Starting phenix.real_space_refine on Thu Jan 16 00:46:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uz1_42830/01_2025/8uz1_42830_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uz1_42830/01_2025/8uz1_42830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uz1_42830/01_2025/8uz1_42830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uz1_42830/01_2025/8uz1_42830.map" model { file = "/net/cci-nas-00/data/ceres_data/8uz1_42830/01_2025/8uz1_42830_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uz1_42830/01_2025/8uz1_42830_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.062 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: 9 Type Number sf(0) Gaussians P 18 5.49 5 Mg 9 5.21 5 S 189 5.16 5 Be 9 3.05 5 C 16668 2.51 5 N 4455 2.21 5 O 5094 1.98 5 F 27 1.80 5 H 25941 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 170 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 52410 Number of models: 1 Model: "" Number of chains: 18 Chain: "J" Number of atoms: 5791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5791 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 5791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5791 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 5792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5792 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 5792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5792 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 5791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5791 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 5792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5792 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 5791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5791 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 5791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5791 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 5791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5791 Classifications: {'peptide': 372} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 19.34, per 1000 atoms: 0.37 Number of scatterers: 52410 At special positions: 0 Unit cell: (94.22, 102.296, 304.196, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) S 189 16.00 P 18 15.00 Mg 9 11.99 F 27 9.00 O 5094 8.00 N 4455 7.00 C 16668 6.00 Be 9 4.00 H 25941 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.68 Conformation dependent library (CDL) restraints added in 3.3 seconds 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6192 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 54 sheets defined 49.2% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'J' and resid 78 through 93 removed outlier: 4.354A pdb=" N LYS J 84 " --> pdb=" O ASP J 80 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU J 93 " --> pdb=" O THR J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 101 Processing helix chain 'J' and resid 112 through 126 removed outlier: 3.597A pdb=" N ARG J 116 " --> pdb=" O PRO J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 144 removed outlier: 3.937A pdb=" N TYR J 143 " --> pdb=" O VAL J 139 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA J 144 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 175 Processing helix chain 'J' and resid 181 through 197 Processing helix chain 'J' and resid 202 through 217 removed outlier: 3.506A pdb=" N GLU J 207 " --> pdb=" O THR J 203 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE J 208 " --> pdb=" O ALA J 204 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS J 217 " --> pdb=" O LYS J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 232 Processing helix chain 'J' and resid 252 through 257 Processing helix chain 'J' and resid 258 through 262 Processing helix chain 'J' and resid 263 through 268 Processing helix chain 'J' and resid 273 through 285 Processing helix chain 'J' and resid 289 through 296 Processing helix chain 'J' and resid 301 through 305 Processing helix chain 'J' and resid 308 through 321 Processing helix chain 'J' and resid 337 through 347 Processing helix chain 'J' and resid 359 through 363 Processing helix chain 'J' and resid 366 through 368 No H-bonds generated for 'chain 'J' and resid 366 through 368' Processing helix chain 'J' and resid 369 through 374 removed outlier: 3.685A pdb=" N LYS J 373 " --> pdb=" O ILE J 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 61 Processing helix chain 'K' and resid 78 through 92 removed outlier: 4.384A pdb=" N LYS K 84 " --> pdb=" O ASP K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 101 Processing helix chain 'K' and resid 112 through 126 removed outlier: 3.658A pdb=" N ARG K 116 " --> pdb=" O PRO K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 146 removed outlier: 3.527A pdb=" N LEU K 142 " --> pdb=" O ALA K 138 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR K 143 " --> pdb=" O VAL K 139 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA K 144 " --> pdb=" O LEU K 140 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER K 145 " --> pdb=" O SER K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 175 removed outlier: 3.674A pdb=" N ILE K 175 " --> pdb=" O PRO K 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 172 through 175' Processing helix chain 'K' and resid 181 through 197 Processing helix chain 'K' and resid 202 through 217 removed outlier: 3.578A pdb=" N GLU K 207 " --> pdb=" O THR K 203 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE K 208 " --> pdb=" O ALA K 204 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS K 217 " --> pdb=" O LYS K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 230 Processing helix chain 'K' and resid 252 through 257 removed outlier: 3.594A pdb=" N CYS K 257 " --> pdb=" O GLU K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 262 Processing helix chain 'K' and resid 263 through 268 Processing helix chain 'K' and resid 273 through 284 Processing helix chain 'K' and resid 286 through 288 No H-bonds generated for 'chain 'K' and resid 286 through 288' Processing helix chain 'K' and resid 289 through 294 Processing helix chain 'K' and resid 301 through 306 removed outlier: 4.356A pdb=" N TYR K 306 " --> pdb=" O THR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 321 Processing helix chain 'K' and resid 334 through 336 No H-bonds generated for 'chain 'K' and resid 334 through 336' Processing helix chain 'K' and resid 337 through 347 Processing helix chain 'K' and resid 351 through 355 removed outlier: 3.829A pdb=" N GLN K 354 " --> pdb=" O THR K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 363 Processing helix chain 'K' and resid 364 through 365 No H-bonds generated for 'chain 'K' and resid 364 through 365' Processing helix chain 'K' and resid 366 through 368 No H-bonds generated for 'chain 'K' and resid 366 through 368' Processing helix chain 'K' and resid 369 through 374 Processing helix chain 'L' and resid 55 through 62 Processing helix chain 'L' and resid 78 through 92 removed outlier: 4.446A pdb=" N LYS L 84 " --> pdb=" O ASP L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 126 removed outlier: 3.645A pdb=" N ARG L 116 " --> pdb=" O PRO L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 146 removed outlier: 3.624A pdb=" N SER L 141 " --> pdb=" O GLN L 137 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU L 142 " --> pdb=" O ALA L 138 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR L 143 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA L 144 " --> pdb=" O LEU L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 175 removed outlier: 3.706A pdb=" N ILE L 175 " --> pdb=" O PRO L 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 172 through 175' Processing helix chain 'L' and resid 181 through 197 removed outlier: 3.775A pdb=" N GLU L 195 " --> pdb=" O LYS L 191 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG L 196 " --> pdb=" O ILE L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 217 removed outlier: 3.848A pdb=" N GLU L 207 " --> pdb=" O THR L 203 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE L 208 " --> pdb=" O ALA L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 222 through 232 removed outlier: 3.539A pdb=" N ALA L 231 " --> pdb=" O MET L 227 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER L 232 " --> pdb=" O ALA L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 257 removed outlier: 3.697A pdb=" N CYS L 257 " --> pdb=" O GLU L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 262 Processing helix chain 'L' and resid 263 through 268 Processing helix chain 'L' and resid 273 through 285 removed outlier: 3.557A pdb=" N CYS L 285 " --> pdb=" O SER L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 289 through 296 Processing helix chain 'L' and resid 301 through 305 Processing helix chain 'L' and resid 308 through 321 Processing helix chain 'L' and resid 337 through 347 Processing helix chain 'L' and resid 350 through 355 removed outlier: 3.687A