 2, 'U10': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 120 Planarities with less than four sites: {'U10:plan-8': 2, 'U10:plan-9': 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: 56 Chain: "3D" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'3PE': 1, 'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 63 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'3PE': 1, 'FES': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 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 72.137 42.051 22.294 1.00156.11 S ATOM 12690 SG CYS3E 236 74.750 40.389 20.099 1.00166.81 S ATOM 28378 SG CYS3R 217 86.275 100.377 41.409 1.00163.27 S ATOM 28514 SG CYS3R 236 82.581 100.360 40.375 1.00159.44 S ATOM 28527 SG CYS3R 238 81.776 100.033 42.107 1.00167.73 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN3N 207 " occ=0.47 ... (16 atoms not shown) pdb=" NE2BGLN3N 207 " occ=0.53 Time building chain proxies: 20.60, per 1000 atoms: 0.61 Number of scatterers: 33543 At special positions: 0 Unit cell: (150.29, 136.99, 171.57, 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 21562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS3E 222 " - pdb=" SG CYS3E 238 " distance=2.04 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 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.52 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES3E 301 " pdb="FE2 FES3E 301 " - pdb=" ND1 HIS3E 239 " pdb="FE1 FES3E 301 " - pdb=" SG CYS3E 236 " pdb="FE1 FES3E 301 " - pdb=" SG CYS3E 217 " pdb="FE2 FES3E 301 " - pdb=" ND1 HIS3E 219 " pdb=" FES3R 301 " pdb="FE2 FES3R 301 " - pdb=" ND1 HIS3R 239 " pdb="FE2 FES3R 301 " - pdb=" ND1 HIS3R 219 " pdb="FE1 FES3R 301 " - pdb=" SG CYS3R 236 " pdb="FE1 FES3R 301 " - pdb=" SG CYS3R 217 " pdb="FE1 FES3R 301 " - pdb=" SG CYS3R 238 " Number of angles added : 9 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 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: 174 helices and 17 sheets defined 56.8% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain '3A' and resid 4 through 11 Processing helix chain '3A' and resid 44 through 48 Processing helix chain '3A' and resid 54 through 65 removed outlier: 4.366A pdb=" N PHE3A 64 " --> pdb=" O GLU3A 60 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS3A 65 " --> pdb=" O HIS3A 61 " (cutoff:3.500A) Processing helix chain '3A' and resid 72 through 82 removed outlier: 4.133A pdb=" N GLU3A 76 " --> pdb=" O GLY3A 72 " (cutoff:3.500A) Processing helix chain '3A' and resid 105 through 118 removed outlier: 3.707A pdb=" N GLU3A 111 " --> pdb=" O PRO3A 107 " (cutoff:3.500A) Processing helix chain '3A' and resid 123 through 143 removed outlier: 3.940A pdb=" N ASP3A 132 " --> pdb=" O GLU3A 128 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL3A 133 " --> pdb=" O LYS3A 129 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER3A 143 " --> pdb=" O GLN3A 139 " (cutoff:3.500A) Processing helix chain '3A' and resid 144 through 158 removed outlier: 3.628A pdb=" N VAL3A 149 " --> pdb=" O MET3A 145 " (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 217 through 219 No H-bonds generated for 'chain '3A' and resid 217 through 219' 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 351 through 369 Processing helix chain '3A' and resid 371 through 385 Processing helix chain '3A' and resid 391 through 402 removed outlier: 3.644A pdb=" N VAL3A 402 " --> pdb=" O ARG3A 398 " (cutoff:3.500A) Processing helix chain '3A' and resid 403 through 415 Processing helix chain '3A' and resid 433 through 441 Processing helix chain '3B' and resid 54 through 58 removed outlier: 3.926A pdb=" N TYR3B 57 " --> pdb=" O GLY3B 54 " (cutoff:3.500A) Processing helix chain '3B' and resid 64 through 72 Processing helix chain '3B' and resid 81 through 93 removed outlier: 3.626A pdb=" N VAL3B 92 " --> pdb=" O GLY3B 88 " (cutoff:3.500A) Processing helix chain '3B' and resid 115 through 129 removed outlier: 3.710A pdb=" N LEU3B 119 " --> pdb=" O ASP3B 115 " (cutoff:3.500A) Processing helix chain '3B' and resid 133 through 141 Processing helix chain '3B' and resid 141 through 153 removed outlier: 4.387A pdb=" N ARG3B 145 " --> pdb=" O GLN3B 141 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE3B 146 " --> pdb=" O SER3B 142 " (cutoff:3.500A) Processing helix chain '3B' and resid 154 through 168 removed outlier: 3.973A pdb=" N GLN3B 158 " --> pdb=" O ASN3B 154 " (cutoff:3.500A) Processing helix chain '3B' and resid 187 through 199 Processing helix chain '3B' and resid 212 through 223 removed outlier: 3.753A pdb=" N PHE3B 223 " --> pdb=" O VAL3B 219 " (cutoff:3.500A) 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 350 removed outlier: 3.549A pdb=" N ALA3B 340 " --> pdb=" O VAL3B 336 " (cutoff:3.500A) Processing helix chain '3B' and resid 353 through 373 Processing helix chain '3B' and resid 374 through 389 Processing helix chain '3B' and resid 394 through 404 Processing helix chain '3B' and resid 406 through 411 Processing helix chain '3B' and resid 413 through 419 Processing helix chain '3C' and resid 3 through 8 Processing helix chain '3C' and resid 8 through 19 Processing helix chain '3C' and resid 28 through 30 No H-bonds generated for 'chain '3C' and resid 28 through 30' Processing helix chain '3C' and resid 31 through 53 removed outlier: 4.214A pdb=" N SER3C 35 " --> pdb=" O TRP3C 31 " (cutoff:3.500A) Processing helix chain '3C' and resid 62 through 72 Processing helix chain '3C' and resid 75 through 104 removed outlier: 4.070A pdb=" N ILE3C 79 " --> pdb=" O TYR3C 75 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER3C 88 " --> pdb=" O ALA3C 84 " (cutoff:3.500A) Processing helix chain '3C' and resid 105 through 108 Processing helix chain '3C' and resid 109 through 133 removed outlier: 3.759A pdb=" N LEU3C 133 " --> pdb=" O MET3C 129 " (cutoff:3.500A) Processing helix chain '3C' and resid 136 through 150 removed outlier: 3.746A pdb=" N LEU3C 150 " --> pdb=" O ILE3C 146 " (cutoff:3.500A) Processing helix chain '3C' and resid 151 through 153 No H-bonds generated for 'chain '3C' and resid 151 through 153' Processing helix chain '3C' and resid 156 through 166 Processing helix chain '3C' and resid 171 through 202 Proline residue: 3C 186 - end of helix removed outlier: 3.603A pdb=" N GLU3C 202 " --> pdb=" O LEU3C 198 " (cutoff:3.500A) Processing helix chain '3C' and resid 220 through 246 removed outlier: 5.093A pdb=" N ILE3C 226 " --> pdb=" O PRO3C 222 " (cutoff:3.500A) Processing helix chain '3C' and resid 252 through 256 Processing helix chain '3C' and resid 271 through 273 No H-bonds generated for 'chain '3C' and resid 271 through 273' Processing helix chain '3C' and resid 274 through 284 removed outlier: 3.694A pdb=" N ILE3C 280 " --> pdb=" O PHE3C 276 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE3C 284 " --> pdb=" O ILE3C 280 " (cutoff:3.500A) Processing helix chain '3C' and resid 286 through 300 removed outlier: 3.979A pdb=" N ILE3C 298 " --> pdb=" O LEU3C 294 " (cutoff:3.500A) Processing helix chain '3C' and resid 303 through 308 Processing helix chain '3C' and resid 318 through 341 removed outlier: 3.785A pdb=" N GLY3C 340 " --> pdb=" O THR3C 336 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN3C 341 " --> pdb=" O TRP3C 337 " (cutoff:3.500A) Processing helix chain '3C' and resid 346 through 364 Processing helix chain '3C' and resid 364 through 377 removed outlier: 3.624A pdb=" N LEU3C 377 " --> pdb=" O GLU3C 373 " (cutoff:3.500A) Processing helix chain '3D' and resid 110 through 124 removed outlier: 3.715A pdb=" N GLN3D 119 " --> pdb=" O ARG3D 115 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL3D 120 " --> pdb=" O ARG3D 116 " (cutoff:3.500A) Processing helix chain '3D' and resid 135 through 140 removed outlier: 3.890A pdb=" N LEU3D 139 " --> pdb=" O ALA3D 135 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL3D 140 " --> pdb=" O TYR3D 136 " (cutoff:3.500A) No H-bonds generated for 'chain '3D' and resid 135 through 140' Processing helix chain '3D' and resid 145 through 156 removed outlier: 3.848A 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 203 through 208 Processing helix chain '3D' and resid 211 through 221 Processing helix chain '3D' and resid 267 through 284 Processing helix chain '3D' and resid 286 through 317 Proline residue: 3D 306 - end of helix Processing helix chain '3D' and resid 318 through 322 removed outlier: 3.901A pdb=" N SER3D 321 " --> pdb=" O VAL3D 318 " (cutoff:3.500A) Processing helix chain '3E' and resid 79 through 83 Processing helix chain '3E' and resid 103 through 141 removed outlier: 4.180A pdb=" N ASP3E 108 " --> pdb=" O LYS3E 104 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA3E 109 " --> pdb=" O GLU3E 105 " (cutoff:3.500A) Processing helix chain '3E' and resid 145 through 150 removed outlier: 4.306A pdb=" N SER3E 150 " --> pdb=" O VAL3E 146 " (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: 4.309A pdb=" N GLY3F 37 " --> pdb=" O TYR3F 33 " (cutoff:3.500A) Processing helix chain '3F' and resid 44 through 49 Processing helix chain '3F' and resid 52 through 61 Processing helix chain '3F' and resid 63 through 84 Processing helix chain '3F' and resid 88 through 92 removed outlier: 3.814A pdb=" N TRP3F 92 " --> pdb=" O LYS3F 89 " (cutoff:3.500A) Processing helix chain '3F' and resid 102 through 121 removed outlier: 3.688A pdb=" N GLU3F 108 " --> pdb=" O PRO3F 104 " (cutoff:3.500A) Processing helix chain '3G' and resid 34 through 72 removed outlier: 4.644A pdb=" N LEU3G 48 " --> pdb=" O ARG3G 44 " (cutoff:3.500A) removed outlier: 5.371A 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: 3.510A pdb=" N THR3H 44 " --> pdb=" O ASP3H 40 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN3H 51 " --> pdb=" O GLU3H 47 " (cutoff:3.500A) Processing helix chain '3H' and resid 52 through 73 Processing helix chain '3H' and resid 79 through 97 Processing helix chain '3H' and resid 98 through 102 Processing helix chain '3J' and resid 6 through 15 Processing helix chain '3J' and resid 17 through 48 removed outlier: 4.025A pdb=" N ARG3J 34 " --> pdb=" O LEU3J 30 " (cutoff:3.500A) Processing helix chain '3N' and resid 44 through 48 Processing helix chain '3N' and resid 54 through 64 removed outlier: 4.596A pdb=" N PHE3N 64 " --> pdb=" O GLU3N 60 " (cutoff:3.500A) Processing helix chain '3N' and resid 72 through 82 removed outlier: 4.090A pdb=" N GLU3N 76 " --> pdb=" O GLY3N 72 " (cutoff:3.500A) removed outlier: 3.560A 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: 3.761A pdb=" N ASP3N 132 " --> pdb=" O GLU3N 128 " (cutoff:3.500A) Processing helix chain '3N' and resid 135 through 144 removed outlier: 3.775A pdb=" N SER3N 143 " --> pdb=" O GLN3N 139 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER3N 144 " --> pdb=" O GLU3N 140 " (cutoff:3.500A) 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 removed outlier: 3.504A pdb=" N VAL3N 272 " --> pdb=" O VAL3N 268 " (cutoff:3.500A) Processing helix chain '3N' and resid 286 through 290 Processing helix chain '3N' and resid 292 through 302 Processing helix chain '3N' and resid 330 through 348 removed outlier: 3.926A 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: 3.717A pdb=" N LEU3N 384 " --> pdb=" O GLY3N 380 " (cutoff:3.500A) Processing helix chain '3N' and resid 391 through 402 removed outlier: 3.537A pdb=" N VAL3N 402 " --> pdb=" O ARG3N 398 " (cutoff:3.500A) 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 92 removed outlier: 3.691A pdb=" N VAL3O 92 " --> pdb=" O GLY3O 88 " (cutoff:3.500A) Processing helix chain '3O' and resid 115 through 128 removed outlier: 3.852A pdb=" N LEU3O 119 " --> pdb=" O ASP3O 115 " (cutoff:3.500A) Processing helix chain '3O' and resid 133 through 153 removed outlier: 4.568A pdb=" N SER3O 142 " --> pdb=" O ALA3O 138 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLN3O 143 " --> pdb=" O ALA3O 139 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU3O 144 " --> pdb=" O LEU3O 140 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG3O 145 " --> pdb=" O GLN3O 141 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE3O 146 " --> pdb=" O SER3O 142 " (cutoff:3.500A) Processing helix chain '3O' and resid 155 through 168 Processing helix chain '3O' and resid 179 through 183 removed outlier: 3.572A pdb=" N ILE3O 183 " --> pdb=" O ASP3O 180 " (cutoff:3.500A) Processing helix chain '3O' and resid 187 through 199 removed outlier: 3.540A pdb=" N LEU3O 191 " --> pdb=" O THR3O 187 " (cutoff:3.500A) 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 Processing helix chain '3O' and resid 225 through 227 No H-bonds generated for 'chain '3O' and resid 225 through 227' Processing helix chain '3O' and resid 266 through 280 removed outlier: 3.527A pdb=" N HIS3O 277 " --> pdb=" O SER3O 273 " (cutoff:3.500A) 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: 3.506A pdb=" N VAL3O 372 " --> pdb=" O TYR3O 368 " (cutoff:3.500A) Processing helix chain '3O' and resid 374 through 388 Processing helix chain '3O' and resid 394 through 404 Processing helix chain '3O' and resid 406 through 411 removed outlier: 3.606A pdb=" N VAL3O 410 " --> pdb=" O ALA3O 406 " (cutoff:3.500A) 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 31 through 53 removed outlier: 4.212A pdb=" N SER3P 35 " --> pdb=" O TRP3P 31 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY3P 38 " --> pdb=" O GLY3P 34 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE3P 50 " --> pdb=" O LEU3P 46 " (cutoff:3.500A) Processing helix chain '3P' and resid 61 through 72 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 109 removed outlier: 3.837A pdb=" N MET3P 108 " --> pdb=" O GLY3P 105 " (cutoff:3.500A) Processing helix chain '3P' and resid 110 through 133 removed outlier: 3.706A pdb=" N VAL3P 132 " --> pdb=" O PHE3P 128 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU3P 133 " --> pdb=" O MET3P 129 " (cutoff:3.500A) Processing helix chain '3P' and resid 136 through 150 removed outlier: 4.010A pdb=" N LEU3P 150 " --> pdb=" O ILE3P 146 " (cutoff:3.500A) Processing helix chain '3P' and resid 151 through 153 No H-bonds generated for 'chain '3P' and resid 151 through 153' Processing helix chain '3P' and resid 157 through 166 Processing helix chain '3P' and resid 171 through 202 Proline residue: 3P 186 - end of helix removed outlier: 3.741A pdb=" N GLU3P 202 " --> pdb=" O LEU3P 198 " (cutoff:3.500A) Processing helix chain '3P' and resid 220 through 246 removed outlier: 3.754A pdb=" N THR3P 225 " --> pdb=" O HIS3P 221 " (cutoff:3.500A) removed outlier: 4.885A 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: 3.512A pdb=" N ILE3P 280 " --> pdb=" O PHE3P 276 " (cutoff:3.500A) Processing helix chain '3P' and resid 286 through 308 removed outlier: 3.975A pdb=" N ILE3P 298 " --> pdb=" O LEU3P 294 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU3P 301 " --> pdb=" O SER3P 297 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE3P 302 " --> pdb=" O ILE3P 298 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU3P 303 " --> pdb=" O LEU3P 299 " (cutoff:3.500A) removed outlier: 3.653A 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: 4.082A pdb=" N ILE3P 349 " --> pdb=" O HIS3P 345 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE3P 350 " --> pdb=" O PRO3P 346 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE3P 362 " --> pdb=" O TYR3P 358 " (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 Processing helix chain '3Q' and resid 57 through 68 removed outlier: 3.936A pdb=" N VAL3Q 68 " --> pdb=" O LEU3Q 64 " (cutoff:3.500A) Processing helix chain '3Q' and resid 97 through 105 removed outlier: 3.678A pdb=" N ARG3Q 102 " --> pdb=" O PRO3Q 98 " (cutoff:3.500A) Processing helix chain '3Q' and resid 115 through 120 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: 4.490A pdb=" N VAL3Q 229 " --> pdb=" O HIS3Q 225 " (cutoff:3.500A) removed outlier: 5.072A 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 103 through 140 removed outlier: 4.295A pdb=" N ASP3R 108 " --> pdb=" O LYS3R 104 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ALA3R 109 " --> pdb=" O GLU3R 105 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN3R 135 " --> pdb=" O ASN3R 131 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE3R 136 " --> pdb=" O ALA3R 132 " (cutoff:3.500A) Processing helix chain '3R' and resid 186 through 190 Processing helix chain '3R' and resid 200 through 205 removed outlier: 3.621A pdb=" N VAL3R 205 " --> pdb=" O ASP3R 201 " (cutoff:3.500A) Processing helix chain '3S' and resid 13 through 25 removed outlier: 3.765A pdb=" N GLY3S 25 " --> pdb=" O TYR3S 21 " (cutoff:3.500A) Processing helix chain '3S' and resid 32 through 36 Processing helix chain '3S' and resid 40 through 49 removed outlier: 3.899A pdb=" N GLU3S 45 " --> pdb=" O ASP3S 41 " (cutoff:3.500A) Processing helix chain '3S' and resid 51 through 71 Processing helix chain '3S' and resid 90 through 109 Processing helix chain '3T' and resid 32 through 71 removed outlier: 4.493A pdb=" N LEU3T 46 " --> pdb=" O ARG3T 42 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ARG3T 47 " --> pdb=" O ALA3T 43 " (cutoff:3.500A) Proline residue: 3T 50 - end of helix removed outlier: 3.874A pdb=" N GLU3T 67 " --> pdb=" O THR3T 63 " (cutoff:3.500A) Processing helix chain '3U' and resid 15 through 25 Processing helix chain '3U' and resid 27 through 47 removed outlier: 4.000A pdb=" N ARG3U 43 " --> pdb=" O LEU3U 39 " (cutoff:3.500A) Processing helix chain '3U' and resid 54 through 72 removed outlier: 3.820A pdb=" N CYS3U 68 " --> pdb=" O ALA3U 64 " (cutoff:3.500A) 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 removed outlier: 3.885A pdb=" N ARG3W 33 " --> pdb=" O LEU3W 29 " (cutoff:3.500A) Processing helix chain '3W' and resid 51 through 55 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 48 through 52 Processing helix chain '3Y' and resid 7 through 36 removed outlier: 3.564A pdb=" N ARG3Y 11 " --> pdb=" O GLY3Y 7 " (cutoff:3.500A) removed outlier: 3.901A 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 46 through 52 removed outlier: 3.697A pdb=" N GLY3Y 50 " --> pdb=" O TYR3Y 47 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '3A' and resid 14 through 16 removed outlier: 3.512A pdb=" N GLY3A 201 " --> pdb=" O GLU3A 28 " (cutoff:3.500A) removed outlier: 3.581A 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: 6.511A pdb=" N VAL3A 325 " --> pdb=" O GLN3A 305 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE3A 307 " --> pdb=" O HIS3A 323 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N HIS3A 323 " --> pdb=" O PHE3A 307 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR3A 309 " --> pdb=" O GLY3A 321 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY3A 321 " --> pdb=" O THR3A 309 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER3A 239 " --> pdb=" O VAL3A 422 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N GLY3A 424 " --> pdb=" O SER3A 239 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE3A 241 " --> pdb=" O GLY3A 424 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N GLY3A 426 " --> pdb=" O ILE3A 241 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N HIS3A 243 " --> pdb=" O GLY3A 426 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU3A 240 " --> pdb=" O SER3G 19 " (cutoff:3.500A) removed outlier: 3.627A 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: 6.445A pdb=" N VAL3B 34 " --> pdb=" O LEU3B 206 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY3B 208 " --> pdb=" O VAL3B 34 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA3B 36 " --> pdb=" O GLY3B 208 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU3B 96 " --> pdb=" O LEU3I 70 " (cutoff:3.500A) removed outlier: 5.545A 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 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 162 removed outlier: 3.554A pdb=" N ARG3D 171 " --> pdb=" O VAL3D 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP3D 160 " --> pdb=" O PHE3D 169 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE3D 169 " --> pdb=" O ASP3D 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '3E' and resid 153 through 154 Processing sheet with id=AA8, first strand: chain '3E' and resid 165 through 169 removed outlier: 3.806A pdb=" N PHE3E 167 " --> pdb=" O LEU3E 174 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3N' and resid 34 through 35 Processing sheet with id=AB1, first strand: chain '3N' and resid 40 through 41 Processing sheet with id=AB2, first strand: chain '3N' and resid 280 through 281 removed outlier: 6.698A pdb=" N VAL3N 325 " --> pdb=" O GLN3N 305 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE3N 307 " --> pdb=" O HIS3N 323 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N HIS3N 323 " --> pdb=" O PHE3N 307 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR3N 309 " --> pdb=" O GLY3N 321 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLY3N 321 " --> pdb=" O THR3N 309 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY3N 318 " --> pdb=" O GLY3N 259 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS3N 326 " --> pdb=" O ALA3N 251 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N GLY3N 424 " --> pdb=" O SER3N 239 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE3N 241 " --> pdb=" O GLY3N 424 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL3T 13 " --> pdb=" O ARG3N 244 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3O' and resid 26 through 28 removed outlier: 3.631A pdb=" N VAL3O 34 " --> pdb=" O MET3O 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3O' and resid 307 through 315 removed outlier: 4.144A pdb=" N GLY3O 320 " --> pdb=" O SER3O 261 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3P' and resid 22 through 23 Processing sheet with id=AB6, first strand: chain '3Q' and resid 69 through 74 removed outlier: 4.923A pdb=" N PHE3Q 81 " --> pdb=" O ASP3Q 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '3R' and resid 166 through 169 Processing sheet with id=AB8, first strand: chain '3R' and resid 225 through 226 1738 hydrogen bonds defined for protein. 4984 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: 10.34 Time building geometry restraints manager: 9.87 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: 14056 1.41 - 1.62: 19987 1.62 - 1.82: 266 1.82 - 2.03: 10 2.03 - 2.24: 24 Bond restraints: 34343 Sorted by residual: bond pdb=" C PHE3I 49 " pdb=" N LEU3I 50 " ideal model delta sigma weight residual 1.332 1.966 -0.634 1.40e-02 5.10e+03 2.05e+03 bond pdb=" C SER3I 48 " pdb=" N PHE3I 49 " ideal model delta sigma weight residual 1.331 1.592 -0.261 1.30e-02 5.92e+03 4.03e+02 bond pdb=" C8 U103C 504 " pdb=" C9 U103C 504 " ideal model delta sigma weight residual 1.470 1.321 0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" C8 U103C 503 " pdb=" C9 U103C 503 " ideal model delta sigma weight residual 1.470 1.322 0.148 2.00e-02 2.50e+03 5.47e+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 5.33e+01 ... (remaining 34338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.50: 46443 7.50 - 15.00: 58 15.00 - 22.50: 8 22.50 - 29.99: 3 29.99 - 37.49: 1 Bond angle restraints: 46513 Sorted by residual: angle pdb=" CA PHE3I 49 " pdb=" C PHE3I 49 " pdb=" N LEU3I 50 " ideal model delta sigma weight residual 115.36 77.87 37.49 1.53e+00 4.27e-01 6.00e+02 angle pdb=" O SER3I 48 " pdb=" C SER3I 48 " pdb=" N PHE3I 49 " ideal model delta sigma weight residual 122.86 146.63 -23.77 1.18e+00 7.18e-01 4.06e+02 angle pdb=" CA SER3I 48 " pdb=" C SER3I 48 " pdb=" N PHE3I 49 " ideal model delta sigma weight residual 115.51 91.10 24.41 1.27e+00 6.20e-01 3.70e+02 angle pdb=" C PHE3I 49 " pdb=" N LEU3I 50 " pdb=" CA LEU3I 50 " ideal model delta sigma weight residual 121.54 95.20 26.34 1.91e+00 2.74e-01 1.90e+02 angle pdb=" C SER3I 48 " pdb=" N PHE3I 49 " pdb=" CA PHE3I 49 " ideal model delta sigma weight residual 122.21 101.02 21.19 1.62e+00 3.81e-01 1.71e+02 ... (remaining 46508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 19566 35.92 - 71.83: 934 71.83 - 107.75: 87 107.75 - 143.66: 7 143.66 - 179.58: 4 Dihedral angle restraints: 20598 sinusoidal: 8654 harmonic: 11944 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 93.00 177.32 -84.32 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" C12 U103P 504 " pdb=" C13 U103P 504 " pdb=" C14 U103P 504 " pdb=" C16 U103P 504 " ideal model delta sinusoidal sigma weight residual 178.80 -1.63 -179.58 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C12 U103P 503 " pdb=" C13 U103P 503 " pdb=" C14 U103P 503 " pdb=" C16 U103P 503 " ideal model delta sinusoidal sigma weight residual 178.80 1.05 177.75 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 20595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4421 0.066 - 0.132: 546 0.132 - 0.198: 30 0.198 - 0.264: 5 0.264 - 0.330: 2 Chirality restraints: 5004 Sorted by residual: chirality pdb=" CA4 CDL3P 506 " pdb=" CA3 CDL3P 506 " pdb=" CA6 CDL3P 506 " pdb=" OA6 CDL3P 506 " both_signs ideal model delta sigma weight residual False -2.57 -2.25 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB4 CDL3Q 502 " pdb=" CB3 CDL3Q 502 " pdb=" CB6 CDL3Q 502 " pdb=" OB6 CDL3Q 502 " both_signs ideal model delta sigma weight residual False -2.57 -2.28 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB4 CDL3P 507 " pdb=" CB3 CDL3P 507 " pdb=" CB6 CDL3P 507 " pdb=" OB6 CDL3P 507 " both_signs ideal model delta sigma weight residual False -2.57 -2.33 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 5001 not shown) Planarity restraints: 5834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE3I 49 " 0.062 2.00e-02 2.50e+03 1.69e-01 2.87e+02 pdb=" C PHE3I 49 " -0.287 2.00e-02 2.50e+03 pdb=" O PHE3I 49 " 0.154 2.00e-02 2.50e+03 pdb=" N LEU3I 50 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 U103C 504 " -0.006 2.00e-02 2.50e+03 7.78e-02 1.06e+02 pdb=" C1M U103C 504 " -0.042 2.00e-02 2.50e+03 pdb=" C2 U103C 504 " -0.038 2.00e-02 2.50e+03 pdb=" C3 U103C 504 " 0.123 2.00e-02 2.50e+03 pdb=" C4 U103C 504 " -0.125 2.00e-02 2.50e+03 pdb=" C5 U103C 504 " -0.004 2.00e-02 2.50e+03 pdb=" C6 U103C 504 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 U103P 503 " -0.004 2.00e-02 2.50e+03 5.61e-02 5.50e+01 pdb=" C1M U103P 503 " -0.018 2.00e-02 2.50e+03 pdb=" C2 U103P 503 " -0.044 2.00e-02 2.50e+03 pdb=" C3 U103P 503 " 0.098 2.00e-02 2.50e+03 pdb=" C4 U103P 503 " -0.087 2.00e-02 2.50e+03 pdb=" C5 U103P 503 " 0.004 2.00e-02 2.50e+03 pdb=" C6 U103P 503 " 0.051 2.00e-02 2.50e+03 ... (remaining 5831 not shown) Histogram of nonbonded interaction distances: 0.91 - 1.71: 1 1.71 - 2.50: 288 2.50 - 3.30: 41813 3.30 - 4.10: 87712 4.10 - 4.90: 161463 Warning: very small nonbonded interaction distances. Nonbonded interactions: 291277 Sorted by model distance: nonbonded pdb=" CD1 TRP3J 53 " pdb=" CE LYS3J 57 " model vdw 0.907 3.660 nonbonded pdb=" NE1 TRP3J 53 " pdb=" CE LYS3J 57 " model vdw 1.720 3.520 nonbonded pdb=" CG TRP3J 53 " pdb=" CE LYS3J 57 " model vdw 1.877 3.660 nonbonded pdb=" CD1 TRP3J 53 " pdb=" NZ LYS3J 57 " model vdw 1.889 3.340 nonbonded pdb=" OG1 THR3N 156 " pdb=" OG SER3N 239 " model vdw 2.153 3.040 ... (remaining 291272 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 and (name C1 or name C10 or name C11 or name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C1M or name C2 or name C3 or name C3M or n \ ame C4 or name C4M or name C5 or name C6 or name C7 or name C8 or name C9 or nam \ e O2 or name O3 or name O4 or name O5 )) or resid 504)) selection = (chain '3P' and (resid 1 through 379 or resid 501 through 504)) } 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' and (resid 79 through 274 or resid 301 through 302)) } 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.110 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 76.520 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.180 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 0.862 34365 Z= 0.646 Angle : 1.002 58.210 46532 Z= 0.471 Chirality : 0.043 0.330 5004 Planarity : 0.006 0.169 5834 Dihedral : 19.748 179.575 12895 Min Nonbonded Distance : 0.907 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.59 % Favored : 94.24 % Rotamer: Outliers : 0.92 % Allowed : 30.38 % Favored : 68.69 % 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: 0.28 (0.14), residues: 4062 helix: 1.46 (0.12), residues: 2006 sheet: -2.32 (0.25), residues: 347 loop : -0.76 (0.16), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP3D 100 HIS 0.010 0.001 HIS3D 289 PHE 0.027 0.002 PHE3A 446 TYR 0.039 0.001 TYR3F 32 ARG 0.011 0.001 ARG3U 34 Details of bonding type rmsd hydrogen bonds : bond 0.14805 ( 1738) hydrogen bonds : angle 6.25244 ( 4984) metal coordination : bond 0.11840 ( 9) metal coordination : angle 29.08967 ( 9) SS BOND : bond 0.00626 ( 5) SS BOND : angle 2.35329 ( 10) covalent geometry : bond 0.00863 (34343) covalent geometry : angle 0.91617 (46513) Misc. bond : bond 0.35598 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 573 time to evaluate : 3.672 Fit side-chains 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: "SER3N 17 " (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: "GLN3N 126 " (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: "THR3N 222 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN3O 125 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE3O 183 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: 3A 136 GLN cc_start: 0.8404 (mt0) cc_final: 0.8149 (mt0) REVERT: 3A 317 THR cc_start: 0.8576 (t) cc_final: 0.8331 (p) REVERT: 3A 332 ASP cc_start: 0.8449 (t0) cc_final: 0.8154 (t0) REVERT: 3A 399 ILE cc_start: 0.9462 (mt) cc_final: 0.9227 (mt) REVERT: 3C 373 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7559 (mm-30) REVERT: 3F 94 LYS cc_start: 0.8590 (mmtm) cc_final: 0.7774 (mmtm) REVERT: 3H 54 LYS cc_start: 0.8693 (tppp) cc_final: 0.8429 (ttpt) REVERT: 3H 100 ASN cc_start: 0.8386 (p0) cc_final: 0.8173 (m-40) REVERT: 3N 343 MET cc_start: 0.8557 (mmp) cc_final: 0.8266 (mmm) REVERT: 3O 144 LEU cc_start: 0.8638 (mt) cc_final: 0.8431 (mt) REVERT: 3O 160 LEU cc_start: 0.8825 (mt) cc_final: 0.8582 (mt) REVERT: 3P 4 ILE cc_start: 0.9433 (OUTLIER) cc_final: 0.9215 (mt) REVERT: 3P 68 HIS cc_start: 0.8835 (OUTLIER) cc_final: 0.8426 (t70) REVERT: 3P 236 MET cc_start: 0.8732 (tpp) cc_final: 0.8410 (tpp) REVERT: 3Q 211 MET cc_start: 0.8648 (tpp) cc_final: 0.8331 (tpt) REVERT: 3Q 222 MET cc_start: 0.7955 (mtp) cc_final: 0.7737 (ttm) REVERT: 3R 167 PHE cc_start: 0.7473 (m-80) cc_final: 0.7194 (m-10) REVERT: 3R 259 GLU cc_start: 0.5409 (tm-30) cc_final: 0.5120 (pp20) REVERT: 3S 21 TYR cc_start: 0.8483 (t80) cc_final: 0.8103 (t80) REVERT: 3S 59 VAL cc_start: 0.9223 (p) cc_final: 0.9010 (m) REVERT: 3U 29 LYS cc_start: 0.9097 (mtpp) cc_final: 0.8815 (ttmt) REVERT: 3U 37 LEU cc_start: 0.8762 (tp) cc_final: 0.8414 (tp) REVERT: 3U 41 ASP cc_start: 0.8702 (m-30) cc_final: 0.8298 (m-30) REVERT: 3X 23 MET cc_start: 0.9156 (tmm) cc_final: 0.8675 (tmm) REVERT: 3Y 39 ARG cc_start: 0.8236 (mpp-170) cc_final: 0.7736 (tpp80) outliers start: 30 outliers final: 18 residues processed: 594 average time/residue: 0.4614 time to fit residues: 449.8850 Evaluate side-chains 433 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 413 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3B residue 223 PHE Chi-restraints excluded: chain 3D residue 276 CYS Chi-restraints excluded: chain 3J residue 13 LEU Chi-restraints excluded: chain 3N residue 8 LEU Chi-restraints excluded: chain 3N residue 17 SER 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 126 GLN 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 195 MET Chi-restraints excluded: chain 3N residue 222 THR Chi-restraints excluded: chain 3O residue 183 ILE Chi-restraints excluded: chain 3P residue 4 ILE Chi-restraints excluded: chain 3P residue 68 HIS Chi-restraints excluded: chain 3T residue 67 GLU Chi-restraints excluded: chain 3V residue 72 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 3.9990 chunk 302 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 312 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 362 optimal weight: 0.0570 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3A 308 GLN 3A 311 ASN 3B 290 ASN ** 3C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3C 85 ASN 3C 312 GLN ** 3D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3E 227 ASN ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3I 58 GLN ** 3J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 9 GLN ** 3N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 311 ASN ** 3N 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 363 ASN 3O 198 HIS 3O 248 ASN 3P 85 ASN ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3Q 35 GLN 3Q 150 ASN 3Q 198 HIS ** 3R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3U 23 GLN 3U 26 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.079368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.065275 restraints weight = 127509.