Starting phenix.real_space_refine on Mon Aug 25 07:28:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uee_42161/08_2025/8uee_42161.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uee_42161/08_2025/8uee_42161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uee_42161/08_2025/8uee_42161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uee_42161/08_2025/8uee_42161.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uee_42161/08_2025/8uee_42161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uee_42161/08_2025/8uee_42161.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 21 5.49 5 Mg 7 5.21 5 S 167 5.16 5 C 16337 2.51 5 N 4410 2.21 5 O 4982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25924 Number of models: 1 Model: "" Number of chains: 19 Chain: "F" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "H" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "I" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "B" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1348 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "C" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1348 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "D" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1348 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "A" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1348 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.49, per 1000 atoms: 0.25 Number of scatterers: 25924 At special positions: 0 Unit cell: (118.8, 111.24, 257.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 167 16.00 P 21 15.00 Mg 7 11.99 O 4982 8.00 N 4410 7.00 C 16337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6090 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 41 sheets defined 53.5% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 91 Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.226A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 117 " --> pdb=" O LYS F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.522A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.563A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.808A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.122A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 350 through 355 removed outlier: 4.025A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 369 through 374 removed outlier: 3.845A pdb=" N LYS F 373 " --> pdb=" O ILE F 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 61 removed outlier: 3.532A pdb=" N LYS H 61 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 92 Processing helix chain 'H' and resid 112 through 125 removed outlier: 3.956A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET H 123 " --> pdb=" O MET H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 145 Processing helix chain 'H' and resid 172 through 175 Processing helix chain 'H' and resid 181 through 193 Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 202 through 217 removed outlier: 3.548A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 233 Processing helix chain 'H' and resid 252 through 257 removed outlier: 3.526A pdb=" N CYS H 257 " --> pdb=" O GLU H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 262 Processing helix chain 'H' and resid 263 through 268 Processing helix chain 'H' and resid 273 through 284 removed outlier: 3.508A pdb=" N LYS H 284 " --> pdb=" O ASN H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 288 removed outlier: 6.318A pdb=" N ASP H 288 " --> pdb=" O CYS H 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 285 through 288' Processing helix chain 'H' and resid 289 through 295 removed outlier: 3.753A pdb=" N ALA H 295 " --> pdb=" O LYS H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 305 Processing helix chain 'H' and resid 308 through 321 Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 337 through 349 Processing helix chain 'H' and resid 350 through 355 removed outlier: 3.553A pdb=" N GLN H 353 " --> pdb=" O SER H 350 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 Processing helix chain 'H' and resid 369 through 374 removed outlier: 3.535A pdb=" N CYS H 374 " --> pdb=" O VAL H 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 61 Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.688A pdb=" N LEU I 65 " --> pdb=" O ARG I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 97 through 101 removed outlier: 3.870A pdb=" N HIS I 101 " --> pdb=" O PRO I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 126 removed outlier: 3.849A pdb=" N ARG I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 145 Processing