Starting phenix.real_space_refine on Thu Oct 10 18:09:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz1_42830/10_2024/8uz1_42830_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz1_42830/10_2024/8uz1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz1_42830/10_2024/8uz1_42830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz1_42830/10_2024/8uz1_42830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz1_42830/10_2024/8uz1_42830_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uz1_42830/10_2024/8uz1_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 19.46, 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: 10.63 Conformation dependent library (CDL) restraints added in 3.2 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: 3.99 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: 20.20 Time building geometry restraints manager: 12.67 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: 0.00 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: 0.610 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: 0.680 Extract box with map and model: 1.620 Check model and map are aligned: 0.300 Set scattering table: 0.390 Process input model: 87.230 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.160 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:2.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.490 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 38 poor density : 498 time to evaluate : 3.201 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: 0.6529 time to fit residues: 563.7464 Evaluate side-chains 327 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 308 time to evaluate : 3.227 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 fitting. rotamer outliers: 45 poor density : 357 time to evaluate : 3.210 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: 0.8465 (tpt) cc_final: 0.7942 (tpt) REVERT: J 137 GLN cc_start: 0.7102 (mt0) cc_final: 0.6876 (mt0) REVERT: K 244 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7204 (p0) REVERT: M 82 MET cc_start: 0.9340 (tpt) cc_final: 0.8885 (tpt) REVERT: M 93 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7109 (pm20) REVERT: M 176 MET cc_start: 0.8892 (mmt) cc_final: 0.8628 (mmt) REVERT: N 80 ASP cc_start: 0.7508 (m-30) cc_final: 0.7308 (t0) REVERT: N 123 MET cc_start: 0.8807 (tpp) cc_final: 0.8568 (mmm) REVERT: N 190 MET cc_start: 0.8255 (mtm) cc_final: 0.7818 (mtp) REVERT: N 227 MET cc_start: 0.8632 (mmm) cc_final: 0.8262 (mmm) REVERT: O 82 MET cc_start: 0.9063 (tpt) cc_final: 0.8350 (tpt) REVERT: O 121 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8199 (tm-30) REVERT: O 123 MET cc_start: 0.8179 (tpp) cc_final: 0.7952 (mmt) REVERT: O 244 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8462 (p0) REVERT: O 269 MET cc_start: 0.8303 (ptp) cc_final: 0.8095 (ptm) REVERT: P 176 MET cc_start: 0.8790 (mmt) cc_final: 0.8579 (mmt) REVERT: P 227 MET cc_start: 0.8798 (mmm) cc_final: 0.8328 (mmm) REVERT: Q 81 ASP cc_start: 0.7607 (m-30) cc_final: 0.7302 (m-30) REVERT: Q 82 MET cc_start: 0.8925 (tpt) cc_final: 0.8533 (tpt) REVERT: Q 93 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6123 (pm20) REVERT: Q 123 MET cc_start: 0.8591 (tpp) cc_final: 0.8358 (mmm) REVERT: Q 291 LYS cc_start: 0.5976 (mmtt) cc_final: 0.5252 (mmtm) REVERT: R 270 GLU cc_start: 0.6711 (mp0) cc_final: 0.6342 (mp0) REVERT: R 330 ILE cc_start: 0.8979 (tp) cc_final: 0.8701 (mt) outliers start: 45 outliers final: 20 residues processed: 391 average time/residue: 0.6402 time to fit residues: 425.0553 Evaluate side-chains 303 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 279 time to evaluate : 3.177 ------------------------------------------------------------------------------- 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 M residue 93 GLU 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 93 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 302 optimal weight: 2.9990 chunk 327 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 300 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 12 ASN Q 137 GLN ** R 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 27036 Z= 0.345 Angle : 0.672 6.979 36684 Z= 0.339 Chirality : 0.046 0.173 4068 Planarity : 0.004 0.040 4689 Dihedral : 10.969 133.847 3780 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.59 % Allowed : 10.12 % Favored : 88.29 % 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: -0.52 (0.14), residues: 3303 helix: -0.47 (0.14), residues: 1377 