pdb=" N GLN L 353 " --> pdb=" O SER L 350 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN L 354 " --> pdb=" O THR L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 363 Processing helix chain 'L' and resid 366 through 372 removed outlier: 3.661A pdb=" N HIS L 371 " --> pdb=" O SER L 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 61 Processing helix chain 'M' and resid 78 through 93 removed outlier: 4.385A pdb=" N LYS M 84 " --> pdb=" O ASP M 80 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU M 93 " --> pdb=" O THR M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 126 removed outlier: 3.716A pdb=" N ARG M 116 " --> pdb=" O PRO M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 146 removed outlier: 3.569A pdb=" N LEU M 142 " --> pdb=" O ALA M 138 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR M 143 " --> pdb=" O VAL M 139 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA M 144 " --> pdb=" O LEU M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 175 removed outlier: 3.516A pdb=" N ILE M 175 " --> pdb=" O PRO M 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 172 through 175' Processing helix chain 'M' and resid 181 through 195 removed outlier: 3.583A pdb=" N THR M 194 " --> pdb=" O MET M 190 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU M 195 " --> pdb=" O LYS M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 202 through 217 removed outlier: 3.982A pdb=" N GLU M 207 " --> pdb=" O THR M 203 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE M 208 " --> pdb=" O ALA M 204 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 232 Processing helix chain 'M' and resid 252 through 257 Processing helix chain 'M' and resid 258 through 268 Proline residue: M 264 - end of helix Processing helix chain 'M' and resid 273 through 283 Processing helix chain 'M' and resid 284 through 285 No H-bonds generated for 'chain 'M' and resid 284 through 285' Processing helix chain 'M' and resid 286 through 288 No H-bonds generated for 'chain 'M' and resid 286 through 288' Processing helix chain 'M' and resid 289 through 296 Processing helix chain 'M' and resid 301 through 306 removed outlier: 4.203A pdb=" N TYR M 306 " --> pdb=" O THR M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 321 Processing helix chain 'M' and resid 334 through 336 No H-bonds generated for 'chain 'M' and resid 334 through 336' Processing helix chain 'M' and resid 337 through 347 Processing helix chain 'M' and resid 359 through 363 Processing helix chain 'M' and resid 364 through 365 No H-bonds generated for 'chain 'M' and resid 364 through 365' Processing helix chain 'M' and resid 366 through 368 No H-bonds generated for 'chain 'M' and resid 366 through 368' Processing helix chain 'M' and resid 369 through 374 Processing helix chain 'N' and resid 55 through 61 Processing helix chain 'N' and resid 78 through 92 removed outlier: 4.455A pdb=" N LYS N 84 " --> pdb=" O ASP N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 126 removed outlier: 3.680A pdb=" N ARG N 116 " --> pdb=" O PRO N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 146 removed outlier: 3.736A pdb=" N SER N 141 " --> pdb=" O GLN N 137 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU N 142 " --> pdb=" O ALA N 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR N 143 " --> pdb=" O VAL N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 175 Processing helix chain 'N' and resid 181 through 195 removed outlier: 3.835A pdb=" N THR N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU N 195 " --> pdb=" O LYS N 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 202 through 217 removed outlier: 3.953A pdb=" N GLU N 207 " --> pdb=" O THR N 203 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE N 208 " --> pdb=" O ALA N 204 " (cutoff:3.500A) Processing helix chain 'N' and resid 222 through 232 Processing helix chain 'N' and resid 251 through 255 Processing helix chain 'N' and resid 257 through 262 Processing helix chain 'N' and resid 263 through 268 Processing helix chain 'N' and resid 273 through 285 Processing helix chain 'N' and resid 286 through 288 No H-bonds generated for 'chain 'N' and resid 286 through 288' Processing helix chain 'N' and resid 289 through 296 Processing helix chain 'N' and resid 301 through 306 removed outlier: 3.964A pdb=" N TYR N 306 " --> pdb=" O THR N 303 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 321 Processing helix chain 'N' and resid 337 through 347 Processing helix chain 'N' and resid 351 through 355 removed outlier: 4.024A pdb=" N GLN N 354 " --> pdb=" O THR N 351 " (cutoff:3.500A) Processing helix chain 'N' and resid 359 through 363 Processing helix chain 'N' and resid 366 through 368 No H-bonds generated for 'chain 'N' and resid 366 through 368' Processing helix chain 'N' and resid 369 through 374 removed outlier: 3.504A pdb=" N LYS N 373 " --> pdb=" O ILE N 369 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 61 Processing helix chain 'O' and resid 78 through 92 removed outlier: 4.365A pdb=" N LYS O 84 " --> pdb=" O ASP O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 126 removed outlier: 3.671A pdb=" N ARG O 116 " --> pdb=" O PRO O 112 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET O 123 " --> pdb=" O MET O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 146 removed outlier: 3.524A pdb=" N SER O 141 " --> pdb=" O GLN O 137 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU O 142 " --> pdb=" O ALA O 138 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR O 143 " --> pdb=" O VAL O 139 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA O 144 " --> pdb=" O LEU O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 194 removed outlier: 3.651A pdb=" N LYS O 191 " --> pdb=" O ASP O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 197 No H-bonds generated for 'chain 'O' and resid 195 through 197' Processing helix chain 'O' and resid 204 through 217 removed outlier: 3.662A pdb=" N ILE O 208 " --> pdb=" O ALA O 204 " (cutoff:3.500A) Processing helix chain 'O' and resid 222 through 230 Processing helix chain 'O' and resid 251 through 255 Processing helix chain 'O' and resid 257 through 262 Processing helix chain 'O' and resid 263 through 268 Processing helix chain 'O' and resid 273 through 284 Processing helix chain 'O' and resid 285 through 288 removed outlier: 6.061A pdb=" N ASP O 288 " --> pdb=" O CYS O 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 285 through 288' Processing helix chain 'O' and resid 289 through 295 Processing helix chain 'O' and resid 301 through 305 Processing helix chain 'O' and resid 308 through 321 Processing helix chain 'O' and resid 337 through 347 Processing helix chain 'O' and resid 359 through 363 Processing helix chain 'O' and resid 364 through 365 No H-bonds generated for 'chain 'O' and resid 364 through 365' Processing helix chain 'O' and resid 366 through 368 No H-bonds generated for 'chain 'O' and resid 366 through 368' Processing helix chain 'O' and resid 369 through 374 removed outlier: 3.586A pdb=" N CYS O 374 " --> pdb=" O VAL O 370 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 61 Processing helix chain 'P' and resid 78 through 92 removed outlier: 4.473A pdb=" N LYS P 84 " --> pdb=" O ASP P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 126 removed outlier: 3.776A pdb=" N ARG P 116 " --> pdb=" O PRO P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 146 removed outlier: 3.575A pdb=" N LEU P 142 " --> pdb=" O ALA P 138 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR P 143 " --> pdb=" O VAL P 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 175 Processing helix chain 'P' and resid 181 through 195 removed outlier: 3.890A pdb=" N GLU P 195 " --> pdb=" O LYS P 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 204 through 217 removed outlier: 3.900A pdb=" N ILE P 208 " --> pdb=" O ALA P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 230 Processing helix chain 'P' and resid 251 through 255 Processing helix chain 'P' and resid 257 through 262 Processing helix chain 'P' and resid 263 through 268 Processing helix chain 'P' and resid 273 through 284 Processing helix chain 'P' and resid 286 through 288 No H-bonds generated for 'chain 'P' and resid 286 through 288' Processing helix chain 'P' and resid 289 through 296 removed outlier: 3.670A pdb=" N ALA P 295 " --> pdb=" O LYS P 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 306 removed outlier: 4.124A pdb=" N TYR P 306 " --> pdb=" O THR P 303 " (cutoff:3.500A) Processing helix chain 'P' and resid 308 through 321 Processing helix chain 'P' and resid 334 through 336 No H-bonds generated for 'chain 'P' and resid 334 through 336' Processing helix chain 'P' and resid 337 through 347 Processing helix chain 'P' and resid 348 through 353 removed outlier: 6.111A pdb=" N THR P 351 " --> pdb=" O SER P 348 " (cutoff:3.500A) Processing helix chain 'P' and resid 359 through 363 Processing helix chain 'P' and