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.067896 restraints weight = 50094.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.069563 restraints weight = 27291.141| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.318 34365 Z= 0.144 Angle : 0.738 43.363 46532 Z= 0.320 Chirality : 0.041 0.183 5004 Planarity : 0.004 0.059 5834 Dihedral : 14.518 177.547 5360 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 3.49 % Allowed : 26.92 % Favored : 69.59 % 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: 0.68 (0.14), residues: 4062 helix: 1.77 (0.11), residues: 2044 sheet: -1.93 (0.27), residues: 315 loop : -0.68 (0.16), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP3N 443 HIS 0.010 0.001 HIS3D 289 PHE 0.034 0.001 PHE3F 72 TYR 0.034 0.001 TYR3F 32 ARG 0.005 0.000 ARG3T 11 Details of bonding type rmsd hydrogen bonds : bond 0.04460 ( 1738) hydrogen bonds : angle 4.99143 ( 4984) metal coordination : bond 0.04272 ( 9) metal coordination : angle 24.44482 ( 9) SS BOND : bond 0.00379 ( 5) SS BOND : angle 0.99233 ( 10) covalent geometry : bond 0.00317 (34343) covalent geometry : angle 0.65522 (46513) Misc. bond : bond 0.15825 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 497 time to evaluate : 3.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR3N 3 " (corrupted residue). Skipping it. 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: "LEU3N 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN3N 126 " (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: "THR3N 222 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER3O 55 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 8 LEU cc_start: 0.8911 (mt) cc_final: 0.8627 (mp) REVERT: 3A 60 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8359 (tm-30) REVERT: 3A 270 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9097 (tp) REVERT: 3B 95 LYS cc_start: 0.8153 (tppp) cc_final: 0.7857 (mmmm) REVERT: 3B 133 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.8026 (mtm180) REVERT: 3E 150 SER cc_start: 0.6970 (OUTLIER) cc_final: 0.6685 (t) REVERT: 3F 82 MET cc_start: 0.9322 (ttp) cc_final: 0.8858 (ttp) REVERT: 3G 67 GLU cc_start: 0.7889 (tp30) cc_final: 0.7650 (tp30) REVERT: 3I 67 SER cc_start: 0.8791 (m) cc_final: 0.8432 (t) REVERT: 3J 48 ASN cc_start: 0.8731 (p0) cc_final: 0.8466 (p0) REVERT: 3O 226 MET cc_start: 0.7116 (pp-130) cc_final: 0.6254 (pp-130) REVERT: 3O 248 ASN cc_start: 0.7876 (t0) cc_final: 0.7644 (t0) REVERT: 3O 370 MET cc_start: 0.8471 (ttm) cc_final: 0.8170 (mtm) REVERT: 3Q 80 MET cc_start: 0.7209 (mmp) cc_final: 0.6972 (mmp) REVERT: 3Q 211 MET cc_start: 0.9019 (tpp) cc_final: 0.8634 (tpt) REVERT: 3R 167 PHE cc_start: 0.7672 (m-80) cc_final: 0.7470 (m-10) REVERT: 3S 44 LYS cc_start: 0.8687 (mtmm) cc_final: 0.8291 (mtmm) REVERT: 3T 68 LYS cc_start: 0.8242 (mtmm) cc_final: 0.8015 (mtmm) REVERT: 3U 29 LYS cc_start: 0.9110 (mtpp) cc_final: 0.8685 (ttmt) REVERT: 3W 44 GLU cc_start: 0.8547 (mt-10) cc_final: 0.7815 (mp0) REVERT: 3X 12 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: 3Y 39 ARG cc_start: 0.8148 (mpp-170) cc_final: 0.7655 (tpp80) outliers start: 119 outliers final: 68 residues processed: 585 average time/residue: 0.4487 time to fit residues: 424.1460 Evaluate side-chains 495 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 422 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 60 GLU Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 149 VAL Chi-restraints excluded: chain 3A residue 217 SER Chi-restraints excluded: chain 3A residue 255 ILE Chi-restraints excluded: chain 3A residue 270 LEU Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 311 ASN Chi-restraints excluded: chain 3A residue 312 ILE Chi-restraints excluded: chain 3A residue 350 THR Chi-restraints excluded: chain 3B residue 29 LEU Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 123 LEU Chi-restraints excluded: chain 3B residue 133 ARG Chi-restraints excluded: chain 3B residue 369 LEU Chi-restraints excluded: chain 3B residue 411 ILE Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 40 CYS Chi-restraints excluded: chain 3C residue 43 LEU Chi-restraints excluded: chain 3C residue 45 ILE Chi-restraints excluded: chain 3C residue 234 PHE Chi-restraints excluded: chain 3C residue 345 HIS Chi-restraints excluded: chain 3D residue 109 LEU Chi-restraints excluded: chain 3D residue 276 CYS Chi-restraints excluded: chain 3D residue 298 LEU Chi-restraints excluded: chain 3E residue 150 SER Chi-restraints excluded: chain 3E residue 220 LEU Chi-restraints excluded: chain 3E residue 271 VAL Chi-restraints excluded: chain 3F residue 71 VAL Chi-restraints excluded: chain 3G residue 17 THR Chi-restraints excluded: chain 3G residue 48 LEU Chi-restraints excluded: chain 3G residue 56 VAL Chi-restraints excluded: chain 3H residue 52 ILE Chi-restraints excluded: chain 3I residue 50 LEU Chi-restraints excluded: chain 3J residue 6 LEU Chi-restraints excluded: chain 3J residue 23 LEU Chi-restraints excluded: chain 3N residue 3 THR Chi-restraints excluded: chain 3N residue 8 LEU Chi-restraints excluded: chain 3N residue 112 LEU Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 126 GLN Chi-restraints excluded: chain 3N residue 132 ASP Chi-restraints excluded: chain 3N residue 134 ILE Chi-restraints excluded: chain 3N residue 222 THR Chi-restraints excluded: chain 3N residue 320 LEU Chi-restraints excluded: chain 3N residue 428 ILE Chi-restraints excluded: chain 3O residue 55 SER Chi-restraints excluded: chain 3O residue 116 ILE Chi-restraints excluded: chain 3O residue 123 LEU Chi-restraints excluded: chain 3O residue 224 LEU Chi-restraints excluded: chain 3O residue 303 VAL Chi-restraints excluded: chain 3P residue 6 LYS Chi-restraints excluded: chain 3P residue 12 LYS Chi-restraints excluded: chain 3P residue 156 ILE Chi-restraints excluded: chain 3P residue 202 GLU Chi-restraints excluded: chain 3P residue 298 ILE Chi-restraints excluded: chain 3P residue 332 LEU Chi-restraints excluded: chain 3P residue 377 LEU Chi-restraints excluded: chain 3Q residue 35 GLN Chi-restraints excluded: chain 3Q residue 141 VAL Chi-restraints excluded: chain 3R residue 174 LEU Chi-restraints excluded: chain 3R residue 212 ILE Chi-restraints excluded: chain 3R residue 262 THR Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3S residue 18 LYS Chi-restraints excluded: chain 3S residue 42 ASP Chi-restraints excluded: chain 3T residue 38 LEU Chi-restraints excluded: chain 3T residue 44 CYS Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3V residue 65 VAL Chi-restraints excluded: chain 3X residue 1 MET Chi-restraints excluded: chain 3X residue 12 GLU Chi-restraints excluded: chain 3X residue 18 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 56 optimal weight: 2.9990 chunk 299 optimal weight: 10.0000 chunk 350 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 328 optimal weight: 7.9990 chunk 269 optimal weight: 0.7980 chunk 233 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 370 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3A 136 GLN 3C 32 ASN ** 3C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3E 194 GLN ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 9 GLN ** 3N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 363 ASN ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3Q 105 ASN ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3R 186 GLN ** 3R 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3U 23 GLN 3V 58 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.076859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.062524 restraints weight = 145253.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.065203 restraints weight = 55148.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.066931 restraints weight = 29369.001| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.432 34365 Z= 0.224 Angle : 0.771 44.261 46532 Z= 0.341 Chirality : 0.044 0.212 5004 Planarity : 0.005 0.050 5834 Dihedral : 13.787 179.237 5335 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.47 % Favored : 94.38 % Rotamer: Outliers : 4.47 % Allowed : 25.92 % 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: 0.63 (0.14), residues: 4062 helix: 1.70 (0.11), residues: 2039 sheet: -1.85 (0.27), residues: 321 loop : -0.67 (0.16), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP3R 169 HIS 0.006 0.001 HIS3P 201 PHE 0.048 0.002 PHE3F 72 TYR 0.026 0.002 TYR3F 32 ARG 0.007 0.001 ARG3W 8 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 1738) hydrogen bonds : angle 4.86483 ( 4984) metal coordination : bond 0.04323 ( 9) metal coordination : angle 23.68702 ( 9) SS BOND : bond 0.00310 ( 5) SS BOND : angle 1.12110 ( 10) covalent geometry : bond 0.00523 (34343) covalent geometry : angle 0.69732 (46513) Misc. bond : bond 0.24447 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 433 time to evaluate : 3.506 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR3N 3 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN3N 9 " (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: "GLN3N 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER3O 55 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: 3A 191 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8868 (mtmm) REVERT: 3A 270 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9116 (tp) REVERT: 3B 84 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8974 (ttpp) REVERT: 3B 95 LYS cc_start: 0.8301 (tppp) cc_final: 0.7995 (mmmm) REVERT: 3B 133 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8384 (mtm180) REVERT: 3B 213 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7618 (m-70) REVERT: 3D 128 CYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7711 (m) REVERT: 3E 150 SER cc_start: 0.6911 (OUTLIER) cc_final: 0.6526 (t) REVERT: 3F 79 ASP cc_start: 0.8585 (t0) cc_final: 0.8286 (t0) REVERT: 3F 82 MET cc_start: 0.9364 (ttp) cc_final: 0.8970 (ttp) REVERT: 3H 50 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6618 (tm-30) REVERT: 3H 53 GLU cc_start: 0.8319 (pm20) cc_final: 0.8098 (pm20) REVERT: 3H 54 LYS cc_start: 0.8799 (ttmm) cc_final: 0.8502 (ttpt) REVERT: 3H 82 GLU cc_start: 0.8502 (mp0) cc_final: 0.8258 (mp0) REVERT: 3I 50 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7716 (pp) REVERT: 3I 67 SER cc_start: 0.8832 (m) cc_final: 0.8454 (t) REVERT: 3J 48 ASN cc_start: 0.8616 (p0) cc_final: 0.8366 (p0) REVERT: 3O 225 ASN cc_start: 0.8525 (p0) cc_final: 0.8320 (p0) REVERT: 3O 226 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6055 (pp-130) REVERT: 3O 248 ASN cc_start: 0.8101 (t0) cc_final: 0.7758 (t0) REVERT: 3P 249 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9383 (tm) REVERT: 3P 313 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7718 (ttt-90) REVERT: 3P 333 ILE cc_start: 0.9633 (OUTLIER) cc_final: 0.9371 (mp) REVERT: 3Q 80 MET cc_start: 0.7201 (mmp) cc_final: 0.6884 (mmp) REVERT: 3Q 160 MET cc_start: 0.8682 (mtt) cc_final: 0.8240 (mtt) REVERT: 3R 143 SER cc_start: 0.8753 (OUTLIER) cc_final: 0.8492 (t) REVERT: 3R 151 LYS cc_start: 0.7968 (mppt) cc_final: 0.7446 (mmmt) REVERT: 3R 155 LYS cc_start: 0.6355 (OUTLIER) cc_final: 0.6068 (ttpt) REVERT: 3R 196 ARG cc_start: 0.6670 (tpt170) cc_final: 0.6395 (tpt170) REVERT: 3R 197 ASP cc_start: 0.3674 (m-30) cc_final: 0.3355 (t0) REVERT: 3S 21 TYR cc_start: 0.8907 (t80) cc_final: 0.8684 (t80) REVERT: 3S 44 LYS cc_start: 0.8854 (mtmm) cc_final: 0.8558 (mtmm) REVERT: 3S 82 LYS cc_start: 0.8888 (mptp) cc_final: 0.8584 (mtmm) REVERT: 3T 70 LYS cc_start: 0.8867 (tmtt) cc_final: 0.8606 (ttpt) REVERT: 3U 41 ASP cc_start: 0.8635 (m-30) cc_final: 0.8199 (m-30) REVERT: 3U 72 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8697 (mtmm) REVERT: 3V 58 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8716 (mm-40) REVERT: 3Y 39 ARG cc_start: 0.8574 (mpp-170) cc_final: 0.7859 (tpp80) outliers start: 153 outliers final: 86 residues processed: 549 average time/residue: 0.4425 time to fit residues: 389.4732 Evaluate side-chains 493 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 392 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 138 LEU Chi-restraints excluded: chain 3A residue 149 VAL Chi-restraints excluded: chain 3A residue 191 LYS Chi-restraints excluded: chain 3A residue 196 VAL Chi-restraints excluded: chain 3A residue 255 ILE Chi-restraints excluded: chain 3A residue 270 LEU Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 346 CYS Chi-restraints excluded: chain 3A residue 350 THR Chi-restraints excluded: chain 3B residue 84 LYS Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 123 LEU Chi-restraints excluded: chain 3B residue 133 ARG Chi-restraints excluded: chain 3B residue 213 HIS Chi-restraints excluded: chain 3B residue 223 PHE Chi-restraints excluded: chain 3B residue 285 VAL Chi-restraints excluded: chain 3B residue 303 VAL Chi-restraints excluded: chain 3B residue 309 VAL Chi-restraints excluded: chain 3B residue 372 VAL Chi-restraints excluded: chain 3B residue 436 VAL Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 40 CYS Chi-restraints excluded: chain 3C residue 43 LEU Chi-restraints excluded: chain 3C