sheet: -0.51 (0.22), residues: 558 loop : 0.15 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 356 HIS 0.003 0.001 HIS R 87 PHE 0.014 0.001 PHE L 31 TYR 0.012 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 331 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 286 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: symmetry clash revert: symmetry clash REVERT: J 360 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7994 (tm-30) REVERT: K 82 MET cc_start: 0.8827 (tpt) cc_final: 0.8512 (tpt) REVERT: K 137 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: K 244 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7062 (p0) REVERT: L 176 MET cc_start: 0.9010 (tpp) cc_final: 0.8792 (mmt) REVERT: M 93 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7331 (pm20) REVERT: N 121 GLN cc_start: 0.8495 (tt0) cc_final: 0.8170 (tt0) REVERT: N 190 MET cc_start: 0.8416 (mtm) cc_final: 0.8102 (mtp) REVERT: N 227 MET cc_start: 0.8662 (mmm) cc_final: 0.8321 (mmm) REVERT: N 244 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7437 (p0) REVERT: N 374 CYS cc_start: 0.6932 (m) cc_final: 0.6704 (m) REVERT: O 41 GLN cc_start: 0.7737 (tt0) cc_final: 0.7458 (tt0) REVERT: O 82 MET cc_start: 0.9085 (tpt) cc_final: 0.8484 (tpt) REVERT: P 54 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.9019 (m) REVERT: P 93 GLU cc_start: 0.7308 (pm20) cc_final: 0.6679 (pt0) REVERT: P 227 MET cc_start: 0.8732 (mmm) cc_final: 0.8355 (mmm) REVERT: P 325 MET cc_start: 0.8125 (ptp) cc_final: 0.7905 (ptp) REVERT: P 360 GLN cc_start: 0.8848 (tp40) cc_final: 0.8610 (tm-30) REVERT: Q 81 ASP cc_start: 0.7724 (m-30) cc_final: 0.7453 (m-30) REVERT: Q 82 MET cc_start: 0.8895 (tpt) cc_final: 0.8559 (tpt) REVERT: Q 93 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6739 (pm20) REVERT: Q 123 MET cc_start: 0.8649 (tpp) cc_final: 0.8085 (mmt) REVERT: Q 244 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8051 (p0) REVERT: Q 291 LYS cc_start: 0.5915 (mmtt) cc_final: 0.5149 (mmtm) REVERT: R 330 ILE cc_start: 0.9030 (tp) cc_final: 0.8736 (mt) outliers start: 45 outliers final: 30 residues processed: 323 average time/residue: 0.6217 time to fit residues: 337.6238 Evaluate side-chains 305 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 268 time to evaluate : 3.207 ------------------------------------------------------------------------------- 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 195 GLU 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 299 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 144 optimal weight: 0.4980 chunk 203 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 321 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 288 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 137 GLN N 41 GLN O 92 ASN Q 12 ASN R 137 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27036 Z= 0.203 Angle : 0.597 6.882 36684 Z= 0.291 Chirality : 0.044 0.163 4068 Planarity : 0.004 0.045 4689 Dihedral : 10.361 140.015 3778 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.88 % Allowed : 10.54 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.14 (0.14), residues: 1377 sheet: -0.47 (0.21), residues: 603 loop : 0.31 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 86 HIS 0.003 0.001 HIS N 101 PHE 0.012 0.001 PHE R 31 TYR 0.009 0.001 TYR N 198 ARG 0.003 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 337 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 284 time to evaluate : 3.240 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: K 244 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7099 (p0) REVERT: L 176 MET cc_start: 0.8931 (tpp) cc_final: 0.8681 (mmt) REVERT: M 93 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7066 (pt0) REVERT: N 47 MET cc_start: 0.5812 (ttp) cc_final: 0.5453 (ttp) REVERT: N 121 GLN cc_start: 0.8440 (tt0) cc_final: 0.8120 (tt0) REVERT: N 190 MET cc_start: 0.8379 (mtm) cc_final: 0.8102 (mtp) REVERT: N 227 MET cc_start: 0.8644 (mmm) cc_final: 0.8344 (mmm) REVERT: N 374 CYS cc_start: 0.6937 (m) cc_final: 0.6677 (m) REVERT: O 82 MET cc_start: 0.9063 (tpt) cc_final: 0.8546 (tpt) REVERT: P 93 GLU cc_start: 0.7187 (pm20) cc_final: 0.6891 (pt0) REVERT: P 227 MET cc_start: 0.8705 (mmm) cc_final: 0.8357 (mmm) REVERT: P 360 GLN cc_start: 0.8748 (tp40) cc_final: 0.8525 (tm-30) REVERT: Q 81 ASP cc_start: 0.7571 (m-30) cc_final: 0.7290 (m-30) REVERT: Q 82 MET cc_start: 0.8864 (tpt) cc_final: 0.8658 (tpt) REVERT: Q 93 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6745 (pt0) REVERT: Q 291 LYS cc_start: 0.5846 (mmtt) cc_final: 0.5541 (mmtt) outliers start: 53 outliers final: 35 residues processed: 331 average time/residue: 0.5949 time to fit residues: 332.9359 Evaluate side-chains 301 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 263 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain K residue 85 ILE 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 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 93 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 89 THR Chi-restraints excluded: chain O residue 139 VAL 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 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 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 Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 268 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 239 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 274 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 27036 Z= 0.403 Angle : 0.663 8.498 36684 Z= 0.331 Chirality : 0.047 0.177 4068 Planarity : 0.004 0.044 4689 Dihedral : 10.358 146.807 3778 Min Nonbonded Distance : 1.411 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.02 % Allowed : 10.72 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.51 (0.15), residues: 3303 helix: -0.31 (0.14), residues: 1422 sheet: -0.57 (0.21), residues: 603 loop : 0.04 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 356 HIS 0.004 0.001 HIS N 40 PHE 0.013 0.001 PHE L 31 TYR 0.011 0.001 TYR M 133 ARG 0.005 0.001 ARG J 95 *********************** 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 329 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 272 time to evaluate : 3.272 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: K 244 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7133 (p0) REVERT: L 176 MET cc_start: 0.8920 (tpp) cc_final: 0.8679 (mmt) REVERT: N 121 GLN cc_start: 0.8494 (tt0) cc_final: 0.8153 (tt0) REVERT: N 190 MET cc_start: 0.8513 (mtm) cc_final: 0.8200 (mtp) REVERT: N 227 MET cc_start: 0.8601 (mmm) cc_final: 0.8307 (mmm) REVERT: N 244 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.7754 (p0) REVERT: N 374 CYS cc_start: 0.6911 (m) cc_final: 0.6667 (m) REVERT: O 77 THR cc_start: 0.9214 (p) cc_final: 0.8818 (t) REVERT: O 82 MET cc_start: 0.9058 (tpt) cc_final: 0.8601 (tpt) REVERT: P 360 GLN cc_start: 0.8840 (tp40) cc_final: 0.8542 (tm-30) REVERT: Q 81 ASP cc_start: 0.7810 (m-30) cc_final: 0.7606 (m-30) REVERT: Q 82 MET cc_start: 0.8888 (tpt) cc_final: 0.8687 (tpt) REVERT: Q 93 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6886 (pt0) REVERT: Q 244 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8133 (p0) REVERT: Q 291 LYS cc_start: 0.6162 (mmtt) cc_final: 0.5610 (mmtm) outliers start: 57 outliers final: 40 residues processed: 319 average time/residue: 0.6108 time to fit residues: 330.7631 Evaluate side-chains 303 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 259 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 244 ASP 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 96 VAL 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 47 MET Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 325 MET 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 139 VAL Chi-restraints excluded: chain O residue 199 SER 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 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 16 LEU Chi-restraints excluded: chain R residue 71 ILE 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 108 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 188 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 322 optimal weight: 0.5980 chunk 267 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3715 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= 0.220 Angle : 0.591 6.892 36684 Z= 0.288 Chirality : 0.044 0.156 4068 Planarity : 0.003 0.045 4689 Dihedral : 10.096 146.042 3775 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.80 % Allowed : 11.39 % Favored : 86.80 % 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: -0.51 (0.21), residues: 603 loop : 0.11 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 356 HIS 0.003 0.001 HIS N 101 PHE 0.009 0.001 PHE L 31 TYR 0.008 0.001 TYR N 198 ARG 0.002 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 327 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 276 time to evaluate : 3.269 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 313 MET cc_start: 0.8596 (mmm) cc_final: 0.8234 (mtp) REVERT: K 244 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7105 (p0) REVERT: L 176 MET cc_start: 0.8861 (tpp) cc_final: 0.8608 (mmt) REVERT: N 121 GLN cc_start: 0.8435 (tt0) cc_final: 0.8098 (tt0) REVERT: N 190 MET cc_start: 0.8412 (mtm) cc_final: 0.8111 (mtp) REVERT: N 227 MET cc_start: 0.8611 (mmm) cc_final: 0.8349 (mmm) REVERT: N 374 CYS cc_start: 0.6884 (m) cc_final: 0.6663 (m) REVERT: O 77 THR cc_start: 0.9177 (p) cc_final: 0.8787 (t) REVERT: O 82 MET cc_start: 0.9065 (tpt) cc_final: 0.8671 (tpt) REVERT: O 334 GLU cc_start: 0.8738 (pm20) cc_final: 0.8515 (pm20) REVERT: P 227 MET cc_start: 0.8538 (tpp) cc_final: 0.8332 (mmm) REVERT: P 360 GLN cc_start: 0.8748 (tp40) cc_final: 0.8495 (tm-30) REVERT: Q 81 ASP cc_start: 0.7698 (m-30) cc_final: 0.7486 (m-30) REVERT: Q 93 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6918 (pt0) REVERT: Q 291 LYS cc_start: 0.6097 (mmtt) cc_final: 0.5851 (mmtt) outliers start: 51 outliers final: 41 residues processed: 320 average time/residue: 0.6205 time to fit residues: 337.3545 Evaluate side-chains 310 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 267 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 137 GLN 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 325 MET 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 334 GLU 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 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 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 16 LEU Chi-restraints excluded: chain R residue 71 ILE 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 310 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 271 optimal weight: 0.4980 chunk 179 optimal weight: 2.9990 chunk 320 optimal weight: 0.6980 chunk 200 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 : 0.003 0.038 27036 Z= 0.225 Angle : 0.579 6.963 36684 Z= 0.281 Chirality : 0.044 0.154 4068 Planarity : 0.003 0.046 4689 Dihedral : 9.919 146.242 3775 Min Nonbonded Distance : 1.631 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.84 % Allowed : 11.61 % Favored : 86.55 % 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: -0.18 (0.15), residues: 3303 helix: 0.10 (0.14), residues: 1440 sheet: -0.68 (0.21), residues: 621 loop : 0.22 (0.18), residues: 1242 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 0.009 0.001 PHE L 31 TYR 0.008 0.001 TYR N 198 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 328 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 276 time to evaluate : 3.251 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 137 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7709 (mt0) REVERT: K 244 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7169 (p0) REVERT: N 121 GLN cc_start: 0.8435 (tt0) cc_final: 0.8095 (tt0) REVERT: N 190 MET cc_start: 0.8317 (mtm) cc_final: 0.8000 (mtp) REVERT: N 227 MET cc_start: 0.8512 (mmm) cc_final: 0.8252 (mmm) REVERT: N 374 CYS cc_start: 0.6908 (m) cc_final: 0.6637 (m) REVERT: O 77 THR cc_start: 0.9193 (p) cc_final: 0.8806 (t) REVERT: O 82 MET cc_start: 0.9073 (tpt) cc_final: 0.8677 (tpt) REVERT: O 334 GLU cc_start: 0.8697 (pm20) cc_final: 0.8479 (pm20) REVERT: P 360 GLN cc_start: 0.8714 (tp40) cc_final: 0.8479 (tm-30) REVERT: Q 82 MET cc_start: 0.8857 (tpt) cc_final: 0.8462 (tpt) REVERT: Q 244 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8036 (p0) REVERT: Q 291 LYS cc_start: 0.5808 (mmtt) cc_final: 0.5278 (mmtm) outliers start: 52 outliers final: 38 residues processed: 322 average time/residue: 0.5913 time to fit residues: 323.0198 Evaluate side-chains 310 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 269 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 137 GLN 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 325 MET 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 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 89 THR 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 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 71 ILE 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 198 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 204 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 252 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 27036 Z= 0.305 Angle : 0.606 7.283 36684 Z= 0.297 Chirality : 0.045 0.170 4068 Planarity : 0.004 0.043 4689 Dihedral : 9.853 148.589 3772 Min Nonbonded Distance : 1.541 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.05 % Allowed : 11.71 % 