helix chain 'I' and resid 172 through 175 Processing helix chain 'I' and resid 181 through 194 removed outlier: 3.776A pdb=" N THR I 194 " --> pdb=" O MET I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 197 No H-bonds generated for 'chain 'I' and resid 195 through 197' Processing helix chain 'I' and resid 202 through 217 Processing helix chain 'I' and resid 222 through 233 Processing helix chain 'I' and resid 252 through 257 removed outlier: 3.522A pdb=" N CYS I 257 " --> pdb=" O GLU I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 262 Processing helix chain 'I' and resid 263 through 268 Processing helix chain 'I' and resid 273 through 284 Processing helix chain 'I' and resid 286 through 288 No H-bonds generated for 'chain 'I' and resid 286 through 288' Processing helix chain 'I' and resid 289 through 295 removed outlier: 3.582A pdb=" N ALA I 295 " --> pdb=" O LYS I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 306 removed outlier: 4.224A pdb=" N TYR I 306 " --> pdb=" O THR I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 321 Processing helix chain 'I' and resid 334 through 336 No H-bonds generated for 'chain 'I' and resid 334 through 336' Processing helix chain 'I' and resid 337 through 349 Processing helix chain 'I' and resid 350 through 353 Processing helix chain 'I' and resid 359 through 366 removed outlier: 3.556A pdb=" N GLU I 364 " --> pdb=" O GLN I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 374 removed outlier: 3.983A pdb=" N ARG I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'J' and resid 78 through 92 Processing helix chain 'J' and resid 97 through 101 Processing helix chain 'J' and resid 112 through 126 removed outlier: 4.005A pdb=" N ARG J 116 " --> pdb=" O PRO J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 144 Processing helix chain 'J' and resid 172 through 175 Processing helix chain 'J' and resid 181 through 193 Processing helix chain 'J' and resid 194 through 197 Processing helix chain 'J' and resid 202 through 217 Processing helix chain 'J' and resid 222 through 233 Processing helix chain 'J' and resid 252 through 257 removed outlier: 3.629A pdb=" N CYS J 257 " --> pdb=" O GLU J 253 " (cutoff:3.500A) 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 284 Processing helix chain 'J' and resid 289 through 295 removed outlier: 3.763A pdb=" N ALA J 295 " --> pdb=" O LYS J 291 " (cutoff:3.500A) 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 349 Processing helix chain 'J' and resid 359 through 366 Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.971A pdb=" N ARG J 372 " --> pdb=" O SER J 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 61 removed outlier: 3.596A pdb=" N LYS K 61 " --> pdb=" O GLU K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 92 Processing helix chain 'K' and resid 97 through 101 removed outlier: 3.564A pdb=" N HIS K 101 " --> pdb=" O PRO K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 126 removed outlier: 4.207A pdb=" N ARG K 116 " --> pdb=" O PRO K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 145 removed outlier: 3.512A pdb=" N LEU K 142 " --> pdb=" O ALA K 138 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER K 145 " --> pdb=" O SER K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 175 Processing helix chain 'K' and resid 181 through 194 removed outlier: 3.754A pdb=" N THR K 194 " --> pdb=" O MET K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 197 No H-bonds generated for 'chain 'K' and resid 195 through 197' Processing helix chain 'K' and resid 202 through 217 removed outlier: 3.735A pdb=" N ILE K 208 " --> pdb=" O ALA K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 233 Processing helix chain 'K' and resid 252 through 257 removed outlier: 3.500A 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 289 through 296 Processing helix chain 'K' and resid 301 through 305 Processing helix chain 'K' and resid 308 through 319 removed outlier: 3.668A pdb=" N ARG K 312 " --> pdb=" O GLY K 308 " (cutoff:3.500A) 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 349 Processing helix chain 'K' and resid 350 through 353 Processing helix chain 'K' and resid 359 through 366 removed outlier: 3.802A pdb=" N GLU K 364 " --> pdb=" O GLN K 360 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA K 365 " --> pdb=" O GLU K 361 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 374 removed outlier: 3.618A pdb=" N CYS K 374 " --> pdb=" O VAL K 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 61 Processing helix chain 'L' and resid 78 through 92 Processing helix chain 'L' and resid 97 