residue 78 VAL Chi-restraints excluded: chain 3C residue 110 LEU Chi-restraints excluded: chain 3C residue 149 LEU Chi-restraints excluded: chain 3C residue 164 ILE Chi-restraints excluded: chain 3C residue 184 ILE Chi-restraints excluded: chain 3C residue 234 PHE Chi-restraints excluded: chain 3C residue 345 HIS Chi-restraints excluded: chain 3C residue 377 LEU Chi-restraints excluded: chain 3D residue 128 CYS Chi-restraints excluded: chain 3D residue 276 CYS Chi-restraints excluded: chain 3D residue 298 LEU Chi-restraints excluded: chain 3D residue 324 LEU Chi-restraints excluded: chain 3E residue 83 ILE Chi-restraints excluded: chain 3E residue 99 SER Chi-restraints excluded: chain 3E residue 150 SER Chi-restraints excluded: chain 3E residue 205 VAL Chi-restraints excluded: chain 3E residue 216 VAL Chi-restraints excluded: chain 3E residue 220 LEU Chi-restraints excluded: chain 3E residue 271 VAL Chi-restraints excluded: chain 3F residue 71 VAL Chi-restraints excluded: chain 3G residue 15 VAL Chi-restraints excluded: chain 3G residue 17 THR Chi-restraints excluded: chain 3H residue 52 ILE Chi-restraints excluded: chain 3H residue 71 SER Chi-restraints excluded: chain 3I residue 50 LEU Chi-restraints excluded: chain 3J residue 6 LEU Chi-restraints excluded: chain 3J residue 24 THR Chi-restraints excluded: chain 3N residue 3 THR Chi-restraints excluded: chain 3N residue 112 LEU Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 126 GLN 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 55 SER Chi-restraints excluded: chain 3O residue 116 ILE Chi-restraints excluded: chain 3O residue 123 LEU Chi-restraints excluded: chain 3O residue 224 LEU Chi-restraints excluded: chain 3O residue 226 MET Chi-restraints excluded: chain 3O residue 309 VAL Chi-restraints excluded: chain 3P residue 6 LYS Chi-restraints excluded: chain 3P residue 112 THR Chi-restraints excluded: chain 3P residue 126 THR Chi-restraints excluded: chain 3P residue 156 ILE Chi-restraints excluded: chain 3P residue 170 VAL Chi-restraints excluded: chain 3P residue 202 GLU Chi-restraints excluded: chain 3P residue 209 THR Chi-restraints excluded: chain 3P residue 233 LEU Chi-restraints excluded: chain 3P residue 249 LEU Chi-restraints excluded: chain 3P residue 298 ILE Chi-restraints excluded: chain 3P residue 313 ARG Chi-restraints excluded: chain 3P residue 333 ILE Chi-restraints excluded: chain 3P residue 377 LEU Chi-restraints excluded: chain 3Q residue 13 SER Chi-restraints excluded: chain 3Q residue 55 CYS Chi-restraints excluded: chain 3Q residue 141 VAL Chi-restraints excluded: chain 3R residue 143 SER Chi-restraints excluded: chain 3R residue 155 LYS Chi-restraints excluded: chain 3R residue 174 LEU Chi-restraints excluded: chain 3R residue 212 ILE Chi-restraints excluded: chain 3R residue 262 THR Chi-restraints excluded: chain 3R residue 266 THR Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3S residue 18 LYS Chi-restraints excluded: chain 3S residue 42 ASP Chi-restraints excluded: chain 3T residue 38 LEU Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3U residue 72 LYS Chi-restraints excluded: chain 3V residue 65 VAL 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 37 ASP Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 13 LEU Chi-restraints excluded: chain 3Y residue 18 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 163 optimal weight: 8.9990 chunk 243 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 396 optimal weight: 8.9990 chunk 276 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 363 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3B 156 GLN 3B 351 ASN ** 3C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3C 114 ASN 3D 287 HIS 3E 194 GLN ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 9 GLN ** 3N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3N 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3Q 35 GLN ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3U 23 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.076704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.062821 restraints weight = 125881.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.065341 restraints weight = 50549.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.066951 restraints weight = 27813.931| |-----------------------------------------------------------------------------| 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) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.415 34365 Z= 0.213 Angle : 0.737 41.319 46532 Z= 0.322 Chirality : 0.043 0.188 5004 Planarity : 0.004 0.045 5834 Dihedral : 13.409 170.045 5328 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.22 % Favored : 94.63 % Rotamer: Outliers : 4.58 % Allowed : 26.15 % 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: 0.69 (0.14), residues: 4062 helix: 1.78 (0.11), residues: 2041 sheet: -1.97 (0.27), residues: 330 loop : -0.65 (0.16), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP3N 443 HIS 0.005 0.001 HIS3P 201 PHE 0.035 0.002 PHE3F 72 TYR 0.024 0.001 TYR3F 32 ARG 0.012 0.001 ARG3E 248 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 1738) hydrogen bonds : angle 4.75309 ( 4984) metal coordination : bond 0.03746 ( 9) metal coordination : angle 23.39637 ( 9) SS BOND : bond 0.00497 ( 5) SS BOND : angle 1.05097 ( 10) covalent geometry : bond 0.00504 (34343) covalent geometry : angle 0.66159 (46513) Misc. bond : bond 0.25282 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 425 time to evaluate : 3.693 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR3N 3 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN3N 9 " (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: "GLN3N 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER3O 55 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 270 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9173 (tp) REVERT: 3B 84 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8985 (ttpp) REVERT: 3B 95 LYS cc_start: 0.8229 (tppp) cc_final: 0.7975 (mmmm) REVERT: 3B 213 HIS cc_start: 0.8224 (OUTLIER) cc_final: 0.7384 (m-70) REVERT: 3B 223 PHE cc_start: 0.6369 (OUTLIER) cc_final: 0.6168 (t80) REVERT: 3B 250 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7075 (p0) REVERT: 3B 430 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9024 (mp) REVERT: 3C 263 ASN cc_start: 0.8897 (t0) cc_final: 0.8606 (t0) REVERT: 3C 327 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8134 (ttm) REVERT: 3D 128 CYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7395 (m) REVERT: 3E 150 SER cc_start: 0.6646 (OUTLIER) cc_final: 0.6384 (t) REVERT: 3E 251 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8557 (mmmt) REVERT: 3F 33 TYR cc_start: 0.8878 (t80) cc_final: 0.8555 (t80) REVERT: 3H 50 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6676 (tm-30) REVERT: 3H 53 GLU cc_start: 0.8178 (pm20) cc_final: 0.7965 (pm20) REVERT: 3H 54 LYS cc_start: 0.8867 (ttmm) cc_final: 0.8543 (ttpt) REVERT: 3H 82 GLU cc_start: 0.8506 (mp0) cc_final: 0.8265 (mp0) REVERT: 3H 100 ASN cc_start: 0.8534 (m110) cc_final: 0.7535 (p0) REVERT: 3I 50 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7917 (pp) REVERT: 3I 67 SER cc_start: 0.8891 (m) cc_final: 0.8481 (t) REVERT: 3O 136 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8721 (mt-10) REVERT: 3O 226 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.5979 (pp-130) REVERT: 3O 248 ASN cc_start: 0.8212 (t0) cc_final: 0.7950 (t0) REVERT: 3P 235 MET cc_start: 0.9192 (tmm) cc_final: 0.8923 (tmm) REVERT: 3P 249 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9315 (tm) REVERT: 3P 313 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8434 (ttt180) REVERT: 3P 333 ILE cc_start: 0.9634 (OUTLIER) cc_final: 0.9418 (mp) REVERT: 3Q 80 MET cc_start: 0.7259 (mmp) cc_final: 0.7040 (mmp) REVERT: 3Q 102 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8097 (mtp85) REVERT: 3Q 160 MET cc_start: 0.8687 (mtt) cc_final: 0.8481 (mtt) REVERT: 3Q 212 MET cc_start: 0.8528 (mmt) cc_final: 0.8261 (mmt) REVERT: 3R 140 MET cc_start: 0.8078 (mtp) cc_final: 0.7861 (mtp) REVERT: 3R 149 MET cc_start: 0.7142 (pmm) cc_final: 0.6916 (pmm) REVERT: 3R 151 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7369 (mmmt) REVERT: 3R 196 ARG cc_start: 0.6746 (tpt170) cc_final: 0.6447 (tpt170) REVERT: 3S 44 LYS cc_start: 0.8904 (mtmm) cc_final: 0.8584 (mtmm) REVERT: 3V 53 GLU cc_start: 0.8421 (mp0) cc_final: 0.7872 (mp0) REVERT: 3Y 39 ARG cc_start: 0.8400 (mpp-170) cc_final: 0.7630 (tpp80) outliers start: 157 outliers final: 93 residues processed: 549 average time/residue: 0.4571 time to fit residues: 405.4050 Evaluate side-chains 505 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 395 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 61 HIS Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 138 LEU Chi-restraints excluded: chain 3A residue 149 VAL Chi-restraints excluded: chain 3A residue 196 VAL Chi-restraints excluded: chain 3A residue 255 ILE Chi-restraints excluded: chain 3A residue 257 VAL Chi-restraints excluded: chain 3A residue 270 LEU Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 346 CYS Chi-restraints excluded: chain 3A residue 350 THR Chi-restraints excluded: chain 3B residue 29 LEU Chi-restraints excluded: chain 3B residue 84 LYS Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 123 LEU Chi-restraints excluded: chain 3B residue 213 HIS Chi-restraints excluded: chain 3B residue 221 GLU Chi-restraints excluded: chain 3B residue 223 PHE Chi-restraints excluded: chain 3B residue 250 ASP Chi-restraints excluded: chain 3B residue 284 HIS Chi-restraints excluded: chain 3B residue 285 VAL Chi-restraints excluded: chain 3B residue 303 VAL Chi-restraints excluded: chain 3B residue 309 VAL Chi-restraints excluded: chain 3B residue 370 MET Chi-restraints excluded: chain 3B residue 372 VAL Chi-restraints excluded: chain 3B residue 411 ILE Chi-restraints excluded: chain 3B residue 430 LEU Chi-restraints excluded: chain 3B residue 436 VAL Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 40 CYS Chi-restraints excluded: chain 3C residue 43 LEU Chi-restraints excluded: chain 3C residue 110 LEU Chi-restraints excluded: chain 3C residue 149 LEU Chi-restraints excluded: chain 3C residue 164 ILE Chi-restraints excluded: chain 3C residue 234 PHE Chi-restraints excluded: chain 3C residue 327 MET Chi-restraints excluded: chain 3C residue 345 HIS Chi-restraints excluded: chain 3C residue 360 LEU Chi-restraints excluded: chain 3C residue 377 LEU Chi-restraints excluded: chain 3D residue 128 CYS Chi-restraints excluded: chain 3D residue 298 LEU Chi-restraints excluded: chain 3E residue 96 VAL Chi-restraints excluded: chain 3E residue 99 SER Chi-restraints excluded: chain 3E residue 150 SER Chi-restraints excluded: chain 3E residue 194 GLN Chi-restraints excluded: chain 3E residue 205 VAL Chi-restraints excluded: chain 3E residue 220 LEU Chi-restraints excluded: chain 3E residue 239 HIS Chi-restraints excluded: chain 3E residue 271 VAL Chi-restraints excluded: chain 3E residue 272 ILE Chi-restraints excluded: chain 3F residue 71 VAL Chi-restraints excluded: chain 3G residue 17 THR Chi-restraints excluded: chain 3H residue 98 LEU Chi-restraints excluded: chain 3I residue 50 LEU Chi-restraints excluded: chain 3J residue 6 LEU Chi-restraints excluded: chain 3J residue 13 LEU Chi-restraints excluded: chain 3J residue 23 LEU Chi-restraints excluded: chain 3J residue 47 ILE Chi-restraints excluded: chain 3N residue 3 THR Chi-restraints excluded: chain 3N residue 112 LEU Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 126 GLN Chi-restraints excluded: chain 3N residue 209 LEU Chi-restraints excluded: chain 3N residue 407 VAL Chi-restraints excluded: chain 3O residue 55 SER Chi-restraints excluded: chain 3O residue 116 ILE Chi-restraints excluded: chain 3O residue 123 LEU Chi-restraints excluded: chain 3O residue 136 GLU Chi-restraints excluded: chain 3O residue 212 SER Chi-restraints excluded: chain 3O residue 224 LEU Chi-restraints excluded: chain 3O residue 226 MET Chi-restraints excluded: chain 3O residue 303 VAL Chi-restraints excluded: chain 3O residue 309 VAL Chi-restraints excluded: chain 3P residue 6 LYS Chi-restraints excluded: chain 3P residue 126 THR Chi-restraints excluded: chain 3P residue 156 ILE Chi-restraints excluded: chain 3P residue 170 VAL Chi-restraints excluded: chain 3P residue 202 GLU Chi-restraints excluded: chain 3P residue 233 LEU Chi-restraints excluded: chain 3P residue 249 LEU Chi-restraints excluded: chain 3P residue 298 ILE Chi-restraints excluded: chain 3P residue 313 ARG Chi-restraints excluded: chain 3P residue 333 ILE Chi-restraints excluded: chain 3Q residue 35 GLN Chi-restraints excluded: chain 3Q residue 55 CYS Chi-restraints excluded: chain 3Q residue 102 ARG Chi-restraints excluded: chain 3Q residue 141 VAL Chi-restraints excluded: chain 3R residue 151 LYS Chi-restraints excluded: chain 3R residue 174 LEU Chi-restraints excluded: chain 3R residue 180 THR Chi-restraints excluded: chain 3R residue 212 ILE Chi-restraints excluded: chain 3R residue 262 THR Chi-restraints excluded: chain 3R residue 266 THR Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3S residue 18 LYS Chi-restraints excluded: chain 3S residue 42 ASP Chi-restraints excluded: chain 3S residue 69 THR Chi-restraints excluded: chain 3S residue 81 THR Chi-restraints excluded: chain 3T residue 38 LEU Chi-restraints excluded: chain 3U residue 52 GLU Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3V residue 65 VAL 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 37 ASP Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 13 LEU Chi-restraints excluded: chain 3Y residue 45 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 264 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 311 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 301 optimal weight: 6.9990 chunk 241 optimal weight: 0.9990 chunk 364 optimal weight: 0.9990 chunk 354 optimal weight: 8.9990 chunk 255 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3E 227 ASN ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 9 GLN 3N 18 GLN ** 3N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 311 ASN ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3U 23 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.076183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.062977 restraints weight = 102711.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.065242 restraints weight = 44766.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.066722 restraints weight = 25879.245| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.438 34365 Z= 0.216 Angle : 0.732 38.986 46532 Z= 0.319 Chirality : 0.042 0.191 5004 Planarity : 0.004 0.051 5834 Dihedral : 13.241 160.547 5327 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.44 % Favored : 94.41 % Rotamer: Outliers : 4.96 % Allowed : 26.23 % Favored : 68.81 % 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: 0.72 (0.14), residues: 4062 helix: 1.80 (0.11), residues: 2040 sheet: -1.87 (0.27), residues: 323 loop : -0.65 (0.16), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP3C 141 HIS 0.005 0.001 HIS3B 213 PHE 0.030 0.002 PHE3F 72 TYR 0.019 0.001 TYR3F 32 ARG 0.006 0.000 ARG3O 46 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 1738) hydrogen bonds : angle 4.74547 ( 4984) metal coordination : bond 0.03127 ( 9) metal coordination : angle 22.87689 ( 9) SS BOND : bond 0.00279 ( 5) SS BOND : angle 1.05054 ( 10) covalent geometry : bond 0.00510 (34343) covalent geometry : angle 0.65972 (46513) Misc. bond : bond 0.27493 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 410 time to evaluate : 4.