resid 366 through 368 No H-bonds generated for 'chain 'P' and resid 366 through 368' Processing helix chain 'P' and resid 369 through 374 Processing helix chain 'Q' and resid 55 through 61 Processing helix chain 'Q' and resid 78 through 92 removed outlier: 4.676A pdb=" N LYS Q 84 " --> pdb=" O ASP Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 97 through 101 Processing helix chain 'Q' and resid 112 through 126 removed outlier: 3.595A pdb=" N ARG Q 116 " --> pdb=" O PRO Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 146 removed outlier: 3.571A pdb=" N LEU Q 142 " --> pdb=" O ALA Q 138 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR Q 143 " --> pdb=" O VAL Q 139 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA Q 144 " --> pdb=" O LEU Q 140 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER Q 145 " --> pdb=" O SER Q 141 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 175 Processing helix chain 'Q' and resid 181 through 196 removed outlier: 3.886A pdb=" N GLU Q 195 " --> pdb=" O LYS Q 191 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG Q 196 " --> pdb=" O ILE Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 202 through 217 removed outlier: 3.848A pdb=" N GLU Q 207 " --> pdb=" O THR Q 203 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE Q 208 " --> pdb=" O ALA Q 204 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 232 Processing helix chain 'Q' and resid 251 through 255 Processing helix chain 'Q' and resid 257 through 262 Processing helix chain 'Q' and resid 263 through 268 Processing helix chain 'Q' and resid 273 through 284 Processing helix chain 'Q' and resid 289 through 294 Processing helix chain 'Q' and resid 301 through 306 removed outlier: 4.276A pdb=" N TYR Q 306 " --> pdb=" O THR Q 303 " (cutoff:3.500A) Processing helix chain 'Q' and resid 308 through 321 Processing helix chain 'Q' and resid 334 through 336 No H-bonds generated for 'chain 'Q' and resid 334 through 336' Processing helix chain 'Q' and resid 337 through 347 Processing helix chain 'Q' and resid 351 through 355 removed outlier: 4.112A pdb=" N GLN Q 354 " --> pdb=" O THR Q 351 " (cutoff:3.500A) Processing helix chain 'Q' and resid 359 through 363 Processing helix chain 'Q' and resid 364 through 365 No H-bonds generated for 'chain 'Q' and resid 364 through 365' Processing helix chain 'Q' and resid 366 through 368 No H-bonds generated for 'chain 'Q' and resid 366 through 368' Processing helix chain 'Q' and resid 369 through 374 Processing helix chain 'R' and resid 55 through 61 Processing helix chain 'R' and resid 78 through 92 removed outlier: 4.344A pdb=" N LYS R 84 " --> pdb=" O ASP R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 126 removed outlier: 3.607A pdb=" N ARG R 116 " --> pdb=" O PRO R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 146 removed outlier: 3.958A pdb=" N SER R 141 " --> pdb=" O GLN R 137 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 175 Processing helix chain 'R' and resid 181 through 195 removed outlier: 3.743A pdb=" N THR R 194 " --> pdb=" O MET R 190 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU R 195 " --> pdb=" O LYS R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 217 removed outlier: 4.011A pdb=" N GLU R 207 " --> pdb=" O THR R 203 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE R 208 " --> pdb=" O ALA R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 230 Processing helix chain 'R' and resid 252 through 257 Processing helix chain 'R' and resid 258 through 262 Processing helix chain 'R' and resid 263 through 268 Processing helix chain 'R' and resid 273 through 284 Processing helix chain 'R' and resid 286 through 294 removed outlier: 3.623A pdb=" N ARG R 290 " --> pdb=" O ASP R 286 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS R 291 " --> pdb=" O ILE R 287 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP R 292 " --> pdb=" O ASP R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 306 removed outlier: 4.299A pdb=" N TYR R 306 " --> pdb=" O THR R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 321 Processing helix chain 'R' and resid 332 through 336 removed outlier: 4.501A pdb=" N LYS R 336 " --> pdb=" O PRO R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 347 Processing helix chain 'R' and resid 359 through 363 Processing helix chain 'R' and resid 366 through 368 No H-bonds generated for 'chain 'R' and resid 366 through 368' Processing helix chain 'R' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'J' and resid 29 through 32 removed outlier: 3.682A pdb=" N THR J 106 " --> pdb=" O CYS J 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'J' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'J' and resid 176 through 178 Processing sheet with id=AA5, first strand: chain 'J' and resid 176 through 178 removed outlier: 3.834A pdb=" N GLN L 41 " --> pdb=" O ALA J 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'K' and resid 29 through 31 removed outlier: 6.663A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N CYS K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR K 133 " --> pdb=" O THR K 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'K' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'K' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'K' and resid 169 through 170 removed outlier: 6.393A pdb=" N ASN K 297 " --> pdb=" O ILE K 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'L' and resid 29 through 33 removed outlier: 4.373A pdb=" N GLY L 15 " --> pdb=" O SER L 33 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU L 8 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N THR L 106 " --> pdb=" O LEU L 8 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N CYS L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA L 135 " --> pdb=" O LEU L 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'L' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'L' and resid 176 through 178 Processing sheet with id=AB8, first strand: chain 'L' and resid 165 through 166 removed outlier: 3.897A pdb=" N GLN N 41 " --> pdb=" O ALA L 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.924A pdb=" N LEU M 8 " --> pdb=" O LEU M 104 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N THR M 106 " --> pdb=" O LEU M 8 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N CYS M 10 " --> pdb=" O THR M 106 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA M 135 " --> pdb=" O LEU M 105 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'M' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'M' and resid 176 through 178 removed outlier: 6.520A pdb=" N ASN M 297 " --> pdb=" O ILE M 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 176 through 178 removed outlier: 3.768A pdb=" N GLN O 41 " --> pdb=" O ALA M 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.784A pdb=" N LEU N 8 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N THR N 106 " --> pdb=" O LEU N 8 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N CYS N 10 " --> pdb=" O THR N 106 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA N 135 " --> pdb=" O LEU N 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'N' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'N' and resid 176 through 178 removed outlier: 3.599A pdb=" N VAL N 163 " --> pdb=" O VAL N 152 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL N 152 " --> pdb=" O VAL N 163 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 176 through 178 removed outlier: 3.756A pdb=" N GLN P 41 " --> pdb=" O ALA N 170 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'O' and resid 29 through 32 removed outlier: 6.841A pdb=" N LEU O 8 " --> pdb=" O LEU O 104 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR O 106 " --> pdb=" O LEU O 8 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS O 10 " --> pdb=" O THR O 106 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA O 135 " --> pdb=" O LEU O 105 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'O' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'O' and resid 176 through 178 Processing sheet with id=AD8, first strand: chain 'O' and resid 165 through 166 Processing sheet with id=AD9, first strand: chain 'O' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'P' and resid 29 through 31 removed outlier: 6.717A pdb=" N LEU P 8 " --> pdb=" O LEU P 104 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N THR P 106 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N CYS P 10 " --> pdb=" O THR P 106 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA P 135 " --> pdb=" O LEU P 105 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'P' and resid 71 through 72 Processing sheet with id=AE4, first strand: chain 'P' and resid 176 through 178 removed outlier: 3.562A pdb=" N VAL P 152 " --> pdb=" O VAL P 163 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 176 through 178 removed outlier: 3.996A pdb=" N GLN R 41 " --> pdb=" O ALA P 170 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 238 through 241 Processing sheet with id=AE7, first strand: chain 'Q' and resid 29 through 32 removed outlier: 6.693A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N THR Q 106 " --> pdb=" O LEU Q 8 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N CYS Q 10 " --> pdb=" O THR Q 106 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 53 through 54 Processing sheet with id=AE9, first strand: chain 'Q' and resid 71 through 72 Processing sheet with id=AF1, first strand: chain 'Q' and resid 169 through 170 Processing sheet with id=AF2, first strand: chain 'Q' and resid 169 through 170 Processing sheet with id=AF3, first strand: chain 'Q' and resid 238 through 241 Processing sheet with id=AF4, first strand: chain 'R' and resid 29 through 32 removed outlier: 4.040A pdb=" N THR R 106 " --> pdb=" O CYS R 10 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 53 through 54 Processing sheet with id=AF6, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AF7, first strand: chain 'R' and resid 169 through 170 Processing sheet with id=AF8, first strand: chain 'R' and resid 169 through 170 removed outlier: 6.392A pdb=" N ASN R 297 " --> pdb=" O ILE R 330 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 238 through 241 1244 hydrogen bonds defined for protein. 