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: -0.26 (0.15), residues: 3303 helix: 0.06 (0.14), residues: 1440 sheet: -0.71 (0.21), residues: 621 loop : 0.13 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.006 0.000 ARG O 147 *********************** 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 329 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 271 time to evaluate : 3.210 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 132 MET cc_start: 0.8902 (ptm) cc_final: 0.8638 (ptm) REVERT: J 137 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7737 (mt0) REVERT: K 244 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7151 (p0) REVERT: N 121 GLN cc_start: 0.8465 (tt0) cc_final: 0.8125 (tt0) REVERT: N 190 MET cc_start: 0.8467 (mtm) cc_final: 0.8147 (mtp) REVERT: N 227 MET cc_start: 0.8512 (mmm) cc_final: 0.8254 (mmm) REVERT: N 244 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7313 (p0) REVERT: N 374 CYS cc_start: 0.6945 (m) cc_final: 0.6646 (m) REVERT: O 77 THR cc_start: 0.9214 (p) cc_final: 0.8817 (t) REVERT: O 82 MET cc_start: 0.9077 (tpt) cc_final: 0.8696 (tpt) REVERT: O 217 CYS cc_start: 0.9177 (m) cc_final: 0.8940 (m) REVERT: O 334 GLU cc_start: 0.8742 (pm20) cc_final: 0.8525 (pm20) REVERT: P 360 GLN cc_start: 0.8735 (tp40) cc_final: 0.8482 (tm-30) REVERT: Q 244 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8113 (p0) REVERT: Q 291 LYS cc_start: 0.5820 (mmtt) cc_final: 0.5502 (mmtt) REVERT: R 41 GLN cc_start: 0.7829 (tt0) cc_final: 0.7382 (tt0) outliers start: 58 outliers final: 45 residues processed: 323 average time/residue: 0.6344 time to fit residues: 348.4763 Evaluate side-chains 315 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 266 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 137 GLN 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 325 MET 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 334 GLU Chi-restraints excluded: chain L residue 344 SER 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 139 VAL 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 288 ASP 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 250 ILE 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 250 ILE 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 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 Chi-restraints excluded: chain R residue 270 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 291 optimal weight: 0.9980 chunk 307 optimal weight: 3.9990 chunk 280 optimal weight: 0.4980 chunk 299 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 282 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27036 Z= 0.253 Angle : 0.588 7.134 36684 Z= 0.285 Chirality : 0.044 0.158 4068 Planarity : 0.003 0.044 4689 Dihedral : 9.767 148.909 3772 Min Nonbonded Distance : 1.621 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.98 % Allowed : 11.89 % Favored : 86.13 % 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: -0.31 (0.15), residues: 3303 helix: 0.01 (0.14), residues: 1494 sheet: -0.67 (0.21), residues: 621 loop : 0.09 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 356 HIS 0.003 0.001 HIS N 101 PHE 0.009 0.001 PHE L 31 TYR 0.008 0.001 TYR M 133 ARG 0.003 0.000 ARG K 183 *********************** 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 332 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 276 time to evaluate : 3.226 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 137 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7673 (mt0) REVERT: K 244 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7163 (p0) REVERT: N 121 GLN cc_start: 0.8442 (tt0) cc_final: 0.8100 (tt0) REVERT: N 190 MET cc_start: 0.8389 (mtm) cc_final: 0.8055 (mtp) REVERT: N 227 MET cc_start: 0.8491 (mmm) cc_final: 0.8240 (mmm) REVERT: N 244 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.7528 (p0) REVERT: N 374 CYS cc_start: 0.6880 (m) cc_final: 0.6618 (m) REVERT: O 77 THR cc_start: 0.9206 (p) cc_final: 0.8819 (t) REVERT: O 82 MET cc_start: 0.9073 (tpt) cc_final: 0.8707 (tpt) REVERT: P 360 GLN cc_start: 0.8715 (tp40) cc_final: 0.8461 (tm-30) REVERT: Q 244 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8027 (p0) REVERT: Q 291 LYS cc_start: 0.5793 (mmtt) cc_final: 0.5472 (mmtt) REVERT: R 41 GLN cc_start: 0.7816 (tt0) cc_final: 0.7361 (tt0) outliers start: 56 outliers final: 44 residues processed: 325 average time/residue: 0.6215 time to fit residues: 345.1097 Evaluate side-chains 315 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 267 