through 101 Processing helix chain 'L' and resid 112 through 126 removed outlier: 3.882A pdb=" N ARG L 116 " --> pdb=" O PRO L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 145 removed outlier: 3.534A pdb=" N TYR L 143 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER L 145 " --> pdb=" O SER L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 175 Processing helix chain 'L' and resid 181 through 194 removed outlier: 3.882A pdb=" N THR L 194 " --> pdb=" O MET L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 197 No H-bonds generated for 'chain 'L' and resid 195 through 197' Processing helix chain 'L' and resid 202 through 217 Processing helix chain 'L' and resid 222 through 231 Processing helix chain 'L' and resid 252 through 260 removed outlier: 3.620A pdb=" N CYS L 257 " --> pdb=" O GLU L 253 " (cutoff:3.500A) Proline residue: L 258 - end of helix Processing helix chain 'L' and resid 261 through 262 No H-bonds generated for 'chain 'L' and resid 261 through 262' Processing helix chain 'L' and resid 263 through 268 Processing helix chain 'L' and resid 273 through 284 Processing helix chain 'L' and resid 289 through 295 removed outlier: 3.590A pdb=" N ALA L 295 " --> pdb=" O LYS L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 301 through 306 removed outlier: 4.022A pdb=" N TYR L 306 " --> pdb=" O THR L 303 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 321 Processing helix chain 'L' and resid 334 through 336 No H-bonds generated for 'chain 'L' and resid 334 through 336' Processing helix chain 'L' and resid 337 through 348 Processing helix chain 'L' and resid 349 through 355 removed outlier: 3.599A pdb=" N GLN L 354 " --> pdb=" O THR L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 366 Processing helix chain 'L' and resid 368 through 374 removed outlier: 4.036A pdb=" N ARG L 372 " --> 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 92 removed outlier: 3.573A pdb=" N MET M 82 " --> pdb=" O ASN M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 101 Processing helix chain 'M' and resid 112 through 126 removed outlier: 4.034A pdb=" N ARG M 116 " --> pdb=" O PRO M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 145 Processing helix chain 'M' and resid 172 through 175 Processing helix chain 'M' and resid 181 through 193 Processing helix chain 'M' and resid 194 through 197 Processing helix chain 'M' and resid 202 through 217 removed outlier: 3.673A pdb=" N GLU M 207 " --> pdb=" O THR M 203 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE M 208 " --> pdb=" O ALA M 204 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 233 Processing helix chain 'M' and resid 252 through 257 Processing helix chain 'M' and resid 258 through 262 Processing helix chain 'M' and resid 263 through 268 Processing helix chain 'M' and resid 273 through 284 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 295 removed outlier: 3.607A pdb=" N ALA M 295 " --> pdb=" O LYS M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 301 through 306 removed outlier: 4.126A 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 348 Processing helix chain 'M' and resid 349 through 355 removed outlier: 3.783A pdb=" N GLN M 354 " --> pdb=" O THR M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 366 Processing helix chain 'M' and resid 367 through 372 removed outlier: 3.607A pdb=" N VAL M 370 " --> pdb=" O PRO M 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 536 removed outlier: 3.552A pdb=" N HIS B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 554 Processing helix chain 'B' and resid 561 through 576 Processing helix chain 'B' and resid 579 through 590 removed outlier: 3.655A pdb=" N GLN B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 612 removed outlier: 3.527A pdb=" N LYS B 602 " --> pdb=" O GLU B 598 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 609 " --> pdb=" O THR B 605 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B 611 " --> pdb=" O LYS B 607 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS B 612 " --> pdb=" O GLU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 630 Processing helix chain 'B' and resid 640 through 651 Processing helix chain 'B' and resid 654 through 659 removed outlier: 3.939A pdb=" N ARG B 657 " --> pdb=" O GLY B 654 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B 658 " --> pdb=" O SER B 655 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY B 659 " --> pdb=" O TRP B 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 654 through 659' Processing helix chain 'B' and resid 676 through 682 removed outlier: 3.971A pdb=" N LEU