3105 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: 20.77 Time building geometry restraints manager: 12.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 25896 1.12 - 1.30: 4562 1.30 - 1.47: 10064 1.47 - 1.64: 12122 1.64 - 1.82: 333 Bond restraints: 52977 Sorted by residual: bond pdb=" N ILE J 212 " pdb=" H ILE J 212 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N VAL J 209 " pdb=" H VAL J 209 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ALA O 365 " pdb=" H ALA O 365 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NE ARG J 312 " pdb=" HE ARG J 312 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASP L 288 " pdb=" H ASP L 288 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 52972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 88156 3.69 - 7.38: 7309 7.38 - 11.07: 199 11.07 - 14.76: 55 14.76 - 18.45: 29 Bond angle restraints: 95748 Sorted by residual: angle pdb=" CA ASP N 80 " pdb=" CB ASP N 80 " pdb=" CG ASP N 80 " ideal model delta sigma weight residual 112.60 119.54 -6.94 1.00e+00 1.00e+00 4.81e+01 angle pdb=" CA ASP Q 244 " pdb=" CB ASP Q 244 " pdb=" CG ASP Q 244 " ideal model delta sigma weight residual 112.60 118.99 -6.39 1.00e+00 1.00e+00 4.08e+01 angle pdb=" CA ASP M 244 " pdb=" CB ASP M 244 " pdb=" CG ASP M 244 " ideal model delta sigma weight residual 112.60 118.97 -6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" CA ASP L 244 " pdb=" CB ASP L 244 " pdb=" CG ASP L 244 " ideal model delta sigma weight residual 112.60 118.84 -6.24 1.00e+00 1.00e+00 3.90e+01 angle pdb=" CA ASP N 244 " pdb=" CB ASP N 244 " pdb=" CG ASP N 244 " ideal model delta sigma weight residual 112.60 118.78 -6.18 1.00e+00 1.00e+00 3.82e+01 ... (remaining 95743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.95: 23571 27.95 - 55.89: 1065 55.89 - 83.84: 284 83.84 - 111.78: 15 111.78 - 139.73: 25 Dihedral angle restraints: 24960 sinusoidal: 13734 harmonic: 11226 Sorted by residual: dihedral pdb=" C GLU M 93 " pdb=" N GLU M 93 " pdb=" CA GLU M 93 " pdb=" CB GLU M 93 " ideal model delta harmonic sigma weight residual -122.60 -141.76 19.16 0 2.50e+00 1.60e-01 5.88e+01 dihedral pdb=" N GLU M 93 " pdb=" C GLU M 93 " pdb=" CA GLU M 93 " pdb=" CB GLU M 93 " ideal model delta harmonic sigma weight residual 122.80 140.48 -17.68 0 2.50e+00 1.60e-01 5.00e+01 dihedral pdb=" C GLU P 93 " pdb=" N GLU P 93 " pdb=" CA GLU P 93 " pdb=" CB GLU P 93 " ideal model delta harmonic sigma weight residual -122.60 -140.02 17.42 0 2.50e+00 1.60e-01 4.86e+01 ... (remaining 24957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 3578 0.153 - 0.306: 443 0.306 - 0.460: 34 0.460 - 0.613: 11 0.613 - 0.766: 2 Chirality restraints: 4068 Sorted by residual: chirality pdb=" CA GLU M 93 " pdb=" N GLU M 93 " pdb=" C GLU M 93 " pdb=" CB GLU M 93 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" CA GLU P 93 " pdb=" N GLU P 93 " pdb=" C GLU P 93 " pdb=" CB GLU P 93 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA GLU O 93 " pdb=" N GLU O 93 " pdb=" C GLU O 93 " pdb=" CB GLU O 93 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.22e+00 ... (remaining 4065 not shown) Planarity restraints: 7857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP P 340 " 0.244 2.00e-02 2.50e+03 9.46e-02 3.58e+02 pdb=" CG TRP P 340 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP P 340 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP P 340 " -0.089 2.00e-02 2.50e+03 pdb=" NE1 TRP P 340 " -0.109 2.00e-02 2.50e+03 pdb=" CE2 TRP P 340 " -0.084 2.00e-02 2.50e+03 pdb=" CE3 TRP P 340 " -0.093 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 340 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 340 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP P 340 " 0.051 2.00e-02 2.50e+03 pdb=" HD1 TRP P 340 " 0.066 2.00e-02 2.50e+03 pdb=" HE1 TRP P 340 " 0.008 2.00e-02 2.50e+03 pdb=" HE3 TRP P 340 " -0.128 2.00e-02 2.50e+03 pdb=" HZ2 TRP P 340 " 0.033 2.00e-02 2.50e+03 pdb=" HZ3 TRP P 340 " 0.034 2.00e-02 2.50e+03 pdb=" HH2 TRP P 340 " 0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 340 " 0.252 2.00e-02 2.50e+03 9.08e-02 3.30e+02 pdb=" CG TRP J 340 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP J 340 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP J 340 " -0.086 2.00e-02 2.50e+03 pdb=" NE1 TRP J 340 " -0.099 2.00e-02 2.50e+03 pdb=" CE2 TRP J 340 " -0.069 2.00e-02 2.50e+03 pdb=" CE3 TRP J 340 " -0.088 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 340 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 340 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP J 340 " 0.037 2.00e-02 2.50e+03 pdb=" HD1 TRP J 340 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TRP J 340 " -0.009 2.00e-02 2.50e+03 pdb=" HE3 TRP J 340 " -0.119 2.00e-02 2.50e+03 pdb=" HZ2 TRP J 340 " 0.067 2.00e-02 2.50e+03 pdb=" HZ3 TRP J 340 " 0.029 2.00e-02 2.50e+03 pdb=" HH2 TRP J 340 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 62 " 0.055 9.50e-02 1.11e+02 1.19e-01 3.11e+02 pdb=" NE ARG R 62 " 0.110 2.00e-02 2.50e+03 pdb=" CZ ARG R 62 " 0.097 2.00e-02 2.50e+03 pdb=" NH1 ARG R 62 " 0.063 2.00e-02 2.50e+03 pdb=" NH2 ARG R 62 " 0.073 2.00e-02 2.50e+03 pdb="HH11 ARG R 62 " -0.205 2.00e-02 2.50e+03 pdb="HH12 ARG R 62 " 0.034 2.00e-02 2.50e+03 pdb="HH21 ARG R 62 " -0.219 2.00e-02 2.50e+03 pdb="HH22 ARG R 62 " 0.045 2.00e-02 2.50e+03 ... (remaining 7854 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 1403 2.01 - 2.66: 62197 2.66 - 3.30: 160882 3.30 - 3.95: 208035 3.95 - 4.60: 317146 Nonbonded interactions: 749663 Sorted by model distance: nonbonded pdb=" HE2 HIS M 173 " pdb=" HE2 HIS O 40 " model vdw 1.360 2.100 nonbonded pdb=" HE2 HIS O 173 " pdb=" HE2 HIS Q 40 " model vdw 1.483 2.100 nonbonded pdb=" OE2 GLU N 270 " pdb=" HG1 THR O 66 " model vdw 1.600 2.450 nonbonded pdb=" OE2 GLU O 270 " pdb=" HG1 THR P 66 " model vdw 1.603 2.450 nonbonded pdb=" HH TYR M 69 " pdb=" OE2 GLU M 207 " model vdw 1.609 2.450 ... (remaining 749658 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: 0.03 Found NCS groups: ncs_group { reference = chain 'J' selection = chain 'K' selection = (chain 'L' and (resid 4 through 172 or (resid 173 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 174 through 375 or resid 401 through 403)) selection = (chain 'M' and (resid 4 through 172 or (resid 173 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 174 through 375 or resid 401 through 403)) selection = chain 'N' selection = (chain 'O' and (resid 4 through 172 or (resid 173 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 174 through 375 or resid 401 through 403)) selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.210 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: 0.690 Extract box with map and model: 1.480 Check model and map are aligned: 0.290 Set scattering table: 0.360 Process input model: 88.590 Find NCS groups from input model: 1.510 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:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.012 0.143 27036 Z= 0.810 Angle : 1.908 18.446 36684 Z= 1.211 Chirality : 0.106 0.766 4068 Planarity : 0.014 0.116 4689 Dihedral : 15.162 139.725 10053 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 0.