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR3N 3 " (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: "LEU3N 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN3N 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER3O 55 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: 3A 270 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9198 (tp) REVERT: 3B 84 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8989 (ttpp) REVERT: 3B 95 LYS cc_start: 0.8276 (tppp) cc_final: 0.8076 (mmmm) REVERT: 3B 153 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8051 (mt0) REVERT: 3B 213 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7546 (m-70) REVERT: 3B 250 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7045 (p0) REVERT: 3B 430 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9058 (mp) REVERT: 3C 110 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8636 (mp) REVERT: 3C 263 ASN cc_start: 0.8893 (t0) cc_final: 0.8690 (t0) REVERT: 3C 373 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8144 (mm-30) REVERT: 3D 128 CYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7220 (m) REVERT: 3D 293 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7690 (mtm) REVERT: 3E 251 LYS cc_start: 0.8895 (mmmt) cc_final: 0.8619 (mmmt) REVERT: 3H 50 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6683 (tm-30) REVERT: 3H 82 GLU cc_start: 0.8447 (mp0) cc_final: 0.8213 (mp0) REVERT: 3I 50 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8034 (pp) REVERT: 3I 77 ARG cc_start: 0.8213 (ttp80) cc_final: 0.7949 (ttp80) REVERT: 3J 16 ARG cc_start: 0.8813 (ttm-80) cc_final: 0.8373 (ttt-90) REVERT: 3J 38 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8137 (mt0) REVERT: 3J 48 ASN cc_start: 0.8482 (p0) cc_final: 0.8225 (p0) REVERT: 3O 136 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8707 (mt-10) REVERT: 3O 226 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6155 (pp-130) REVERT: 3O 248 ASN cc_start: 0.8219 (t0) cc_final: 0.7944 (t0) REVERT: 3P 235 MET cc_start: 0.9140 (tmm) cc_final: 0.8857 (tmm) REVERT: 3P 249 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9291 (tm) REVERT: 3P 313 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8477 (ttt180) REVERT: 3P 333 ILE cc_start: 0.9648 (OUTLIER) cc_final: 0.9441 (mp) REVERT: 3Q 102 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7980 (mtp85) REVERT: 3Q 212 MET cc_start: 0.8586 (mmt) cc_final: 0.8143 (mmt) REVERT: 3R 140 MET cc_start: 0.8280 (mtp) cc_final: 0.7719 (mtp) REVERT: 3R 149 MET cc_start: 0.7162 (pmm) cc_final: 0.6812 (pmm) REVERT: 3R 151 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7337 (mmmt) REVERT: 3R 191 GLU cc_start: 0.7221 (tp30) cc_final: 0.6978 (tp30) REVERT: 3R 204 ARG cc_start: 0.7418 (tpp-160) cc_final: 0.6894 (ttm170) REVERT: 3S 44 LYS cc_start: 0.8885 (mtmm) cc_final: 0.8613 (mtmm) REVERT: 3V 53 GLU cc_start: 0.8389 (mp0) cc_final: 0.7794 (mp0) REVERT: 3X 47 TYR cc_start: 0.8910 (t80) cc_final: 0.8601 (t80) REVERT: 3Y 39 ARG cc_start: 0.8380 (mpp-170) cc_final: 0.7745 (tpp80) outliers start: 170 outliers final: 112 residues processed: 538 average time/residue: 0.4497 time to fit residues: 392.3749 Evaluate side-chains 518 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 389 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 61 HIS Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 138 LEU Chi-restraints excluded: chain 3A residue 149 VAL Chi-restraints excluded: chain 3A residue 196 VAL Chi-restraints excluded: chain 3A residue 255 ILE Chi-restraints excluded: chain 3A residue 257 VAL Chi-restraints excluded: chain 3A residue 270 LEU Chi-restraints excluded: chain 3A residue 282 SER Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 320 LEU Chi-restraints excluded: chain 3A residue 346 CYS Chi-restraints excluded: chain 3A residue 350 THR Chi-restraints excluded: chain 3B residue 84 LYS Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 123 LEU Chi-restraints excluded: chain 3B residue 153 GLN Chi-restraints excluded: chain 3B residue 213 HIS Chi-restraints excluded: chain 3B residue 221 GLU Chi-restraints excluded: chain 3B residue 250 ASP Chi-restraints excluded: chain 3B residue 284 HIS Chi-restraints excluded: chain 3B residue 285 VAL Chi-restraints excluded: chain 3B residue 303 VAL Chi-restraints excluded: chain 3B residue 309 VAL Chi-restraints excluded: chain 3B residue 370 MET Chi-restraints excluded: chain 3B residue 372 VAL Chi-restraints excluded: chain 3B residue 430 LEU Chi-restraints excluded: chain 3B residue 436 VAL Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 40 CYS Chi-restraints excluded: chain 3C residue 43 LEU Chi-restraints excluded: chain 3C residue 78 VAL Chi-restraints excluded: chain 3C residue 110 LEU Chi-restraints excluded: chain 3C residue 149 LEU Chi-restraints excluded: chain 3C residue 164 ILE Chi-restraints excluded: chain 3C residue 192 LEU Chi-restraints excluded: chain 3C residue 212 SER Chi-restraints excluded: chain 3C residue 234 PHE Chi-restraints excluded: chain 3C residue 281 LEU Chi-restraints excluded: chain 3C residue 345 HIS Chi-restraints excluded: chain 3C residue 377 LEU Chi-restraints excluded: chain 3D residue 128 CYS Chi-restraints excluded: chain 3D residue 276 CYS Chi-restraints excluded: chain 3D residue 293 MET Chi-restraints excluded: chain 3D residue 298 LEU Chi-restraints excluded: chain 3E residue 83 ILE Chi-restraints excluded: chain 3E residue 96 VAL Chi-restraints excluded: chain 3E residue 99 SER Chi-restraints excluded: chain 3E residue 205 VAL Chi-restraints excluded: chain 3E residue 216 VAL Chi-restraints excluded: chain 3E residue 220 LEU Chi-restraints excluded: chain 3E residue 238 CYS Chi-restraints excluded: chain 3E residue 239 HIS Chi-restraints excluded: chain 3E residue 269 ASP Chi-restraints excluded: chain 3E residue 271 VAL Chi-restraints excluded: chain 3F residue 71 VAL Chi-restraints excluded: chain 3G residue 17 THR Chi-restraints excluded: chain 3H residue 52 ILE Chi-restraints excluded: chain 3H residue 98 LEU Chi-restraints excluded: chain 3I residue 50 LEU Chi-restraints excluded: chain 3J residue 6 LEU Chi-restraints excluded: chain 3J residue 13 LEU Chi-restraints excluded: chain 3J residue 23 LEU Chi-restraints excluded: chain 3J residue 24 THR Chi-restraints excluded: chain 3J residue 47 ILE Chi-restraints excluded: chain 3N residue 3 THR Chi-restraints excluded: chain 3N residue 112 LEU Chi-restraints excluded: chain 3N residue 117 VAL Chi-restraints excluded: chain 3N residue 126 GLN Chi-restraints excluded: chain 3N residue 167 VAL Chi-restraints excluded: chain 3N residue 209 LEU Chi-restraints excluded: chain 3N residue 407 VAL Chi-restraints excluded: chain 3N residue 444 LEU Chi-restraints excluded: chain 3O residue 51 ILE Chi-restraints excluded: chain 3O residue 55 SER Chi-restraints excluded: chain 3O residue 68 LEU Chi-restraints excluded: chain 3O residue 116 ILE Chi-restraints excluded: chain 3O residue 123 LEU Chi-restraints excluded: chain 3O residue 136 GLU Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 226 MET Chi-restraints excluded: chain 3O residue 303 VAL Chi-restraints excluded: chain 3O residue 309 VAL Chi-restraints excluded: chain 3O residue 347 ILE Chi-restraints excluded: chain 3P residue 6 LYS Chi-restraints excluded: chain 3P residue 112 THR Chi-restraints excluded: chain 3P residue 126 THR Chi-restraints excluded: chain 3P residue 144 THR Chi-restraints excluded: chain 3P residue 156 ILE Chi-restraints excluded: chain 3P residue 170 VAL Chi-restraints excluded: chain 3P residue 202 GLU Chi-restraints excluded: chain 3P residue 233 LEU Chi-restraints excluded: chain 3P residue 249 LEU Chi-restraints excluded: chain 3P residue 298 ILE Chi-restraints excluded: chain 3P residue 313 ARG Chi-restraints excluded: chain 3P residue 332 LEU Chi-restraints excluded: chain 3P residue 333 ILE Chi-restraints excluded: chain 3Q residue 55 CYS Chi-restraints excluded: chain 3Q residue 66 GLU Chi-restraints excluded: chain 3Q residue 102 ARG Chi-restraints excluded: chain 3Q residue 113 LEU Chi-restraints excluded: chain 3Q residue 141 VAL Chi-restraints excluded: chain 3R residue 151 LYS Chi-restraints excluded: chain 3R residue 174 LEU Chi-restraints excluded: chain 3R residue 180 THR Chi-restraints excluded: chain 3R residue 212 ILE Chi-restraints excluded: chain 3R residue 262 THR Chi-restraints excluded: chain 3R residue 266 THR Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3S residue 18 LYS Chi-restraints excluded: chain 3S residue 42 ASP Chi-restraints excluded: chain 3S residue 69 THR Chi-restraints excluded: chain 3S residue 81 THR Chi-restraints excluded: chain 3T residue 38 LEU Chi-restraints excluded: chain 3T residue 41 THR Chi-restraints excluded: chain 3U residue 30 CYS Chi-restraints excluded: chain 3U residue 52 GLU Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3V residue 65 VAL 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 4 THR Chi-restraints excluded: chain 3X residue 1 MET Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 37 ASP Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 13 LEU Chi-restraints excluded: chain 3Y residue 18 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 119 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 chunk 369 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 394 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3B 343 GLN 3C 85 ASN 3E 194 GLN 3E 227 ASN ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3F 91 GLN ** 3J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 9 GLN ** 3N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3P 312 GLN ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3Q 35 GLN ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3U 23 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.076473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.062625 restraints weight = 128309.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.065125 restraints weight = 51753.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.066738 restraints weight = 28529.723| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.448 34365 Z= 0.195 Angle : 0.713 37.219 46532 Z= 0.315 Chirality : 0.042 0.194 5004 Planarity : 0.004 0.047 5834 Dihedral : 13.054 142.258 5327 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.10 % Favored : 94.75 % Rotamer: Outliers : 4.81 % Allowed : 26.52 % 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: 0.78 (0.14), residues: 4062 helix: 1.83 (0.11), residues: 2047 sheet: -1.85 (0.26), residues: 340 loop : -0.59 (0.16), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP3C 141 HIS 0.006 0.001 HIS3B 213 PHE 0.026 0.001 PHE3F 72 TYR 0.018 0.001 TYR3C 224 ARG 0.007 0.000 ARG3V 52 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 1738) hydrogen bonds : angle 4.69926 ( 4984) metal coordination : bond 0.03185 ( 9) metal coordination : angle 20.55575 ( 9) SS BOND : bond 0.00358 ( 5) SS BOND : angle 1.00647 ( 10) covalent geometry : bond 0.00461 (34343) covalent geometry : angle 0.65327 (46513) Misc. bond : bond 0.26151 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 427 time to evaluate : 3.707 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR3N 3 " (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: "LEU3N 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN3N 126 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER3O 55 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 3A 270 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9180 (tp) REVERT: 3B 84 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.9049 (ttpp) REVERT: 3B 153 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8062 (mt0) REVERT: 3B 213 HIS cc_start: 0.8404 (OUTLIER) cc_final: 0.7585 (m-70) REVERT: 3B 250 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.6997 (p0) REVERT: 3B 430 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9006 (mp) REVERT: 3C 19 ILE cc_start: 0.9385 (mm) cc_final: 0.9164 (mm) REVERT: 3C 110 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8612 (mp) REVERT: 3C 373 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8083 (mm-30) REVERT: 3D 293 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7647 (mtm) REVERT: 3E 251 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8670 (mmmt) REVERT: 3F 56 LYS cc_start: 0.8809 (mttp) cc_final: 0.8576 (mtmm) REVERT: 3F 85 GLN cc_start: 0.8555 (mt0) cc_final: 0.8334 (mp10) REVERT: 3H 50 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6732 (tm-30) REVERT: 3I 50 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8197 (pp) REVERT: 3J 38 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8141 (mt0) REVERT: 3O 105 MET cc_start: 0.8922 (mtp) cc_final: 0.8542 (ttp) REVERT: 3O 136 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8442 (mt-10) REVERT: 3O 226 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6361 (pp-130) REVERT: 3O 248 ASN cc_start: 0.8230 (t0) cc_final: 0.7767 (t0) REVERT: 3P 235 MET cc_start: 0.9147 (tmm) cc_final: 0.8864 (tmm) REVERT: 3P 248 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8183 (p0) REVERT: 3P 249 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9266 (tm) REVERT: 3Q 102 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8008 (mtp85) REVERT: 3Q 212 MET cc_start: 0.8606 (mmt) cc_final: 0.8184 (mmt) REVERT: 3R 140 MET cc_start: 0.8303 (mtp) cc_final: 0.7735 (mtp) REVERT: 3R 149 MET cc_start: 0.7133 (pmm) cc_final: 0.6894 (pmm) REVERT: 3R 151 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7385 (mmmt) REVERT: 3R 204 ARG cc_start: 0.7403 (tpp-160) cc_final: 0.6977 (ttm170) REVERT: 3S 44 LYS cc_start: 0.8925 (mtmm) cc_final: 0.8635 (mtmm) REVERT: 3T 70 LYS cc_start: 0.8914 (tmtt) cc_final: 0.8689 (tttt) REVERT: 3U 32 LYS cc_start: 0.9115 (mmtm) cc_final: 0.8878 (mmtm) REVERT: 3V 53 GLU cc_start: 0.8350 (mp0) cc_final: 0.7732 (mp0) REVERT: 3X 6 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7433 (tm) REVERT: 3X 23 MET cc_start: 0.9076 (tmm) cc_final: 0.8531 (tmm) REVERT: 3Y 39 ARG cc_start: 0.8433 (mpp-170) cc_final: 0.7748 (tpp80) outliers start: 165 outliers final: 113 residues processed: 556 average time/residue: 0.4445 time to fit residues: 402.7551 Evaluate side-chains 526 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 397 time to evaluate : 3.