B 681 " --> pdb=" O THR B 677 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS B 682 " --> pdb=" O VAL B 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 536 removed outlier: 4.065A pdb=" N HIS C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 554 Processing helix chain 'C' and resid 561 through 576 Processing helix chain 'C' and resid 579 through 590 Processing helix chain 'C' and resid 591 through 595 removed outlier: 5.840A pdb=" N ASP C 594 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS C 595 " --> pdb=" O ASP C 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 591 through 595' Processing helix chain 'C' and resid 596 through 611 Processing helix chain 'C' and resid 615 through 629 Processing helix chain 'C' and resid 640 through 651 removed outlier: 3.526A pdb=" N VAL C 646 " --> pdb=" O VAL C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 658 Processing helix chain 'C' and resid 676 through 682 removed outlier: 3.604A pdb=" N LEU C 681 " --> pdb=" O THR C 677 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N HIS C 682 " --> pdb=" O VAL C 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 537 Processing helix chain 'D' and resid 543 through 554 Processing helix chain 'D' and resid 561 through 576 removed outlier: 3.507A pdb=" N ALA D 567 " --> pdb=" O PRO D 563 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 574 " --> pdb=" O GLY D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 591 removed outlier: 3.540A pdb=" N GLN D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER D 591 " --> pdb=" O LYS D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 595 removed outlier: 3.566A pdb=" N LYS D 595 " --> pdb=" O ASP D 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 592 through 595' Processing helix chain 'D' and resid 596 through 612 removed outlier: 3.828A pdb=" N LEU D 606 " --> pdb=" O LYS D 602 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU D 608 " --> pdb=" O GLU D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 629 Processing helix chain 'D' and resid 640 through 651 Processing helix chain 'D' and resid 654 through 658 Processing helix chain 'D' and resid 676 through 682 removed outlier: 3.782A pdb=" N HIS D 682 " --> pdb=" O VAL D 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 removed outlier: 4.003A pdb=" N SER A 527 " --> pdb=" O SER A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'A' and resid 541 through 554 Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.508A pdb=" N ALA A 567 " --> pdb=" O PRO A 563 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 570 " --> pdb=" O ARG A 566 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 574 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 590 Processing helix chain 'A' and resid 592 through 595 Processing helix chain 'A' and resid 596 through 612 removed outlier: 3.652A pdb=" N LYS A 600 " --> pdb=" O HIS A 596 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 601 " --> pdb=" O PRO A 597 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 609 " --> pdb=" O THR A 605 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 630 Processing helix chain 'A' and resid 641 through 651 removed outlier: 3.860A pdb=" N ASN A 645 " --> pdb=" O TYR A 641 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 646 " --> pdb=" O VAL A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 678 through 682 removed outlier: 3.706A pdb=" N HIS A 682 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 29 through 32 removed outlier: 3.534A pdb=" N PHE F 31 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.647A pdb=" N ARG F 37 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.540A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 32 removed outlier: 3.565A pdb=" N PHE H 31 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'H' and resid 169 through 170 removed outlier: 6.560A pdb=" N ASN H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'I' and resid 8 through 12 Processing sheet with id=AB5, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'I' and resid 105 through 107 removed outlier: 6.542A pdb=" N LEU I 105 " --> pdb=" O ALA I 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'I' and resid 131 through 132 Processing sheet with id=AB8, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AB9, first strand: chain 'I' and resid 169 through 170 removed outlier: 6.306A pdb=" N ASN I 297 " --> pdb=" O ILE I 330 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 238 through 241 Processing sheet with id=AC2, first strand: chain 'J' and resid 29 through 32 removed