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.87 % Favored : 94.91 % Rotamer: Outliers : 1.34 % Allowed : 5.13 % Favored : 93.52 % Cbeta Deviations : 0.97 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3303 helix: -1.94 (0.12), residues: 1341 sheet: -0.13 (0.24), residues: 360 loop : -0.55 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.169 0.033 TRP J 340 HIS 0.011 0.004 HIS L 101 PHE 0.068 0.010 PHE L 31 TYR 0.098 0.016 TYR L 53 ARG 0.015 0.001 ARG M 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 498 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 82 MET cc_start: 0.8256 (tpt) cc_final: 0.7858 (tpt) REVERT: J 137 GLN cc_start: 0.7550 (mt0) cc_final: 0.7347 (mt0) REVERT: J 176 MET cc_start: 0.7982 (mmm) cc_final: 0.7770 (mmt) REVERT: L 244 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7387 (p0) REVERT: M 82 MET cc_start: 0.9287 (tpt) cc_final: 0.8873 (tpt) REVERT: M 157 ASP cc_start: 0.8483 (t70) cc_final: 0.8154 (t0) REVERT: M 176 MET cc_start: 0.8814 (mmt) cc_final: 0.8494 (mmt) REVERT: N 47 MET cc_start: 0.5402 (ttp) cc_final: 0.5184 (ttt) REVERT: N 82 MET cc_start: 0.8888 (tpt) cc_final: 0.8670 (tpt) REVERT: N 190 MET cc_start: 0.8384 (mtm) cc_final: 0.7889 (mtm) REVERT: N 227 MET cc_start: 0.8893 (mmm) cc_final: 0.8653 (mmm) REVERT: O 82 MET cc_start: 0.9049 (tpt) cc_final: 0.8259 (tpt) REVERT: O 123 MET cc_start: 0.8201 (tpp) cc_final: 0.7988 (mmt) REVERT: O 244 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7991 (p0) REVERT: O 269 MET cc_start: 0.8234 (ptp) cc_final: 0.7965 (ptm) REVERT: O 283 MET cc_start: 0.8618 (mmt) cc_final: 0.8361 (mmm) REVERT: P 93 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6767 (pm20) REVERT: P 132 MET cc_start: 0.8767 (ptm) cc_final: 0.8558 (ppp) REVERT: P 176 MET cc_start: 0.8846 (mmt) cc_final: 0.8546 (mmt) REVERT: P 227 MET cc_start: 0.8939 (mmm) cc_final: 0.8521 (mmm) REVERT: P 374 CYS cc_start: 0.7936 (m) cc_final: 0.7599 (m) REVERT: Q 82 MET cc_start: 0.9028 (tpt) cc_final: 0.8827 (tpt) REVERT: Q 244 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.7916 (p0) REVERT: Q 291 LYS cc_start: 0.6249 (mmtt) cc_final: 0.5442 (mptt) REVERT: R 41 GLN cc_start: 0.7870 (tt0) cc_final: 0.7552 (tt0) REVERT: R 330 ILE cc_start: 0.9272 (tp) cc_final: 0.9005 (mt) outliers start: 38 outliers final: 15 residues processed: 531 average time/residue: 0.6727 time to fit residues: 582.9690 Evaluate side-chains 327 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 308 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain N residue 93 GLU Chi-restraints excluded: chain N residue 244 ASP Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 278 THR Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 93 GLU Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 244 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 0.9980 chunk 252 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 170 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 302 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 162 ASN N 162 ASN ** O 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.109153 restraints weight = 112176.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.113370 restraints weight = 39720.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.115635 restraints weight = 18535.825| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27036 Z= 0.207 Angle : 0.695 7.114 36684 Z= 0.352 Chirality : 0.046 0.170 4068 Planarity : 0.004 0.059 4689 Dihedral : 11.848 136.739 3797 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.59 % Allowed : 7.78 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.14), residues: 3303 helix: -0.81 (0.13), residues: 1377 sheet: -0.53 (0.21), residues: 558 loop : 0.25 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 356 HIS 0.004 0.001 HIS L 275 PHE 0.012 0.002 PHE L 31 TYR 0.013 0.001 TYR J 294 ARG 0.003 0.001 ARG P 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 357 time to evaluate : 3.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 82 MET cc_start: 0.7962 (tpt) cc_final: 0.7448 (tpt) REVERT: J 123 MET cc_start: 0.8581 (tpp) cc_final: 0.8336 (tpp) REVERT: J 137 GLN cc_start: 0.6276 (mt0) cc_final: 0.5920 (mt0) REVERT: J 238 LYS cc_start: 0.8183 (mmmm) cc_final: 0.7868 (mptt) REVERT: J 354 GLN cc_start: 0.8576 (mm110) cc_final: 0.8290 (tp-100) REVERT: K 76 ILE cc_start: 0.9416 (mt) cc_final: 0.9122 (mt) REVERT: K 244 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8357 (p0) REVERT: L 80 ASP cc_start: 0.7428 (m-30) cc_final: 0.7186 (t0) REVERT: L 241 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7634 (mm-30) REVERT: L 328 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8460 (ttpt) REVERT: M 82 MET cc_start: 0.9146 (tpt) cc_final: 0.8617 (tpt) REVERT: M 93 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7117 (pm20) REVERT: M 111 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.8727 (t0) REVERT: M 157 ASP cc_start: 0.8426 (t70) cc_final: 0.8140 (t0) REVERT: N 80 ASP cc_start: 0.7604 (m-30) cc_final: 0.6851 (t0) REVERT: N 123 MET cc_start: 0.9156 (tpp) cc_final: 0.8825 (mmm) REVERT: N 159 VAL cc_start: 0.8941 (p) cc_final: 0.8669 (m) REVERT: N 190 MET cc_start: 0.7485 (mtm) cc_final: 0.6968 (mtp) REVERT: N 227 MET cc_start: 0.8377 (mmm) cc_final: 0.8129 (mmm) REVERT: O 82 MET cc_start: 0.8782 (tpt) cc_final: 0.7894 (tpt) REVERT: O 121 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7511 (tm-30) REVERT: O 123 MET cc_start: 0.8278 (tpp) cc_final: 0.8054 (mmt) REVERT: O 215 LYS cc_start: 0.8654 (mmtp) cc_final: 0.8358 (mptt) REVERT: O 244 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8580 (p0) REVERT: O 269 MET cc_start: 0.8110 (ptp) cc_final: 0.7907 (ptm) REVERT: P 119 MET cc_start: 0.8480 (ttm) cc_final: 0.8236 (ttp) REVERT: P 132 MET cc_start: 0.8616 (ptm) cc_final: 0.8341 (ppp) REVERT: P 176 MET cc_start: 0.8574 (mmt) cc_final: 0.8298 (mmt) REVERT: P 227 MET cc_start: 0.8504 (mmm) cc_final: 0.7928 (mmm) REVERT: P 374 CYS cc_start: 0.7813 (m) cc_final: 0.7511 (m) REVERT: Q 16 LEU cc_start: 0.8377 (tp) cc_final: 0.8160 (tp) REVERT: Q 82 MET cc_start: 0.8763 (tpt) cc_final: 0.8315 (tpt) REVERT: Q 93 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6100 (pm20) REVERT: Q 123 MET cc_start: 0.8899 (tpp) cc_final: 0.8638 (mmm) REVERT: Q 291 LYS cc_start: 0.4616 (mmtt) cc_final: 0.4061 (mmtm) REVERT: R 81 ASP cc_start: 0.8055 (m-30) cc_final: 0.7845 (m-30) REVERT: R 270 GLU cc_start: 0.6252 (mp0) cc_final: 0.5947 (mp0) REVERT: R 283 MET cc_start: 0.8535 (mmt) cc_final: 0.8261 (tpp) REVERT: R 330 ILE cc_start: 0.8639 (tp) cc_final: 0.8372 (mt) outliers start: 45 outliers final: 20 residues processed: 391 average time/residue: 0.6619 time to fit residues: 439.7023 Evaluate side-chains 312 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 286 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 237 GLU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 328 LYS Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 111 ASN Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 244 ASP Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 85 ILE Chi-restraints excluded: chain Q residue 93 GLU Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 205 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 168 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 319 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 316 optimal weight: 3.9990 chunk 307 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: K 137 GLN K 246 GLN L 137 GLN N 40 HIS N 137 GLN O 92 ASN Q 12 ASN Q 137 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109594 restraints weight = 117177.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.113826 restraints weight = 41603.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116165 restraints weight = 19699.505| |-----------------------------------------------------------------------------| r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 27036 Z= 0.376 Angle : 0.687 7.009 36684 Z= 0.348 Chirality : 0.047 0.174 4068 Planarity : 0.004 0.038 4689 Dihedral : 10.973 137.260 3780 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.77 % Allowed : 10.19 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3303 helix: -0.60 (0.13), residues: 1431 sheet: -0.53 (0.22), residues: 558 loop : 0.07 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 356 HIS 0.003 0.001 HIS L 161 PHE 0.014 0.002 PHE L 31 TYR 0.013 0.001 TYR N 294 ARG 0.004 0.001 ARG P 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 290 time to evaluate : 3.