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 137 GLN 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 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 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 288 ASP 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 195 GLU Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 250 ILE 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 71 ILE 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 Chi-restraints excluded: chain R residue 270 GLU Chi-restraints excluded: chain R residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 196 optimal weight: 3.9990 chunk 316 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 150 optimal weight: 0.0980 chunk 219 optimal weight: 2.9990 chunk 331 optimal weight: 4.9990 chunk 305 optimal weight: 1.9990 chunk 264 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27036 Z= 0.247 Angle : 0.584 7.030 36684 Z= 0.283 Chirality : 0.044 0.167 4068 Planarity : 0.003 0.044 4689 Dihedral : 9.680 149.052 3772 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.80 % Allowed : 12.21 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.27 (0.15), residues: 3303 helix: 0.06 (0.14), residues: 1494 sheet: -0.65 (0.21), residues: 621 loop : 0.09 (0.18), residues: 1188 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 0.008 0.001 PHE L 31 TYR 0.011 0.001 TYR P 279 ARG 0.002 0.000 ARG J 177 ********************** 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 326 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 275 time to evaluate : 3.282 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 137 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7677 (mt0) REVERT: K 244 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7102 (p0) REVERT: N 121 GLN cc_start: 0.8438 (tt0) cc_final: 0.8097 (tt0) REVERT: N 190 MET cc_start: 0.8386 (mtm) cc_final: 0.8045 (mtp) REVERT: N 227 MET cc_start: 0.8485 (mmm) cc_final: 0.8235 (mmm) REVERT: N 374 CYS cc_start: 0.6989 (m) cc_final: 0.6622 (m) REVERT: O 77 THR cc_start: 0.9204 (p) cc_final: 0.8816 (t) REVERT: O 82 MET cc_start: 0.9078 (tpt) cc_final: 0.8394 (tpt) REVERT: P 360 GLN cc_start: 0.8697 (tp40) cc_final: 0.8449 (tm-30) REVERT: Q 82 MET cc_start: 0.8795 (tpt) cc_final: 0.8439 (tpt) REVERT: Q 244 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8019 (p0) REVERT: Q 291 LYS cc_start: 0.5557 (mmtt) cc_final: 0.5229 (mmtt) REVERT: R 41 GLN cc_start: 0.7806 (tt0) cc_final: 0.7353 (tt0) outliers start: 51 outliers final: 44 residues processed: 321 average time/residue: 0.6180 time to fit residues: 337.0932 Evaluate side-chains 317 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 270 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 137 GLN 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 325 MET 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 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 288 ASP Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 334 GLU 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 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 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 71 ILE 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 Chi-restraints excluded: chain R residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 209 optimal weight: 0.0970 chunk 281 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 243 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 264 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.123146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.104532 restraints weight = 113481.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.108812 restraints weight = 40367.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.111125 restraints weight = 18956.040| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27036 Z= 0.152 Angle : 0.552 7.279 36684 Z= 0.262 Chirality : 0.042 0.168 4068 Planarity : 0.003 0.047 4689 Dihedral : 9.425 147.122 3772 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.66 % Allowed : 12.35 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.15), residues: 3303 helix: 0.39 (0.14), residues: 1440 sheet: -0.52 (0.21), residues: 621 loop : 0.32 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 356 HIS 0.003 0.001 HIS M 161 PHE 0.007 0.001 PHE M 31 TYR 0.009 0.001 TYR N 143 ARG 0.003 0.000 ARG K 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7806.04 seconds wall clock time: 136 minutes 20.26 seconds (8180.26 seconds total)