outlier: 3.538A pdb=" N PHE J 31 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR J 106 " --> pdb=" O CYS J 10 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASN J 12 " --> pdb=" O THR J 106 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.552A pdb=" N ARG J 37 " --> pdb=" O THR J 66 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 71 through 72 Processing sheet with id=AC5, first strand: chain 'J' and resid 176 through 178 removed outlier: 6.424A pdb=" N ASN J 297 " --> pdb=" O ILE J 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 176 through 178 removed outlier: 4.232A pdb=" N GLN K 41 " --> pdb=" O ALA J 170 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 238 through 241 Processing sheet with id=AC8, first strand: chain 'K' and resid 29 through 32 removed outlier: 3.878A pdb=" N THR K 106 " --> pdb=" O CYS K 10 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASN K 12 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'K' and resid 71 through 72 Processing sheet with id=AD2, first strand: chain 'K' and resid 169 through 170 Processing sheet with id=AD3, first strand: chain 'K' and resid 169 through 170 removed outlier: 6.232A pdb=" N ILE K 151 " --> pdb=" O VAL K 298 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N SER K 300 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU K 153 " --> pdb=" O SER K 300 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN K 297 " --> pdb=" O ILE K 330 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 238 through 241 Processing sheet with id=AD5, first strand: chain 'L' and resid 29 through 32 removed outlier: 3.502A pdb=" N PHE L 31 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR L 106 " --> pdb=" O CYS L 10 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASN L 12 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR L 133 " --> pdb=" O THR L 103 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'L' and resid 71 through 72 Processing sheet with id=AD8, first strand: chain 'L' and resid 169 through 170 removed outlier: 6.217A pdb=" N ILE L 151 " --> pdb=" O VAL L 298 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N SER L 300 " --> pdb=" O ILE L 151 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU L 153 " --> pdb=" O SER L 300 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASN L 297 " --> pdb=" O ILE L 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.840A pdb=" N LEU M 8 " --> pdb=" O LEU M 104 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N THR M 106 " --> pdb=" O LEU M 8 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N CYS M 10 " --> pdb=" O THR M 106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'M' and resid 169 through 170 Processing sheet with id=AE4, first strand: chain 'M' and resid 169 through 170 removed outlier: 6.541A pdb=" N ASN M 297 " --> pdb=" O ILE M 330 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 238 through 241 1236 hydrogen bonds defined for protein. 3195 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: 5.78 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4723 1.32 - 1.45: 6509 1.45 - 1.57: 14928 1.57 - 1.69: 21 1.69 - 1.81: 295 Bond restraints: 26476 Sorted by residual: bond pdb=" C ILE H 75 " pdb=" O ILE H 75 " ideal model delta sigma weight residual 1.236 1.202 0.034 1.02e-02 9.61e+03 1.13e+01 bond pdb=" CA HIC H 73 " pdb=" C HIC H 73 " ideal model delta sigma weight residual 1.525 1.455 0.070 2.10e-02 2.27e+03 1.10e+01 bond pdb=" O3 PO4 M 403 " pdb=" P PO4 M 403 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" CA ASN A 534 " pdb=" C ASN A 534 " ideal model delta sigma weight residual 1.522 1.478 0.045 1.41e-02 5.03e+03 9.97e+00 bond pdb=" CG HIC K 73 " pdb=" ND1 HIC K 73 " ideal model delta sigma weight residual 1.370 1.308 0.062 2.00e-02 2.50e+03 9.73e+00 ... (remaining 26471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 35305 2.21 - 4.42: 511 4.42 - 6.63: 85 6.63 - 8.83: 3 8.83 - 11.04: 1 Bond angle restraints: 35905 Sorted by residual: angle pdb=" N HIC H 73 " pdb=" CA HIC H 73 " pdb=" CB HIC H 73 " ideal model delta sigma weight residual 110.50 117.34 -6.84 1.70e+00 3.46e-01 1.62e+01 angle pdb=" C ILE I 71 " pdb=" CA ILE I 71 " pdb=" CB ILE I 71 " ideal model delta sigma weight residual 111.29 105.44 5.85 1.64e+00 3.72e-01 1.27e+01 angle pdb=" N ARG B 628 " pdb=" CA ARG B 628 " pdb=" C ARG B 628 " ideal model delta sigma weight residual 111.28 115.13 -3.85 1.09e+00 8.42e-01 1.25e+01 angle pdb=" O TYR H 69 " pdb=" C TYR H 69 " pdb=" N PRO H 70 " ideal model delta sigma weight residual 121.35 124.47 -3.12 9.20e-01 