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 82 MET cc_start: 0.8006 (tpt) cc_final: 0.7602 (tpt) REVERT: J 238 LYS cc_start: 0.8100 (mmmm) cc_final: 0.7741 (mptt) REVERT: J 311 ASP cc_start: 0.8578 (m-30) cc_final: 0.8265 (t0) REVERT: J 354 GLN cc_start: 0.8579 (mm110) cc_final: 0.8300 (tp-100) REVERT: J 360 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7331 (tm-30) REVERT: K 80 ASP cc_start: 0.8243 (m-30) cc_final: 0.7799 (t0) REVERT: K 137 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7471 (mt0) REVERT: K 244 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8132 (p0) REVERT: L 80 ASP cc_start: 0.7563 (m-30) cc_final: 0.7285 (t0) REVERT: L 137 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7833 (mt0) REVERT: L 328 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8570 (ttpt) REVERT: M 93 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: N 121 GLN cc_start: 0.8298 (tt0) cc_final: 0.8008 (tt0) REVERT: N 159 VAL cc_start: 0.9118 (p) cc_final: 0.8842 (m) REVERT: N 190 MET cc_start: 0.7802 (mtm) cc_final: 0.7423 (mtp) REVERT: N 227 MET cc_start: 0.8436 (mmm) cc_final: 0.8211 (mmm) REVERT: N 244 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7328 (p0) REVERT: N 374 CYS cc_start: 0.6754 (m) cc_final: 0.6449 (m) REVERT: O 41 GLN cc_start: 0.7386 (tt0) cc_final: 0.6948 (tt0) REVERT: O 82 MET cc_start: 0.8825 (tpt) cc_final: 0.8074 (tpt) REVERT: O 215 LYS cc_start: 0.8704 (mmtp) cc_final: 0.8235 (mttp) REVERT: O 269 MET cc_start: 0.8149 (ptp) cc_final: 0.7936 (ptm) REVERT: P 54 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8684 (m) REVERT: P 93 GLU cc_start: 0.7512 (pm20) cc_final: 0.6904 (pt0) REVERT: P 132 MET cc_start: 0.8669 (ptm) cc_final: 0.8259 (ppp) REVERT: P 176 MET cc_start: 0.8653 (mmt) cc_final: 0.8427 (mmt) REVERT: P 227 MET cc_start: 0.8422 (mmm) cc_final: 0.8000 (mmm) REVERT: P 360 GLN cc_start: 0.8792 (tp40) cc_final: 0.8344 (tm-30) REVERT: P 374 CYS cc_start: 0.7683 (m) cc_final: 0.7366 (m) REVERT: Q 82 MET cc_start: 0.8779 (tpt) cc_final: 0.8396 (tpt) REVERT: Q 93 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6833 (pm20) REVERT: Q 123 MET cc_start: 0.8989 (tpp) cc_final: 0.8364 (mmt) REVERT: Q 244 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8067 (p0) REVERT: R 283 MET cc_start: 0.8567 (mmt) cc_final: 0.8338 (tpp) REVERT: R 328 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8093 (ttpp) REVERT: R 330 ILE cc_start: 0.8648 (tp) cc_final: 0.8358 (mt) outliers start: 50 outliers final: 34 residues processed: 333 average time/residue: 0.6223 time to fit residues: 346.0647 Evaluate side-chains 316 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 137 GLN Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 237 GLU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 325 MET Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 137 GLN Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 328 LYS Chi-restraints excluded: chain L residue 344 SER Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 244 ASP Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 271 SER Chi-restraints excluded: chain O residue 278 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 93 GLU Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 328 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 1 optimal weight: 7.9990 chunk 210 optimal weight: 1.9990 chunk 322 optimal weight: 0.0370 chunk 298 optimal weight: 0.4980 chunk 206 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 231 optimal weight: 0.8980 chunk 319 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 41 GLN Q 12 ASN R 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.107800 restraints weight = 112606.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.112057 restraints weight = 39563.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.114362 restraints weight = 18419.361| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 27036 Z= 0.146 Angle : 0.582 6.676 36684 Z= 0.281 Chirality : 0.043 0.164 4068 Planarity : 0.003 0.045 4689 Dihedral : 10.268 141.717 3778 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.66 % Allowed : 10.58 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.15), residues: 3303 helix: -0.04 (0.14), residues: 1386 sheet: -0.45 (0.21), residues: 603 loop : 0.33 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 356 HIS 0.003 0.001 HIS N 101 PHE 0.010 0.001 PHE K 127 TYR 0.011 0.001 TYR K 143 ARG 0.002 0.000 ARG P 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 291 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 ARG cc_start: 0.7255 (ptp-170) cc_final: 0.6893 (ptp90) REVERT: J 238 LYS cc_start: 0.8117 (mmmm) cc_final: 0.7736 (mptt) REVERT: J 253 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: J 311 ASP cc_start: 0.8582 (m-30) cc_final: 0.8290 (t0) REVERT: J 354 GLN cc_start: 0.8511 (mm110) cc_final: 0.8283 (tp-100) REVERT: K 44 MET cc_start: 0.7899 (mmt) cc_final: 0.7639 (mmm) REVERT: K 80 ASP cc_start: 0.8167 (m-30) cc_final: 0.7774 (t0) REVERT: K 244 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8232 (p0) REVERT: L 80 ASP cc_start: 0.7464 (m-30) cc_final: 0.7163 (t0) REVERT: L 313 MET cc_start: 0.8912 (tpp) cc_final: 0.8658 (tpp) REVERT: N 47 MET cc_start: 0.5759 (ttp) cc_final: 0.5527 (ttp) REVERT: N 80 ASP cc_start: 0.7852 (m-30) cc_final: 0.7131 (t0) REVERT: N 121 GLN cc_start: 0.8225 (tt0) cc_final: 0.7913 (tt0) REVERT: N 159 VAL cc_start: 0.9079 (p) cc_final: 0.8797 (m) REVERT: N 190 MET cc_start: 0.7669 (mtm) cc_final: 0.7254 (mtp) REVERT: N 374 CYS cc_start: 0.6764 (m) cc_final: 0.6430 (m) REVERT: O 82 MET cc_start: 0.8794 (tpt) cc_final: 0.8164 (tpt) REVERT: O 195 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8217 (pt0) REVERT: O 215 LYS cc_start: 0.8710 (mmtp) cc_final: 0.8227 (mttp) REVERT: P 54 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8680 (m) REVERT: P 132 MET cc_start: 0.8543 (ptm) cc_final: 0.8287 (ppp) REVERT: P 176 MET cc_start: 0.8682 (mmt) cc_final: 0.8465 (mmt) REVERT: P 227 MET cc_start: 0.8457 (mmm) cc_final: 0.8075 (mmm) REVERT: P 360 GLN cc_start: 0.8654 (tp40) cc_final: 0.8404 (tm-30) REVERT: P 374 CYS cc_start: 0.7668 (m) cc_final: 0.7374 (m) REVERT: Q 82 MET cc_start: 0.8759 (tpt) cc_final: 0.8485 (tpt) REVERT: Q 325 MET cc_start: 0.6876 (ptp) cc_final: 0.6636 (ptp) REVERT: R 283 MET cc_start: 0.8435 (mmt) cc_final: 0.8198 (tpp) outliers start: 47 outliers final: 26 residues processed: 332 average time/residue: 0.6048 time to fit residues: 337.7367 Evaluate side-chains 301 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 271 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 253 GLU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 244 ASP Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain R residue 205 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 55 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 314 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 137 GLN O 41 GLN O 137 GLN Q 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.101877 restraints weight = 114855.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.106083 restraints weight = 41100.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.108378 restraints weight = 19440.110| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27036 Z= 0.289 Angle : 0.611 7.678 36684 Z= 0.300 Chirality : 0.044 0.168 4068 Planarity : 0.004 0.043 4689 Dihedral : 10.061 143.080 3772 Min Nonbonded Distance : 1.399 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.63 % Allowed : 10.44 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.15), residues: 3303 helix: 0.06 (0.14), residues: 1377 sheet: -0.45 (0.21), residues: 603 loop : 0.23 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 86 HIS 0.003 0.001 HIS N 101 PHE 0.010 0.001 PHE L 31 TYR 0.010 0.001 TYR N 198 ARG 0.003 0.000 ARG P 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 286 time to evaluate : 3.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 ARG cc_start: 0.7382 (ptp-170) cc_final: 0.7073 (ptp90) REVERT: J 238 LYS cc_start: 0.8191 (mmmm) cc_final: 0.7772 (mptt) REVERT: J 311 ASP cc_start: 0.8555 (m-30) cc_final: 0.8310 (t0) REVERT: J 354 GLN cc_start: 0.8565 (mm110) cc_final: 0.8316 (tp-100) REVERT: K 44 MET cc_start: 0.7878 (mmt) cc_final: 0.7623 (mmm) REVERT: K 244 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8179 (p0) REVERT: N 47 MET cc_start: 0.5713 (ttp) cc_final: 0.5393 (ttp) REVERT: N 121 GLN cc_start: 0.8286 (tt0) cc_final: 0.7962 (tt0) REVERT: N 190 MET cc_start: 0.7931 (mtm) cc_final: 0.7577 (mtp) REVERT: N 244 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.7723 (p0) REVERT: N 374 CYS cc_start: 0.6785 (m) cc_final: 0.6427 (m) REVERT: O 45 VAL cc_start: 0.8844 (t) cc_final: 0.8612 (m) REVERT: O 77 THR cc_start: 0.9383 (p) cc_final: 0.9087 (t) REVERT: O 82 MET cc_start: 0.8923 (tpt) cc_final: 0.8347 (tpt) REVERT: O 137 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7533 (mt0) REVERT: P 132 MET cc_start: 0.8553 (ptm) cc_final: 0.8297 (ppp) REVERT: P 176 MET cc_start: 0.8680 (mmt) cc_final: 0.8458 (mmt) REVERT: P 227 MET cc_start: 0.8474 (mmm) cc_final: 0.8093 (mmm) REVERT: P 360 GLN cc_start: 0.8667 (tp40) cc_final: 0.8338 (tm-30) REVERT: P 374 CYS cc_start: 0.7575 (m) cc_final: 0.7291 (m) REVERT: Q 82 MET cc_start: 0.8767 (tpt) cc_final: 0.8515 (tpt) REVERT: Q 244 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8138 (p0) outliers start: 46 outliers final: 28 residues processed: 325 average time/residue: 0.6546 time to fit residues: 359.1983 Evaluate side-chains 304 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 344 SER Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 244 ASP Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 137 GLN Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 chunk 260 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 169 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 157 optimal weight: 0.0270 chunk 135 optimal weight: 3.