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 61 HIS Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 138 LEU Chi-restraints excluded: chain 3A residue 145 MET Chi-restraints excluded: chain 3A residue 149 VAL Chi-restraints excluded: chain 3A residue 196 VAL Chi-restraints excluded: chain 3A residue 255 ILE Chi-restraints excluded: chain 3A residue 257 VAL Chi-restraints excluded: chain 3A residue 270 LEU Chi-restraints excluded: chain 3A residue 282 SER Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 320 LEU Chi-restraints excluded: chain 3A residue 346 CYS Chi-restraints excluded: chain 3A residue 350 THR Chi-restraints excluded: chain 3B residue 84 LYS Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 133 ARG Chi-restraints excluded: chain 3B residue 153 GLN Chi-restraints excluded: chain 3B residue 213 HIS Chi-restraints excluded: chain 3B residue 221 GLU Chi-restraints excluded: chain 3B residue 250 ASP Chi-restraints excluded: chain 3B residue 284 HIS Chi-restraints excluded: chain 3B residue 285 VAL Chi-restraints excluded: chain 3B residue 309 VAL Chi-restraints excluded: chain 3B residue 370 MET Chi-restraints excluded: chain 3B residue 372 VAL Chi-restraints excluded: chain 3B residue 430 LEU Chi-restraints excluded: chain 3B residue 436 VAL Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 40 CYS Chi-restraints excluded: chain 3C residue 43 LEU Chi-restraints excluded: chain 3C residue 78 VAL Chi-restraints excluded: chain 3C residue 110 LEU Chi-restraints excluded: chain 3C residue 146 ILE Chi-restraints excluded: chain 3C residue 149 LEU Chi-restraints excluded: chain 3C residue 164 ILE Chi-restraints excluded: chain 3C residue 192 LEU Chi-restraints excluded: chain 3C residue 212 SER Chi-restraints excluded: chain 3C residue 234 PHE Chi-restraints excluded: chain 3C residue 345 HIS Chi-restraints excluded: chain 3C residue 377 LEU Chi-restraints excluded: chain 3D residue 276 CYS Chi-restraints excluded: chain 3D residue 293 MET Chi-restraints excluded: chain 3D residue 298 LEU Chi-restraints excluded: chain 3E residue 83 ILE Chi-restraints excluded: chain 3E residue 96 VAL Chi-restraints excluded: chain 3E residue 99 SER Chi-restraints excluded: chain 3E residue 194 GLN Chi-restraints excluded: chain 3E residue 205 VAL Chi-restraints excluded: chain 3E residue 216 VAL Chi-restraints excluded: chain 3E residue 220 LEU Chi-restraints excluded: chain 3E residue 238 CYS Chi-restraints excluded: chain 3E residue 239 HIS Chi-restraints excluded: chain 3E residue 269 ASP Chi-restraints excluded: chain 3E residue 271 VAL Chi-restraints excluded: chain 3F residue 71 VAL Chi-restraints excluded: chain 3G residue 17 THR Chi-restraints excluded: chain 3H residue 52 ILE Chi-restraints excluded: chain 3H residue 98 LEU Chi-restraints excluded: chain 3I residue 50 LEU Chi-restraints excluded: chain 3J residue 6 LEU Chi-restraints excluded: chain 3J residue 13 LEU Chi-restraints excluded: chain 3J residue 23 LEU Chi-restraints excluded: chain 3J residue 24 THR Chi-restraints excluded: chain 3N residue 3 THR 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 126 GLN Chi-restraints excluded: chain 3N residue 167 VAL Chi-restraints excluded: chain 3N residue 209 LEU Chi-restraints excluded: chain 3N residue 444 LEU Chi-restraints excluded: chain 3O residue 51 ILE Chi-restraints excluded: chain 3O residue 55 SER Chi-restraints excluded: chain 3O residue 116 ILE Chi-restraints excluded: chain 3O residue 123 LEU Chi-restraints excluded: chain 3O residue 136 GLU Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 212 SER Chi-restraints excluded: chain 3O residue 226 MET Chi-restraints excluded: chain 3O residue 303 VAL Chi-restraints excluded: chain 3O residue 309 VAL Chi-restraints excluded: chain 3O residue 347 ILE Chi-restraints excluded: chain 3P residue 6 LYS Chi-restraints excluded: chain 3P residue 112 THR Chi-restraints excluded: chain 3P residue 126 THR Chi-restraints excluded: chain 3P residue 156 ILE Chi-restraints excluded: chain 3P residue 170 VAL Chi-restraints excluded: chain 3P residue 202 GLU Chi-restraints excluded: chain 3P residue 233 LEU Chi-restraints excluded: chain 3P residue 248 ASP Chi-restraints excluded: chain 3P residue 249 LEU Chi-restraints excluded: chain 3P residue 298 ILE Chi-restraints excluded: chain 3P residue 332 LEU Chi-restraints excluded: chain 3Q residue 35 GLN Chi-restraints excluded: chain 3Q residue 55 CYS Chi-restraints excluded: chain 3Q residue 66 GLU Chi-restraints excluded: chain 3Q residue 102 ARG Chi-restraints excluded: chain 3Q residue 113 LEU Chi-restraints excluded: chain 3Q residue 141 VAL Chi-restraints excluded: chain 3R residue 143 SER Chi-restraints excluded: chain 3R residue 151 LYS Chi-restraints excluded: chain 3R residue 174 LEU Chi-restraints excluded: chain 3R residue 180 THR Chi-restraints excluded: chain 3R residue 212 ILE Chi-restraints excluded: chain 3R residue 262 THR Chi-restraints excluded: chain 3R residue 266 THR Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3S residue 18 LYS Chi-restraints excluded: chain 3S residue 42 ASP Chi-restraints excluded: chain 3S residue 69 THR Chi-restraints excluded: chain 3S residue 81 THR Chi-restraints excluded: chain 3T residue 38 LEU Chi-restraints excluded: chain 3T residue 41 THR Chi-restraints excluded: chain 3U residue 30 CYS Chi-restraints excluded: chain 3U residue 52 GLU Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3V residue 50 LEU Chi-restraints excluded: chain 3V residue 65 VAL 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 3X residue 1 MET Chi-restraints excluded: chain 3X residue 6 LEU Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 37 ASP Chi-restraints excluded: chain 3X residue 40 LEU Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 18 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 300 optimal weight: 5.9990 chunk 278 optimal weight: 8.9990 chunk 384 optimal weight: 0.3980 chunk 364 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 134 optimal weight: 0.0970 chunk 217 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3C 85 ASN 3C 201 HIS 3E 200 HIS 3E 227 ASN ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 9 GLN ** 3N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 289 HIS ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3Q 35 GLN ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3U 23 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.065085 restraints weight = 103906.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.067474 restraints weight = 44585.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.069009 restraints weight = 25334.310| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.368 34365 Z= 0.124 Angle : 0.676 33.792 46532 Z= 0.301 Chirality : 0.041 0.204 5004 Planarity : 0.004 0.047 5834 Dihedral : 12.778 125.142 5327 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.80 % Favored : 95.05 % Rotamer: Outliers : 4.21 % Allowed : 27.27 % Favored : 68.52 % 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: 0.87 (0.14), residues: 4062 helix: 1.96 (0.11), residues: 2038 sheet: -1.80 (0.26), residues: 361 loop : -0.57 (0.16), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP3C 141 HIS 0.005 0.001 HIS3C 182 PHE 0.023 0.001 PHE3F 72 TYR 0.020 0.001 TYR3Y 47 ARG 0.006 0.000 ARG3G 4 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 1738) hydrogen bonds : angle 4.58556 ( 4984) metal coordination : bond 0.03290 ( 9) metal coordination : angle 18.39554 ( 9) SS BOND : bond 0.00301 ( 5) SS BOND : angle 0.86928 ( 10) covalent geometry : bond 0.00282 (34343) covalent geometry : angle 0.62592 (46513) Misc. bond : bond 0.21458 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 434 time to evaluate : 3.702 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 11 " (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: "SER3O 55 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 3A 9 GLN cc_start: 0.8309 (tm-30) cc_final: 0.8080 (tm-30) REVERT: 3A 270 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9130 (tp) REVERT: 3A 430 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: 3B 153 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7891 (mt0) REVERT: 3B 213 HIS cc_start: 0.8312 (OUTLIER) cc_final: 0.7418 (m-70) REVERT: 3B 250 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7249 (p0) REVERT: 3B 430 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8939 (mp) REVERT: 3C 19 ILE cc_start: 0.9345 (mm) cc_final: 0.9099 (mm) REVERT: 3C 373 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8107 (mm-30) REVERT: 3D 293 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7481 (mtm) REVERT: 3F 56 LYS cc_start: 0.8792 (mttp) cc_final: 0.8536 (mtmm) REVERT: 3F 85 GLN cc_start: 0.8504 (mt0) cc_final: 0.8276 (mp10) REVERT: 3H 50 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6712 (tm-30) REVERT: 3I 50 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8152 (pp) REVERT: 3I 77 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7675 (ttp80) REVERT: 3J 38 GLN cc_start: 0.8238 (mm-40) cc_final: 0.8037 (mt0) REVERT: 3N 226 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7234 (p0) REVERT: 3O 105 MET cc_start: 0.8925 (mtp) cc_final: 0.8545 (mtp) REVERT: 3O 226 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6313 (pp-130) REVERT: 3O 248 ASN cc_start: 0.8290 (t0) cc_final: 0.7769 (t0) REVERT: 3P 235 MET cc_start: 0.9147 (tmm) cc_final: 0.8855 (tmm) REVERT: 3P 249 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9227 (tm) REVERT: 3Q 35 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8355 (pt0) REVERT: 3Q 102 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.7937 (mtp85) REVERT: 3Q 212 MET cc_start: 0.8647 (mmt) cc_final: 0.8222 (mmt) REVERT: 3R 191 GLU cc_start: 0.7087 (tp30) cc_final: 0.6864 (tp30) REVERT: 3R 204 ARG cc_start: 0.7312 (tpp-160) cc_final: 0.6895 (ttm170) REVERT: 3S 44 LYS cc_start: 0.8925 (mtmm) cc_final: 0.8637 (mtmm) REVERT: 3V 53 GLU cc_start: 0.8508 (mp0) cc_final: 0.7925 (mp0) REVERT: 3X 6 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7477 (tm) REVERT: 3Y 39 ARG cc_start: 0.8334 (mpp-170) cc_final: 0.7864 (tpp80) outliers start: 144 outliers final: 96 residues processed: 533 average time/residue: 0.4522 time to fit residues: 391.5134 Evaluate side-chains 519 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 409 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 58 PHE Chi-restraints excluded: chain 3A residue 61 HIS Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 138 LEU Chi-restraints excluded: chain 3A residue 145 MET Chi-restraints excluded: chain 3A residue 149 VAL Chi-restraints excluded: chain 3A residue 196 VAL Chi-restraints excluded: chain 3A residue 255 ILE Chi-restraints excluded: chain 3A residue 257 VAL Chi-restraints excluded: chain 3A residue 270 LEU Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 320 LEU Chi-restraints excluded: chain 3A residue 346 CYS Chi-restraints excluded: chain 3A residue 430 GLN Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 133 ARG Chi-restraints excluded: chain 3B residue 153 GLN Chi-restraints excluded: chain 3B residue 213 HIS Chi-restraints excluded: chain 3B residue 221 GLU Chi-restraints excluded: chain 3B residue 250 ASP Chi-restraints excluded: chain 3B residue 285 VAL Chi-restraints excluded: chain 3B residue 309 VAL Chi-restraints excluded: chain 3B residue 372 VAL Chi-restraints excluded: chain 3B residue 430 LEU Chi-restraints excluded: chain 3B residue 436 VAL Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 40 CYS Chi-restraints excluded: chain 3C residue 43 LEU Chi-restraints excluded: chain 3C residue 68 HIS Chi-restraints excluded: chain 3C residue 110 LEU Chi-restraints excluded: chain 3C residue 146 ILE Chi-restraints excluded: chain 3C residue 149 LEU Chi-restraints excluded: chain 3C residue 164 ILE Chi-restraints excluded: chain 3C residue 192 LEU Chi-restraints excluded: chain 3C residue 212 SER Chi-restraints excluded: chain 3C residue 234 PHE Chi-restraints excluded: chain 3C residue 345 HIS Chi-restraints excluded: chain 3C residue 377 LEU Chi-restraints excluded: chain 3D residue 109 LEU Chi-restraints excluded: chain 3D residue 276 CYS Chi-restraints excluded: chain 3D residue 293 MET Chi-restraints excluded: chain 3D residue 298 LEU Chi-restraints excluded: chain 3E residue 83 ILE Chi-restraints excluded: chain 3E residue 97 LEU Chi-restraints excluded: chain 3E residue 205 VAL Chi-restraints excluded: chain 3E residue 216 VAL Chi-restraints excluded: chain 3E residue 220 LEU Chi-restraints excluded: chain 3E residue 238 CYS Chi-restraints excluded: chain 3E residue 239 HIS Chi-restraints excluded: chain 3E residue 271 VAL Chi-restraints excluded: chain 3F residue 71 VAL Chi-restraints excluded: chain 3H residue 52 ILE Chi-restraints excluded: chain 3H residue 98 LEU Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 50 LEU Chi-restraints excluded: chain 3J residue 6 LEU Chi-restraints excluded: chain 3J residue 13 LEU Chi-restraints excluded: chain 3J residue 23 LEU 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 226 ASP Chi-restraints excluded: chain 3O residue 51 ILE Chi-restraints excluded: chain 3O residue 55 SER Chi-restraints excluded: chain 3O residue 123 LEU Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 212 SER Chi-restraints excluded: chain 3O residue 226 MET Chi-restraints excluded: chain 3O residue 303 VAL Chi-restraints excluded: chain 3O residue 309 VAL Chi-restraints excluded: chain 3O residue 347 ILE Chi-restraints excluded: chain 3P residue 6 LYS Chi-restraints excluded: chain 3P residue 112 THR Chi-restraints excluded: chain 3P residue 126 THR Chi-restraints excluded: chain 3P residue 156 ILE Chi-restraints excluded: chain 3P residue 170 VAL Chi-restraints excluded: chain 3P residue 202 GLU Chi-restraints excluded: chain 3P residue 233 LEU Chi-restraints excluded: chain 3P residue 249 LEU Chi-restraints excluded: chain 3P residue 332 LEU Chi-restraints excluded: chain 3Q residue 35 GLN Chi-restraints excluded: chain 3Q residue 66 GLU Chi-restraints excluded: chain 3Q residue 102 ARG Chi-restraints excluded: chain 3Q residue 141 VAL Chi-restraints excluded: chain 3R residue 147 LEU Chi-restraints excluded: chain 3R residue 174 LEU Chi-restraints excluded: chain 3R residue 192 VAL Chi-restraints excluded: chain 3R residue 212 ILE Chi-restraints excluded: chain 3R residue 262 THR Chi-restraints excluded: chain 3R residue 266 THR Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3S residue 18 LYS Chi-restraints excluded: chain 3S residue 42 ASP Chi-restraints excluded: chain 3S residue 69 THR Chi-restraints excluded: chain 3S residue 81 THR Chi-restraints excluded: chain 3T residue 38 LEU Chi-restraints excluded: chain 3U residue 30 CYS Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3V residue 50 LEU Chi-restraints excluded: chain 3V residue 55 LEU Chi-restraints excluded: chain 3V residue 65 VAL Chi-restraints excluded: chain 3V residue 72 VAL Chi-restraints excluded: chain 3W residue 24 ILE Chi-restraints excluded: chain 3X residue 1 MET Chi-restraints excluded: chain 3X residue 6 LEU Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 37 ASP Chi-restraints excluded: chain 3X residue 40 LEU Chi-restraints excluded: chain 3X residue 45 VAL Chi-restraints excluded: chain 3Y residue 18 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 378 optimal weight: 6.9990 chunk 200 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 103 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 125 optimal weight: 0.0970 chunk 55 optimal weight: 5.9990 chunk 385 optimal weight: 4.9990 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3E 227 ASN ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3J 49 GLN 3N 9 GLN ** 3N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3O 343 GLN ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3Q 35 GLN ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3T 23 GLN ** 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 = 0.3213 r_free = 0.3213 target = 0.078457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.064957 restraints weight = 107076.