1.18e+00 1.15e+01 angle pdb=" N ASN A 534 " pdb=" CA ASN A 534 " pdb=" C ASN A 534 " ideal model delta sigma weight residual 112.38 108.33 4.05 1.22e+00 6.72e-01 1.10e+01 ... (remaining 35900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.70: 15627 34.70 - 69.41: 290 69.41 - 104.11: 41 104.11 - 138.81: 0 138.81 - 173.52: 7 Dihedral angle restraints: 15965 sinusoidal: 6477 harmonic: 9488 Sorted by residual: dihedral pdb=" C5' ADP K 401 " pdb=" O5' ADP K 401 " pdb=" PA ADP K 401 " pdb=" O2A ADP K 401 " ideal model delta sinusoidal sigma weight residual -60.00 113.52 -173.52 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP L 401 " pdb=" O5' ADP L 401 " pdb=" PA ADP L 401 " pdb=" O2A ADP L 401 " ideal model delta sinusoidal sigma weight residual 300.00 128.95 171.05 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' ADP I 401 " pdb=" O5' ADP I 401 " pdb=" PA ADP I 401 " pdb=" O2A ADP I 401 " ideal model delta sinusoidal sigma weight residual -60.00 107.61 -167.61 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 15962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2298 0.033 - 0.067: 1164 0.067 - 0.100: 341 0.100 - 0.133: 181 0.133 - 0.167: 9 Chirality restraints: 3993 Sorted by residual: chirality pdb=" CB THR C 633 " pdb=" CA THR C 633 " pdb=" OG1 THR C 633 " pdb=" CG2 THR C 633 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" C2' ADP J 401 " pdb=" C1' ADP J 401 " pdb=" C3' ADP J 401 " pdb=" O2' ADP J 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA ILE K 75 " pdb=" N ILE K 75 " pdb=" C ILE K 75 " pdb=" CB ILE K 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 3990 not shown) Planarity restraints: 4597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 340 " -0.021 2.00e-02 2.50e+03 1.95e-02 9.52e+00 pdb=" CG TRP F 340 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP F 340 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 340 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 340 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 340 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 340 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 340 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 340 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP F 340 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN J 111 " -0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO J 112 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO J 112 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO J 112 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR H 304 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C THR H 304 " 0.026 2.00e-02 2.50e+03 pdb=" O THR H 304 " -0.009 2.00e-02 2.50e+03 pdb=" N MET H 305 " -0.009 2.00e-02 2.50e+03 ... (remaining 4594 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 110 2.49 - 3.10: 18505 3.10 - 3.70: 38151 3.70 - 4.30: 56814 4.30 - 4.90: 95076 Nonbonded interactions: 208656 Sorted by model distance: nonbonded pdb=" O1B ADP L 401 " pdb="MG MG L 402 " model vdw 1.893 2.170 nonbonded pdb=" O1B ADP J 401 " pdb="MG MG J 402 " model vdw 1.902 2.170 nonbonded pdb="MG MG H 402 " pdb=" O2 PO4 H 403 " model vdw 1.904 2.170 nonbonded pdb=" O1B ADP H 401 " pdb="MG MG H 402 " model vdw 1.907 2.170 nonbonded pdb="MG MG F 402 " pdb=" O4 PO4 F 403 " model vdw 1.987 2.170 ... (remaining 208651 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 25.710 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.011 0.897 26479 Z= 0.976 Angle : 0.634 11.042 35905 Z= 0.313 Chirality : 0.045 0.167 3993 Planarity : 0.004 0.046 4597 Dihedral : 14.505 173.516 9875 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.43 % Allowed : 0.43 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.15), residues: 3242 helix: 0.44 (0.14), residues: 1419 sheet: -0.05 (0.23), residues: 483 loop : 0.24 (0.18), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 565 TYR 0.022 0.001 TYR D 662 PHE 0.012 0.001 PHE L 200 TRP 0.051 0.002 TRP F 340 HIS 0.011 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00494 (26476) covalent geometry : angle 0.63382 (35905) hydrogen bonds : bond 0.23914 ( 1222) hydrogen bonds : angle 7.05803 ( 3195) Misc. bond : bond 0.89139 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 436 time to evaluate : 1.116 Fit side-chains REVERT: F 43 VAL cc_start: 0.8948 (t) cc_final: 0.8741 (t) REVERT: F 44 MET cc_start: 0.5682 (mmm) cc_final: 0.5273 (mmm) REVERT: F 76 ILE cc_start: 0.8962 (mt) cc_final: 0.8753 (mt) REVERT: F 107 GLU cc_start: 0.8121 (tt0) cc_final: 0.7846 (pt0) REVERT: H 65 LEU cc_start: 0.9311 (mt) cc_final: 