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 137 GLN Q 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.121682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103079 restraints weight = 113912.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.107271 restraints weight = 40639.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.109557 restraints weight = 19190.004| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 27036 Z= 0.329 Angle : 0.616 7.082 36684 Z= 0.304 Chirality : 0.045 0.164 4068 Planarity : 0.004 0.043 4689 Dihedral : 9.999 145.954 3772 Min Nonbonded Distance : 1.503 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.59 % Allowed : 10.86 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.15), residues: 3303 helix: 0.05 (0.14), residues: 1377 sheet: -0.52 (0.21), residues: 603 loop : 0.14 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 356 HIS 0.004 0.001 HIS Q 101 PHE 0.011 0.001 PHE L 31 TYR 0.010 0.001 TYR M 133 ARG 0.003 0.000 ARG L 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 3.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 ARG cc_start: 0.7392 (ptp-170) cc_final: 0.7171 (ptp90) REVERT: J 238 LYS cc_start: 0.8149 (mmmm) cc_final: 0.7693 (mptt) REVERT: J 354 GLN cc_start: 0.8591 (mm110) cc_final: 0.8310 (tp-100) REVERT: K 44 MET cc_start: 0.7893 (mmt) cc_final: 0.7632 (mmm) REVERT: K 244 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8213 (p0) REVERT: K 334 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8158 (pm20) REVERT: N 47 MET cc_start: 0.5702 (ttp) cc_final: 0.5345 (ttp) REVERT: N 121 GLN cc_start: 0.8295 (tt0) cc_final: 0.7971 (tt0) REVERT: N 190 MET cc_start: 0.7934 (mtm) cc_final: 0.7593 (mtp) REVERT: N 374 CYS cc_start: 0.6750 (m) cc_final: 0.6391 (m) REVERT: O 45 VAL cc_start: 0.8872 (t) cc_final: 0.8658 (m) REVERT: O 77 THR cc_start: 0.9372 (p) cc_final: 0.9078 (t) REVERT: O 82 MET cc_start: 0.8925 (tpt) cc_final: 0.8399 (tpt) REVERT: O 195 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8251 (pt0) REVERT: O 334 GLU cc_start: 0.8370 (pm20) cc_final: 0.7944 (pm20) REVERT: P 132 MET cc_start: 0.8566 (ptm) cc_final: 0.8306 (ppp) REVERT: P 176 MET cc_start: 0.8722 (mmt) cc_final: 0.8488 (mmt) REVERT: P 360 GLN cc_start: 0.8666 (tp40) cc_final: 0.8340 (tm-30) REVERT: P 374 CYS cc_start: 0.7544 (m) cc_final: 0.7269 (m) REVERT: Q 82 MET cc_start: 0.8728 (tpt) cc_final: 0.8514 (tpt) REVERT: Q 244 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8122 (p0) outliers start: 45 outliers final: 35 residues processed: 314 average time/residue: 0.6243 time to fit residues: 330.3548 Evaluate side-chains 304 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 334 GLU Chi-restraints excluded: chain L residue 344 SER Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 244 ASP Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain O residue 271 SER Chi-restraints excluded: chain O residue 278 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain P residue 344 SER Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 203 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 332 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 300 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 137 GLN Q 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.121364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102265 restraints weight = 115188.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.106571 restraints weight = 41688.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.108924 restraints weight = 19815.889| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27036 Z= 0.282 Angle : 0.597 7.130 36684 Z= 0.292 Chirality : 0.044 0.157 4068 Planarity : 0.004 0.043 4689 Dihedral : 9.901 146.172 3772 Min Nonbonded Distance : 1.554 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.02 % Allowed : 11.00 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.15), residues: 3303 helix: 0.04 (0.14), residues: 1440 sheet: -0.72 (0.21), residues: 621 loop : 0.14 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 356 HIS 0.003 0.001 HIS Q 101 PHE 0.010 0.001 PHE L 31 TYR 0.010 0.001 TYR M 133 ARG 0.003 0.000 ARG L 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 274 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 ARG cc_start: 0.7463 (ptp-170) cc_final: 0.7002 (mtt90) REVERT: J 354 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8380 (tp-100) REVERT: J 363 ASP cc_start: 0.8576 (p0) cc_final: 0.8191 (m-30) REVERT: K 44 MET cc_start: 0.7881 (mmt) cc_final: 0.7605 (mmm) REVERT: K 244 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8243 (p0) REVERT: K 334 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8112 (pm20) REVERT: L 137 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7935 (mt0) REVERT: L 325 MET cc_start: 0.7988 (ptp) cc_final: 0.7699 (ptp) REVERT: M 16 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8699 (mt) REVERT: N 72 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7331 (mm-30) REVERT: N 121 GLN cc_start: 0.8251 (tt0) cc_final: 0.7933 (tt0) REVERT: N 190 MET cc_start: 0.7787 (mtm) cc_final: 0.7470 (mtp) REVERT: N 374 CYS cc_start: 0.6737 (m) cc_final: 0.6359 (m) REVERT: O 77 THR cc_start: 0.9361 (p) cc_final: 0.9088 (t) REVERT: O 82 MET cc_start: 0.8889 (tpt) cc_final: 0.8391 (tpt) REVERT: O 217 CYS cc_start: 0.9339 (m) cc_final: 0.8879 (m) REVERT: O 334 GLU cc_start: 0.8297 (pm20) cc_final: 0.7896 (pm20) REVERT: P 132 MET cc_start: 0.8593 (ptm) cc_final: 0.8373 (ppp) REVERT: P 176 MET cc_start: 0.8646 (mmt) cc_final: 0.8380 (mmt) REVERT: P 205 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: P 360 GLN cc_start: 0.8602 (tp40) cc_final: 0.8321 (tm-30) REVERT: P 374 CYS cc_start: 0.7551 (m) cc_final: 0.7201 (m) REVERT: Q 244 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8100 (p0) outliers start: 57 outliers final: 38 residues processed: 326 average time/residue: 0.6079 time to fit residues: 335.9860 Evaluate side-chains 318 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 274 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 137 GLN Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 334 GLU Chi-restraints excluded: chain L residue 344 SER Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 330 ILE Chi-restraints excluded: chain N residue 244 ASP Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain O residue 271 SER Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 278 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 194 THR Chi-restraints excluded: chain P residue 205 GLU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain P residue 344 SER Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 85 ILE Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 221 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 120 optimal weight: 0.4980 chunk 30 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 4 optimal weight: 30.0000 chunk 283 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 137 GLN O 137 GLN Q 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101460 restraints weight = 114805.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.105739 restraints weight = 40754.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.108073 restraints weight = 19115.256| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27036 Z= 0.245 Angle : 0.584 7.000 36684 Z= 0.284 Chirality : 0.044 0.153 4068 Planarity : 0.003 0.042 4689 Dihedral : 9.830 146.161 3772 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.70 % Allowed : 11.82 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.22 (0.15), residues: 3303 helix: 0.11 (0.14), residues: 1440 sheet: -0.70 (0.21), residues: 621 loop : 0.15 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 356 HIS 0.003 0.001 HIS O 371 PHE 0.009 0.001 PHE L 31 TYR 0.008 0.001 TYR M 133 ARG 0.003 0.000 ARG L 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 279 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 ARG cc_start: 0.7468 (ptp-170) cc_final: 0.7041 (mtt90) REVERT: J 121 GLN cc_start: 0.8737 (tt0) cc_final: 0.7851 (tm-30) REVERT: J 354 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8378 (tp-100) REVERT: J 363 ASP cc_start: 0.8523 (p0) cc_final: 0.8198 (m-30) REVERT: K 44 MET cc_start: 0.7871 (mmt) cc_final: 0.7612 (mmm) REVERT: K 80 ASP cc_start: 0.8300 (m-30) cc_final: 0.7856 (t0) REVERT: K 244 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8231 (p0) REVERT: K 334 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8096 (pm20) REVERT: N 72 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7324 (mm-30) REVERT: N 121 GLN cc_start: 0.8242 (tt0) cc_final: 0.7924 (tt0) REVERT: N 190 MET cc_start: 0.7755 (mtm) cc_final: 0.7432 (mtp) REVERT: N 374 CYS cc_start: 0.6640 (m) cc_final: 0.6303 (m) REVERT: O 77 THR cc_start: 0.9358 (p) cc_final: 0.9084 (t) REVERT: O 82 MET cc_start: 