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.067355 restraints weight = 45484.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.068916 restraints weight = 25768.082| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.371 34365 Z= 0.134 Angle : 0.676 29.412 46532 Z= 0.304 Chirality : 0.041 0.196 5004 Planarity : 0.004 0.045 5834 Dihedral : 12.561 117.517 5322 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.75 % Favored : 95.10 % Rotamer: Outliers : 3.86 % Allowed : 27.30 % Favored : 68.84 % 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: 0.91 (0.14), residues: 4062 helix: 1.94 (0.11), residues: 2048 sheet: -1.68 (0.26), residues: 353 loop : -0.54 (0.16), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP3C 141 HIS 0.004 0.001 HIS3C 182 PHE 0.028 0.001 PHE3J 36 TYR 0.019 0.001 TYR3G 61 ARG 0.007 0.000 ARG3A 381 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 1738) hydrogen bonds : angle 4.54722 ( 4984) metal coordination : bond 0.03268 ( 9) metal coordination : angle 16.10495 ( 9) SS BOND : bond 0.00256 ( 5) SS BOND : angle 0.86714 ( 10) covalent geometry : bond 0.00318 (34343) covalent geometry : angle 0.63801 (46513) Misc. bond : bond 0.21347 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 424 time to evaluate : 3.802 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR3N 3 " (corrupted residue). Skipping it. 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 11 " (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: "SER3O 55 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3A 270 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9161 (tp) REVERT: 3A 430 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: 3B 153 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: 3B 204 MET cc_start: 0.8785 (mtp) cc_final: 0.8391 (mtp) REVERT: 3B 213 HIS cc_start: 0.8287 (OUTLIER) cc_final: 0.7419 (m-70) REVERT: 3B 250 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7266 (p0) REVERT: 3B 430 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8959 (mp) REVERT: 3C 19 ILE cc_start: 0.9357 (mm) cc_final: 0.9098 (mm) REVERT: 3C 373 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8080 (mm-30) REVERT: 3D 293 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7506 (mtm) REVERT: 3E 84 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7867 (mtp-110) REVERT: 3F 56 LYS cc_start: 0.8853 (mttp) cc_final: 0.8610 (mtmm) REVERT: 3F 85 GLN cc_start: 0.8474 (mt0) cc_final: 0.8226 (mp10) REVERT: 3H 50 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6766 (tm-30) REVERT: 3I 50 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8111 (pp) REVERT: 3N 226 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7219 (p0) REVERT: 3O 226 MET cc_start: 0.6842 (OUTLIER) cc_final: 0.6253 (pp-130) REVERT: 3O 248 ASN cc_start: 0.8323 (t0) cc_final: 0.7820 (t0) REVERT: 3P 235 MET cc_start: 0.9156 (tmm) cc_final: 0.8864 (tmm) REVERT: 3P 248 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8131 (p0) REVERT: 3P 249 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9186 (tm) REVERT: 3Q 102 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8025 (mtp85) REVERT: 3Q 212 MET cc_start: 0.8649 (mmt) cc_final: 0.8229 (mmt) REVERT: 3R 204 ARG cc_start: 0.7297 (tpp-160) cc_final: 0.6931 (ttm170) REVERT: 3S 44 LYS cc_start: 0.8932 (mtmm) cc_final: 0.8630 (mtmm) REVERT: 3S 82 LYS cc_start: 0.9089 (mtmm) cc_final: 0.8531 (mtmm) REVERT: 3T 10 MET cc_start: 0.7573 (mtt) cc_final: 0.6916 (mtt) REVERT: 3V 53 GLU cc_start: 0.8458 (mp0) cc_final: 0.8111 (mp0) REVERT: 3X 6 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7564 (tm) REVERT: 3X 12 GLU cc_start: 0.8788 (tt0) cc_final: 0.8002 (tm-30) REVERT: 3Y 39 ARG cc_start: 0.8359 (mpp-170) cc_final: 0.7858 (tpp80) outliers start: 132 outliers final: 101 residues processed: 513 average time/residue: 0.4456 time to fit residues: 370.3361 Evaluate side-chains 514 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 398 time to evaluate : 3.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 58 PHE Chi-restraints excluded: chain 3A residue 61 HIS Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 149 VAL Chi-restraints excluded: chain 3A residue 196 VAL Chi-restraints excluded: chain 3A residue 255 ILE Chi-restraints excluded: chain 3A residue 257 VAL Chi-restraints excluded: chain 3A residue 270 LEU Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 320 LEU Chi-restraints excluded: chain 3A residue 346 CYS Chi-restraints excluded: chain 3A residue 430 GLN Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 133 ARG Chi-restraints excluded: chain 3B residue 153 GLN Chi-restraints excluded: chain 3B residue 213 HIS Chi-restraints excluded: chain 3B residue 221 GLU Chi-restraints excluded: chain 3B residue 250 ASP Chi-restraints excluded: chain 3B residue 285 VAL Chi-restraints excluded: chain 3B residue 309 VAL Chi-restraints excluded: chain 3B residue 372 VAL Chi-restraints excluded: chain 3B residue 411 ILE Chi-restraints excluded: chain 3B residue 430 LEU Chi-restraints excluded: chain 3B residue 436 VAL Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 40 CYS Chi-restraints excluded: chain 3C residue 43 LEU Chi-restraints excluded: chain 3C residue 68 HIS Chi-restraints excluded: chain 3C residue 78 VAL Chi-restraints excluded: chain 3C residue 110 LEU Chi-restraints excluded: chain 3C residue 146 ILE Chi-restraints excluded: chain 3C residue 164 ILE Chi-restraints excluded: chain 3C residue 192 LEU Chi-restraints excluded: chain 3C residue 212 SER Chi-restraints excluded: chain 3C residue 234 PHE Chi-restraints excluded: chain 3C residue 345 HIS Chi-restraints excluded: chain 3C residue 363 LEU Chi-restraints excluded: chain 3C residue 377 LEU Chi-restraints excluded: chain 3D residue 109 LEU Chi-restraints excluded: chain 3D residue 276 CYS Chi-restraints excluded: chain 3D residue 293 MET Chi-restraints excluded: chain 3D residue 298 LEU Chi-restraints excluded: chain 3E residue 83 ILE Chi-restraints excluded: chain 3E residue 84 ARG Chi-restraints excluded: chain 3E residue 97 LEU Chi-restraints excluded: chain 3E residue 205 VAL Chi-restraints excluded: chain 3E residue 216 VAL Chi-restraints excluded: chain 3E residue 220 LEU Chi-restraints excluded: chain 3E residue 238 CYS Chi-restraints excluded: chain 3E residue 239 HIS Chi-restraints excluded: chain 3E residue 271 VAL Chi-restraints excluded: chain 3E residue 272 ILE Chi-restraints excluded: chain 3F residue 71 VAL Chi-restraints excluded: chain 3G residue 48 LEU Chi-restraints excluded: chain 3H residue 52 ILE Chi-restraints excluded: chain 3H residue 98 LEU Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 42 VAL Chi-restraints excluded: chain 3I residue 50 LEU Chi-restraints excluded: chain 3J residue 6 LEU Chi-restraints excluded: chain 3J residue 23 LEU Chi-restraints excluded: chain 3N residue 3 THR 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 226 ASP Chi-restraints excluded: chain 3O residue 51 ILE Chi-restraints excluded: chain 3O residue 55 SER Chi-restraints excluded: chain 3O residue 123 LEU Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 212 SER Chi-restraints excluded: chain 3O residue 226 MET Chi-restraints excluded: chain 3O residue 303 VAL Chi-restraints excluded: chain 3O residue 309 VAL Chi-restraints excluded: chain 3O residue 347 ILE Chi-restraints excluded: chain 3P residue 6 LYS Chi-restraints excluded: chain 3P residue 112 THR Chi-restraints excluded: chain 3P residue 126 THR Chi-restraints excluded: chain 3P residue 156 ILE Chi-restraints excluded: chain 3P residue 170 VAL Chi-restraints excluded: chain 3P residue 202 GLU Chi-restraints excluded: chain 3P residue 233 LEU Chi-restraints excluded: chain 3P residue 248 ASP Chi-restraints excluded: chain 3P residue 249 LEU Chi-restraints excluded: chain 3P residue 332 LEU Chi-restraints excluded: chain 3Q residue 66 GLU Chi-restraints excluded: chain 3Q residue 102 ARG Chi-restraints excluded: chain 3Q residue 141 VAL Chi-restraints excluded: chain 3R residue 146 VAL Chi-restraints excluded: chain 3R residue 174 LEU Chi-restraints excluded: chain 3R residue 192 VAL Chi-restraints excluded: chain 3R residue 212 ILE Chi-restraints excluded: chain 3R residue 262 THR Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3S residue 18 LYS Chi-restraints excluded: chain 3S residue 42 ASP Chi-restraints excluded: chain 3S residue 81 THR Chi-restraints excluded: chain 3T residue 38 LEU Chi-restraints excluded: chain 3U residue 30 CYS Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3V residue 50 LEU Chi-restraints excluded: chain 3V residue 55 LEU Chi-restraints excluded: chain 3V residue 65 VAL 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 24 ILE Chi-restraints excluded: chain 3X residue 1 MET Chi-restraints excluded: chain 3X residue 6 LEU Chi-restraints excluded: chain 3X residue 18 ILE Chi-restraints excluded: chain 3X residue 37 ASP 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 42 LEU Chi-restraints excluded: chain 3Y residue 45 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 201 optimal weight: 6.9990 chunk 380 optimal weight: 6.9990 chunk 326 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 162 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 336 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3E 227 ASN ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3J 38 GLN ** 3J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 9 GLN ** 3N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.077435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.063219 restraints weight = 140016.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.065870 restraints weight = 53747.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.067570 restraints weight = 28779.856| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.388 34365 Z= 0.176 Angle : 0.702 27.237 46532 Z= 0.319 Chirality : 0.042 0.197 5004 Planarity : 0.004 0.098 5834 Dihedral : 12.516 113.057 5322 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.00 % Favored : 94.85 % Rotamer: Outliers : 3.89 % Allowed : 27.70 % Favored : 68.41 % 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: 0.92 (0.14), residues: 4062 helix: 1.93 (0.11), residues: 2048 sheet: -1.66 (0.27), residues: 343 loop : -0.53 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP3C 141 HIS 0.004 0.001 HIS3B 213 PHE 0.031 0.001 PHE3J 36 TYR 0.020 0.001 TYR3Y 47 ARG 0.007 0.000 ARG3A 381 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 1738) hydrogen bonds : angle 4.57967 ( 4984) metal coordination : bond 0.03262 ( 9) metal coordination : angle 15.22497 ( 9) SS BOND : bond 0.00260 ( 5) SS BOND : angle 0.90817 ( 10) covalent geometry : bond 0.00419 (34343) covalent geometry : angle 0.66928 (46513) Misc. bond : bond 0.23652 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 402 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR3N 3 " (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: "VAL3N 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET3N 195 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER3O 55 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 3A 270 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9190 (tp) REVERT: 3A 430 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: 3B 213 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.7565 (m-70) REVERT: 3B 250 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7095 (p0) REVERT: 3B 430 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9006 (mp) REVERT: 3C 19 ILE cc_start: 0.9350 (mm) cc_final: 0.9096 (mm) REVERT: 3C 234 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8182 (t80) REVERT: 3C 373 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8199 (mm-30) REVERT: 3D 293 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7680 (mtm) REVERT: 3F 56 LYS cc_start: 0.8866 (mttp) cc_final: 0.8617 (mtmm) REVERT: 3F 85 GLN cc_start: 0.8493 (mt0) cc_final: 0.8230 (mp10) REVERT: 3H 50 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6849 (tm-30) REVERT: 3I 50 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8254 (pp) REVERT: 3I 77 ARG cc_start: 0.8065 (ttp80) cc_final: 0.6753 (tmm160) REVERT: 3N 226 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7222 (p0) REVERT: 3O 226 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6360 (pp-130) REVERT: 3O 248 ASN cc_start: 0.8385 (t0) cc_final: 0.7880 (t0) REVERT: 3P 108 MET cc_start: 0.8916 (mmp) cc_final: 0.8680 (mmp) REVERT: 3P 235 MET cc_start: 0.9167 (tmm) cc_final: 0.8874 (tmm) REVERT: 3Q 102 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.7434 (mtp85) REVERT: 3Q 212 MET cc_start: 0.8686 (mmt) cc_final: 0.8263 (mmt) REVERT: 3Q 233 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7467 (ptp-170) REVERT: 3R 140 MET cc_start: 0.8285 (mtp) cc_final: 0.8010 (mtp) REVERT: 3R 204 ARG cc_start: 0.7334 (tpp-160) cc_final: 0.7085 (ttm170) REVERT: 3R 231 PHE cc_start: 0.5158 (t80) cc_final: 0.4924 (t80) REVERT: 3S 44 LYS cc_start: 0.8958 (mtmm) cc_final: 0.8657 (mtmm) REVERT: 3U 32 LYS cc_start: 0.9070 (mmtm) cc_final: 0.8721 (mmtm) REVERT: 3V 53 GLU cc_start: 0.8489 (mp0) cc_final: 0.8102 (mp0) REVERT: 3X 6 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7610 (tm) REVERT: 3X 12 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: 3Y 39 ARG cc_start: 0.8455 (mpp-170) cc_final: 0.7914 (tpp80) outliers start: 133 outliers final: 106 residues processed: 490 average time/residue: 0.4534 time to fit residues: 358.9038 Evaluate side-chains 519 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 399 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 58 PHE Chi-restraints excluded: chain 3A residue 61 HIS Chi-restraints excluded: chain 3A residue 99 ILE Chi-restraints excluded: chain 3A residue 138 LEU Chi-restraints excluded: chain 3A residue 149 VAL Chi-restraints excluded: chain 3A residue 196 VAL Chi-restraints excluded: chain 3A residue 255 ILE Chi-restraints excluded: chain 3A residue 257 VAL Chi-restraints excluded: chain 3A residue 270 LEU Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 320 LEU Chi-restraints excluded: chain 3A residue 346 CYS Chi-restraints excluded: chain 3A residue 430 GLN Chi-restraints excluded: chain 3B residue 99 THR Chi-restraints excluded: chain 3B residue 133 ARG Chi-restraints excluded: chain 3B residue 213 HIS Chi-restraints excluded: chain 3B residue 221 GLU Chi-restraints excluded: chain 3B residue 250 ASP Chi-restraints excluded: chain 3B residue 285 VAL Chi-restraints excluded: chain 3B residue 309 VAL Chi-restraints excluded: chain 3B residue 372 VAL Chi-restraints excluded: chain 3B residue 430 LEU Chi-restraints excluded: chain 3B residue 436 VAL Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 40 CYS Chi-restraints excluded: chain 3C residue 43 LEU Chi-restraints excluded: chain 3C residue 68 HIS Chi-restraints excluded: chain 3C residue 78 VAL Chi-restraints excluded: chain 3C residue 110 LEU Chi-restraints excluded: chain 3C residue 146 ILE Chi-restraints excluded: chain 3C residue 149 LEU Chi-restraints excluded: chain 3C residue 164 ILE