0.8892 (tpt) cc_final: 0.8002 (tpt) REVERT: O 217 CYS cc_start: 0.9350 (m) cc_final: 0.8887 (m) REVERT: O 334 GLU cc_start: 0.8282 (pm20) cc_final: 0.7915 (pm20) REVERT: P 191 LYS cc_start: 0.8462 (ttmt) cc_final: 0.7935 (tttp) REVERT: P 360 GLN cc_start: 0.8573 (tp40) cc_final: 0.8324 (tm-30) REVERT: P 374 CYS cc_start: 0.7540 (m) cc_final: 0.7189 (m) REVERT: Q 244 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8069 (p0) REVERT: Q 291 LYS cc_start: 0.5937 (mptt) cc_final: 0.5616 (mptt) outliers start: 48 outliers final: 39 residues processed: 324 average time/residue: 0.6170 time to fit residues: 337.4806 Evaluate side-chains 314 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 272 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 334 GLU Chi-restraints excluded: chain L residue 344 SER Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 330 ILE Chi-restraints excluded: chain N residue 244 ASP Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 137 GLN Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain O residue 271 SER Chi-restraints excluded: chain O residue 278 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 194 THR Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain P residue 344 SER Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 85 ILE Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 92 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 chunk 106 optimal weight: 0.0870 chunk 95 optimal weight: 2.9990 chunk 244 optimal weight: 0.5980 chunk 273 optimal weight: 0.8980 chunk 240 optimal weight: 2.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.123997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.105484 restraints weight = 113011.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.109759 restraints weight = 39927.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.112062 restraints weight = 18608.975| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27036 Z= 0.171 Angle : 0.560 6.809 36684 Z= 0.269 Chirality : 0.043 0.178 4068 Planarity : 0.003 0.043 4689 Dihedral : 9.696 145.222 3772 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.34 % Allowed : 12.31 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.08 (0.15), residues: 3303 helix: 0.39 (0.15), residues: 1386 sheet: -0.62 (0.21), residues: 621 loop : 0.30 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 356 HIS 0.003 0.001 HIS O 371 PHE 0.008 0.001 PHE Q 31 TYR 0.011 0.001 TYR J 169 ARG 0.002 0.000 ARG P 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 285 time to evaluate : 3.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 ARG cc_start: 0.7484 (ptp-170) cc_final: 0.7084 (mtt90) REVERT: J 121 GLN cc_start: 0.8727 (tt0) cc_final: 0.7854 (tm-30) REVERT: J 354 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8351 (tp-100) REVERT: J 363 ASP cc_start: 0.8531 (p0) cc_final: 0.8329 (m-30) REVERT: K 44 MET cc_start: 0.7815 (mmt) cc_final: 0.7562 (mmm) REVERT: K 244 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8127 (p0) REVERT: K 334 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8167 (pm20) REVERT: N 72 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7299 (mm-30) REVERT: N 121 GLN cc_start: 0.8276 (tt0) cc_final: 0.7942 (tt0) REVERT: N 159 VAL cc_start: 0.9158 (p) cc_final: 0.8923 (m) REVERT: N 190 MET cc_start: 0.7659 (mtm) cc_final: 0.7353 (mtp) REVERT: N 374 CYS cc_start: 0.6692 (m) cc_final: 0.6324 (m) REVERT: O 77 THR cc_start: 0.9371 (p) cc_final: 0.9070 (t) REVERT: O 82 MET cc_start: 0.8872 (tpt) cc_final: 0.7951 (tpt) REVERT: O 217 CYS cc_start: 0.9316 (m) cc_final: 0.8855 (m) REVERT: O 334 GLU cc_start: 0.8275 (pm20) cc_final: 0.7958 (pm20) REVERT: P 191 LYS cc_start: 0.8515 (ttmt) cc_final: 0.8075 (ttpp) REVERT: P 246 GLN cc_start: 0.8355 (mt0) cc_final: 0.8142 (mt0) REVERT: P 374 CYS cc_start: 0.7502 (m) cc_final: 0.7177 (m) REVERT: Q 82 MET cc_start: 0.8757 (tpt) cc_final: 0.8034 (tpt) REVERT: Q 291 LYS cc_start: 0.6005 (mptt) cc_final: 0.5683 (mptt) outliers start: 38 outliers final: 32 residues processed: 320 average time/residue: 0.6230 time to fit residues: 334.2874 Evaluate side-chains 310 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 334 GLU Chi-restraints excluded: chain L residue 344 SER Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 330 ILE Chi-restraints excluded: chain N residue 244 ASP Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain O residue 271 SER Chi-restraints excluded: chain O residue 278 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 85 ILE Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 152 optimal weight: 0.9980 chunk 87 optimal weight: 0.2980 chunk 180 optimal weight: 1.9990 chunk 258 optimal weight: 1.9990 chunk 269 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106852 restraints weight = 112888.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.111102 restraints weight = 39749.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113391 restraints weight = 18519.946| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27036 Z= 0.168 Angle : 0.553 6.846 36684 Z= 0.264 Chirality : 0.043 0.162 4068 Planarity : 0.003 0.045 4689 Dihedral : 9.485 142.409 3772 Min Nonbonded Distance : 1.562 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.20 % Allowed : 12.56 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.15), residues: 3303 helix: 0.37 (0.14), residues: 1440 sheet: -0.50 (0.21), residues: 621 loop : 0.32 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 356 HIS 0.003 0.001 HIS O 371 PHE 0.006 0.001 PHE Q 31 TYR 0.011 0.001 TYR P 279 ARG 0.004 0.000 ARG Q 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 293 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 ARG cc_start: 0.7715 (ptp-170) cc_final: 0.7409 (mtt90) REVERT: J 121 GLN cc_start: 0.8707 (tt0) cc_final: 0.7960 (tm-30) REVERT: J 354 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8341 (tp-100) REVERT: K 44 MET cc_start: 0.7773 (mmt) cc_final: 0.7517 (mmm) REVERT: K 244 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8157 (p0) REVERT: K 334 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8127 (pm20) REVERT: M 16 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8473 (mt) REVERT: N 121 GLN cc_start: 0.8281 (tt0) cc_final: 0.7934 (tt0) REVERT: N 132 MET cc_start: 0.8610 (ppp) cc_final: 0.8343 (ppp) REVERT: N 159 VAL cc_start: 0.9156 (p) cc_final: 0.8911 (m) REVERT: N 179 ASP cc_start: 0.8568 (m-30) cc_final: 0.8312 (m-30) REVERT: N 190 MET cc_start: 0.7629 (mtm) cc_final: 0.7315 (mtp) REVERT: N 374 CYS cc_start: 0.6731 (m) cc_final: 0.6271 (m) REVERT: O 77 THR cc_start: 0.9390 (p) cc_final: 0.9092 (t) REVERT: O 82 MET cc_start: 0.8871 (tpt) cc_final: 0.7972 (tpt) REVERT: O 217 CYS cc_start: 0.9317 (m) cc_final: 0.8860 (m) REVERT: O 334 GLU cc_start: 0.8182 (pm20) cc_final: 0.7959 (pm20) REVERT: P 191 LYS cc_start: 0.8363 (ttmt) cc_final: 0.7929 (ttpp) REVERT: P 374 CYS cc_start: 0.7489 (m) cc_final: 0.7172 (m) REVERT: Q 82 MET cc_start: 0.8766 (tpt) cc_final: 0.8109 (tpt) REVERT: Q 132 MET cc_start: 0.8671 (ptm) cc_final: 0.8338 (tmm) REVERT: Q 244 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8140 (p0) outliers start: 34 outliers final: 27 residues processed: 326 average time/residue: 0.6749 time to fit residues: 372.6454 Evaluate side-chains 313 residues out of total 2826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 282 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 334 GLU Chi-restraints excluded: chain L residue 344 SER Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 244 ASP Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 257 CYS Chi-restraints excluded: chain O residue 271 SER Chi-restraints excluded: chain O residue 278 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 257 CYS Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 85 ILE Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 1 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 12 ASN R 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.104016 restraints weight = 113573.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.108225 restraints weight = 40392.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.110482 restraints weight = 18924.974| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 27036 Z= 0.309 Angle : 0.593 7.194 36684 Z= 0.288 Chirality : 0.045 0.192 4068 Planarity : 0.004 0.045 4689 Dihedral : 9.502 144.469 3772 Min Nonbonded Distance : 1.408 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.49 % Allowed : 12.67 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.15), residues: 3303 helix: 0.28 (0.14), residues: 1440 sheet: -0.54 (0.21), residues: 621 loop : 0.19 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 356 HIS 0.003 0.001 HIS Q 101 PHE 0.009 0.001 PHE L 31 TYR 0.008 0.001 TYR M 133 ARG 0.003 0.000 ARG L 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10966.08 seconds wall clock time: 189 minutes 48.27 seconds (11388.27 seconds total)