Chi-restraints excluded: chain 3C residue 192 LEU Chi-restraints excluded: chain 3C residue 212 SER Chi-restraints excluded: chain 3C residue 234 PHE Chi-restraints excluded: chain 3C residue 345 HIS Chi-restraints excluded: chain 3C residue 377 LEU Chi-restraints excluded: chain 3D residue 109 LEU Chi-restraints excluded: chain 3D residue 276 CYS Chi-restraints excluded: chain 3D residue 293 MET Chi-restraints excluded: chain 3D residue 298 LEU Chi-restraints excluded: chain 3E residue 83 ILE Chi-restraints excluded: chain 3E residue 97 LEU Chi-restraints excluded: chain 3E residue 139 SER Chi-restraints excluded: chain 3E residue 205 VAL Chi-restraints excluded: chain 3E residue 216 VAL Chi-restraints excluded: chain 3E residue 220 LEU Chi-restraints excluded: chain 3E residue 238 CYS Chi-restraints excluded: chain 3E residue 239 HIS Chi-restraints excluded: chain 3E residue 262 THR Chi-restraints excluded: chain 3E residue 271 VAL Chi-restraints excluded: chain 3F residue 71 VAL Chi-restraints excluded: chain 3G residue 17 THR Chi-restraints excluded: chain 3G residue 48 LEU Chi-restraints excluded: chain 3H residue 52 ILE Chi-restraints excluded: chain 3H residue 98 LEU Chi-restraints excluded: chain 3H residue 99 PHE Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 42 VAL Chi-restraints excluded: chain 3I residue 50 LEU Chi-restraints excluded: chain 3J residue 6 LEU Chi-restraints excluded: chain 3J residue 13 LEU Chi-restraints excluded: chain 3J residue 23 LEU Chi-restraints excluded: chain 3N residue 3 THR 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 226 ASP Chi-restraints excluded: chain 3N residue 444 LEU Chi-restraints excluded: chain 3O residue 51 ILE Chi-restraints excluded: chain 3O residue 55 SER Chi-restraints excluded: chain 3O residue 123 LEU Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 212 SER Chi-restraints excluded: chain 3O residue 226 MET Chi-restraints excluded: chain 3O residue 303 VAL Chi-restraints excluded: chain 3O residue 309 VAL Chi-restraints excluded: chain 3O residue 347 ILE Chi-restraints excluded: chain 3P residue 6 LYS Chi-restraints excluded: chain 3P residue 112 THR Chi-restraints excluded: chain 3P residue 126 THR Chi-restraints excluded: chain 3P residue 156 ILE Chi-restraints excluded: chain 3P residue 170 VAL Chi-restraints excluded: chain 3P residue 202 GLU Chi-restraints excluded: chain 3P residue 233 LEU Chi-restraints excluded: chain 3P residue 332 LEU Chi-restraints excluded: chain 3Q residue 66 GLU Chi-restraints excluded: chain 3Q residue 102 ARG Chi-restraints excluded: chain 3Q residue 141 VAL Chi-restraints excluded: chain 3Q residue 233 ARG Chi-restraints excluded: chain 3R residue 146 VAL Chi-restraints excluded: chain 3R residue 149 MET Chi-restraints excluded: chain 3R residue 174 LEU Chi-restraints excluded: chain 3R residue 192 VAL Chi-restraints excluded: chain 3R residue 212 ILE Chi-restraints excluded: chain 3R residue 262 THR Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3S residue 18 LYS Chi-restraints excluded: chain 3S residue 42 ASP Chi-restraints excluded: chain 3S residue 81 THR Chi-restraints excluded: chain 3T residue 38 LEU Chi-restraints excluded: chain 3U residue 30 CYS Chi-restraints excluded: chain 3U residue 52 GLU Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3U residue 72 LYS Chi-restraints excluded: chain 3V residue 50 LEU Chi-restraints excluded: chain 3V residue 55 LEU Chi-restraints excluded: chain 3V residue 65 VAL 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 24 ILE Chi-restraints excluded: chain 3X residue 1 MET Chi-restraints excluded: chain 3X residue 6 LEU Chi-restraints excluded: chain 3X residue 12 GLU Chi-restraints excluded: chain 3X residue 18 ILE 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 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 104 optimal weight: 0.0770 chunk 113 optimal weight: 9.9990 chunk 288 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 344 optimal weight: 0.9990 chunk 100 optimal weight: 0.0000 chunk 165 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 193 optimal weight: 0.9990 chunk 359 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 overall best weight: 0.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3E 194 GLN 3E 227 ASN ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3F 65 ASN 3J 38 GLN ** 3J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 9 GLN ** 3N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3Q 105 ASN ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.079802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.065230 restraints weight = 157279.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.068003 restraints weight = 57412.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.069806 restraints weight = 30054.275| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.317 34365 Z= 0.121 Angle : 0.678 24.272 46532 Z= 0.310 Chirality : 0.041 0.208 5004 Planarity : 0.004 0.045 5834 Dihedral : 12.261 95.544 5322 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.73 % Favored : 95.12 % Rotamer: Outliers : 3.37 % Allowed : 27.96 % Favored : 68.67 % 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: 0.99 (0.14), residues: 4062 helix: 1.98 (0.12), residues: 2045 sheet: -1.53 (0.27), residues: 336 loop : -0.50 (0.16), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP3C 141 HIS 0.007 0.001 HIS3E 239 PHE 0.034 0.001 PHE3J 36 TYR 0.021 0.001 TYR3G 61 ARG 0.032 0.000 ARG3Q 144 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 1738) hydrogen bonds : angle 4.50663 ( 4984) metal coordination : bond 0.04038 ( 9) metal coordination : angle 14.33365 ( 9) SS BOND : bond 0.00137 ( 5) SS BOND : angle 0.98189 ( 10) covalent geometry : bond 0.00281 (34343) covalent geometry : angle 0.64819 (46513) Misc. bond : bond 0.18771 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 442 time to evaluate : 3.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR3N 3 " (corrupted residue). Skipping it. 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 11 " (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: "SER3O 55 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 3A 50 GLU cc_start: 0.8326 (tp30) cc_final: 0.7756 (tp30) REVERT: 3A 270 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9149 (tp) REVERT: 3A 430 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7832 (tt0) REVERT: 3B 153 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8022 (mt0) REVERT: 3B 213 HIS cc_start: 0.8304 (OUTLIER) cc_final: 0.7460 (m-70) REVERT: 3B 222 ARG cc_start: 0.8344 (tpp80) cc_final: 0.7864 (ttp80) REVERT: 3B 250 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7308 (p0) REVERT: 3B 430 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8938 (mp) REVERT: 3C 19 ILE cc_start: 0.9361 (mm) cc_final: 0.9111 (mm) REVERT: 3C 234 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.8121 (t80) REVERT: 3C 373 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8150 (mm-30) REVERT: 3D 293 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7359 (mtm) REVERT: 3F 56 LYS cc_start: 0.8854 (mttp) cc_final: 0.8593 (mtmm) REVERT: 3F 72 PHE cc_start: 0.8611 (t80) cc_final: 0.8331 (t80) REVERT: 3F 97 GLU cc_start: 0.8617 (pm20) cc_final: 0.8304 (pm20) REVERT: 3H 50 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6829 (tm-30) REVERT: 3I 50 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8294 (pp) REVERT: 3N 226 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7218 (p0) REVERT: 3O 105 MET cc_start: 0.8882 (mtp) cc_final: 0.8469 (ttp) REVERT: 3O 226 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6594 (pp-130) REVERT: 3O 248 ASN cc_start: 0.8363 (t0) cc_final: 0.7895 (t0) REVERT: 3P 235 MET cc_start: 0.9133 (tmm) cc_final: 0.8874 (tmm) REVERT: 3Q 102 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.7989 (mtp85) REVERT: 3Q 212 MET cc_start: 0.8638 (mmt) cc_final: 0.8224 (mmt) REVERT: 3R 204 ARG cc_start: 0.7250 (tpp-160) cc_final: 0.6981 (ttm170) REVERT: 3R 231 PHE cc_start: 0.5100 (t80) cc_final: 0.4893 (t80) REVERT: 3S 44 LYS cc_start: 0.8930 (mtmm) cc_final: 0.8629 (mtmm) REVERT: 3V 53 GLU cc_start: 0.8406 (mp0) cc_final: 0.8045 (mp0) REVERT: 3X 6 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7537 (tm) REVERT: 3X 12 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8085 (tm-30) REVERT: 3Y 39 ARG cc_start: 0.8257 (mpp-170) cc_final: 0.7836 (tpp80) outliers start: 115 outliers final: 87 residues processed: 515 average time/residue: 0.4535 time to fit residues: 376.5978 Evaluate side-chains 516 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 415 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3A residue 58 PHE Chi-restraints excluded: chain 3A residue 138 LEU Chi-restraints excluded: chain 3A residue 149 VAL Chi-restraints excluded: chain 3A residue 196 VAL Chi-restraints excluded: chain 3A residue 255 ILE Chi-restraints excluded: chain 3A residue 257 VAL Chi-restraints excluded: chain 3A residue 270 LEU Chi-restraints excluded: chain 3A residue 307 PHE Chi-restraints excluded: chain 3A residue 320 LEU Chi-restraints excluded: chain 3A residue 346 CYS Chi-restraints excluded: chain 3A residue 430 GLN Chi-restraints excluded: chain 3B residue 133 ARG Chi-restraints excluded: chain 3B residue 153 GLN Chi-restraints excluded: chain 3B residue 213 HIS Chi-restraints excluded: chain 3B residue 221 GLU Chi-restraints excluded: chain 3B residue 250 ASP Chi-restraints excluded: chain 3B residue 285 VAL Chi-restraints excluded: chain 3B residue 372 VAL Chi-restraints excluded: chain 3B residue 411 ILE Chi-restraints excluded: chain 3B residue 430 LEU Chi-restraints excluded: chain 3C residue 18 PHE Chi-restraints excluded: chain 3C residue 40 CYS Chi-restraints excluded: chain 3C residue 43 LEU Chi-restraints excluded: chain 3C residue 68 HIS Chi-restraints excluded: chain 3C residue 78 VAL Chi-restraints excluded: chain 3C residue 146 ILE Chi-restraints excluded: chain 3C residue 192 LEU Chi-restraints excluded: chain 3C residue 234 PHE Chi-restraints excluded: chain 3C residue 345 HIS Chi-restraints excluded: chain 3C residue 363 LEU Chi-restraints excluded: chain 3C residue 377 LEU Chi-restraints excluded: chain 3D residue 109 LEU Chi-restraints excluded: chain 3D residue 276 CYS Chi-restraints excluded: chain 3D residue 293 MET Chi-restraints excluded: chain 3D residue 298 LEU Chi-restraints excluded: chain 3E residue 83 ILE Chi-restraints excluded: chain 3E residue 205 VAL Chi-restraints excluded: chain 3E residue 238 CYS Chi-restraints excluded: chain 3E residue 239 HIS Chi-restraints excluded: chain 3E residue 271 VAL Chi-restraints excluded: chain 3E residue 272 ILE Chi-restraints excluded: chain 3F residue 71 VAL Chi-restraints excluded: chain 3G residue 48 LEU Chi-restraints excluded: chain 3H residue 52 ILE Chi-restraints excluded: chain 3H residue 98 LEU Chi-restraints excluded: chain 3I residue 34 LEU Chi-restraints excluded: chain 3I residue 42 VAL Chi-restraints excluded: chain 3I residue 50 LEU Chi-restraints excluded: chain 3J residue 6 LEU Chi-restraints excluded: chain 3J residue 13 LEU Chi-restraints excluded: chain 3J residue 23 LEU Chi-restraints excluded: chain 3N residue 3 THR 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 226 ASP Chi-restraints excluded: chain 3N residue 444 LEU Chi-restraints excluded: chain 3O residue 51 ILE Chi-restraints excluded: chain 3O residue 55 SER Chi-restraints excluded: chain 3O residue 123 LEU Chi-restraints excluded: chain 3O residue 187 THR Chi-restraints excluded: chain 3O residue 212 SER Chi-restraints excluded: chain 3O residue 226 MET Chi-restraints excluded: chain 3O residue 303 VAL Chi-restraints excluded: chain 3O residue 309 VAL Chi-restraints excluded: chain 3O residue 347 ILE Chi-restraints excluded: chain 3P residue 6 LYS Chi-restraints excluded: chain 3P residue 112 THR Chi-restraints excluded: chain 3P residue 126 THR Chi-restraints excluded: chain 3P residue 156 ILE Chi-restraints excluded: chain 3P residue 170 VAL Chi-restraints excluded: chain 3P residue 202 GLU Chi-restraints excluded: chain 3P residue 332 LEU Chi-restraints excluded: chain 3Q residue 66 GLU Chi-restraints excluded: chain 3Q residue 102 ARG Chi-restraints excluded: chain 3Q residue 141 VAL Chi-restraints excluded: chain 3R residue 143 SER Chi-restraints excluded: chain 3R residue 212 ILE Chi-restraints excluded: chain 3R residue 262 THR Chi-restraints excluded: chain 3R residue 273 VAL Chi-restraints excluded: chain 3S residue 42 ASP Chi-restraints excluded: chain 3S residue 81 THR Chi-restraints excluded: chain 3T residue 38 LEU Chi-restraints excluded: chain 3T residue 44 CYS Chi-restraints excluded: chain 3U residue 68 CYS Chi-restraints excluded: chain 3V residue 50 LEU Chi-restraints excluded: chain 3V residue 55 LEU Chi-restraints excluded: chain 3V residue 65 VAL 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 4 THR Chi-restraints excluded: chain 3W residue 24 ILE Chi-restraints excluded: chain 3X residue 1 MET Chi-restraints excluded: chain 3X residue 6 LEU Chi-restraints excluded: chain 3X residue 12 GLU Chi-restraints excluded: chain 3X residue 18 ILE 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 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 81 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 174 optimal weight: 0.0470 chunk 304 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 384 optimal weight: 3.9990 chunk 348 optimal weight: 0.7980 chunk 343 optimal weight: 3.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3E 227 ASN ** 3E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3J 38 GLN ** 3J 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3N 9 GLN ** 3N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3P 44 GLN ** 3P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3R 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.079802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.065476 restraints weight = 143802.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.068161 restraints weight = 54329.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.069914 restraints weight = 28890.240| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.407 34365 Z= 0.124 Angle : 0.685 24.581 46532 Z= 0.309 Chirality : 0.041 0.210 5004 Planarity : 0.004 0.044 5834 Dihedral : 12.079 88.730 5322 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.93 % Favored : 94.92 % Rotamer: Outliers : 3.20 % Allowed : 28.28 % Favored : 68.52 % 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: 1.04 (0.14), residues: 4062 helix: 2.03 (0.12), residues: 2042 sheet: -1.44 (0.27), residues: 338 loop : -0.50 (0.16), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP3R 169 HIS 0.004 0.001 HIS3B 277 PHE 0.038 0.001 PHE3J 36 TYR 0.020 0.001 TYR3B 193 ARG 0.012 0.000 ARG3Q 144 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 1738) hydrogen bonds : angle 4.46768 ( 4984) metal coordination : bond 0.03237 ( 9) metal coordination : angle 14.50150 ( 9) SS BOND : bond 0.00132 ( 5) SS BOND : angle 0.83777 ( 10) covalent geometry : bond 0.00288 (34343) covalent geometry : angle 0.65497 (46513) Misc. bond : bond 0.22466 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11939.62 seconds wall clock time: 210 minutes 7.42 seconds (12607.42 seconds total)