0.9107 (mt) REVERT: H 227 MET cc_start: 0.8006 (tpp) cc_final: 0.7775 (tpp) REVERT: H 305 MET cc_start: 0.8397 (mmm) cc_final: 0.8179 (mmt) REVERT: H 326 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7837 (tttm) REVERT: I 374 CYS cc_start: 0.7039 (m) cc_final: 0.6665 (m) REVERT: K 191 LYS cc_start: 0.8057 (ttpt) cc_final: 0.7846 (ttpt) REVERT: K 206 ARG cc_start: 0.7349 (ttp-170) cc_final: 0.7102 (tpp80) REVERT: L 118 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7350 (tppp) REVERT: B 536 HIS cc_start: 0.7751 (m170) cc_final: 0.7464 (m-70) REVERT: D 538 MET cc_start: 0.8422 (tpp) cc_final: 0.8150 (ttm) REVERT: A 638 GLU cc_start: 0.6603 (pm20) cc_final: 0.6013 (tm-30) outliers start: 12 outliers final: 3 residues processed: 443 average time/residue: 0.1573 time to fit residues: 114.9644 Evaluate side-chains 348 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 344 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain A residue 533 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.4980 chunk 298 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 12 ASN H 12 ASN H 162 ASN K 101 HIS K 162 ASN C 645 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.132017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.105942 restraints weight = 40217.619| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.50 r_work: 0.3174 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26479 Z= 0.140 Angle : 0.592 10.198 35905 Z= 0.293 Chirality : 0.044 0.146 3993 Planarity : 0.004 0.039 4597 Dihedral : 8.184 178.131 3668 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.04 % Allowed : 7.59 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.15), residues: 3242 helix: 0.91 (0.15), residues: 1399 sheet: 0.11 (0.24), residues: 469 loop : 0.34 (0.18), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 37 TYR 0.035 0.001 TYR C 641 PHE 0.011 0.001 PHE A 626 TRP 0.028 0.001 TRP F 340 HIS 0.005 0.001 HIS C 613 Details of bonding type rmsd covalent geometry : bond 0.00315 (26476) covalent geometry : angle 0.59240 (35905) hydrogen bonds : bond 0.03901 ( 1222) hydrogen bonds : angle 4.86978 ( 3195) Misc. bond : bond 0.00306 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 371 time to evaluate : 1.112 Fit side-chains REVERT: F 41 GLN cc_start: 0.7957 (pm20) cc_final: 0.7205 (tp40) REVERT: F 44 MET cc_start: 0.5486 (mmm) cc_final: 0.5279 (mtp) REVERT: F 59 GLN cc_start: 0.8401 (mm110) cc_final: 0.8163 (tp40) REVERT: F 225 ASN cc_start: 0.8089 (t0) cc_final: 0.7866 (t0) REVERT: H 47 MET cc_start: 0.5739 (ppp) cc_final: 0.5446 (ppp) REVERT: H 65 LEU cc_start: 0.9282 (mt) cc_final: 0.9057 (mt) REVERT: H 227 MET cc_start: 0.8058 (tpp) cc_final: 0.7790 (tpp) REVERT: H 286 ASP cc_start: 0.8556 (t0) cc_final: 0.7862 (m-30) REVERT: H 326 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7864 (tttm) REVERT: I 72 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7011 (tp30) REVERT: I 148 THR cc_start: 0.8655 (p) cc_final: 0.8400 (m) REVERT: I 286 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: I 374 CYS cc_start: 0.6797 (m) cc_final: 0.6445 (m) REVERT: J 10 CYS cc_start: 0.8401 (t) cc_final: 0.8172 (t) REVERT: J 132 MET cc_start: 0.8497 (ppp) cc_final: 0.8266 (ptm) REVERT: K 82 MET cc_start: 0.8164 (tpt) cc_final: 0.7593 (tpt) REVERT: K 191 LYS cc_start: 0.8097 (ttpt) cc_final: 0.7732 (ttpt) REVERT: L 25 ASP cc_start: 0.8022 (p0) cc_final: 0.7667 (t0) REVERT: L 136 ILE cc_start: 0.8538 (mm) cc_final: 0.8334 (mm) REVERT: M 270 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8572 (tp30) REVERT: B 536 HIS cc_start: 0.7885 (m170) cc_final: 0.7579 (m-70) REVERT: B 574 GLU cc_start: 0.7428 (tt0) cc_final: 0.6996 (pt0) outliers start: 29 outliers final: 14 residues processed: 388 average time/residue: 0.1707 time to fit residues: 107.4753 Evaluate side-chains 349 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 332 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 594 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 115 optimal weight: 4.9990 chunk 253 optimal weight: 0.1980 chunk 42 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 38 optimal weight: 0.1980 chunk 119 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 249 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 ASN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 ASN K 101 HIS K 162 ASN ** K 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105290 restraints weight = 40726.665| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.52 r_work: 0.3167 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26479 Z= 0.129 Angle : 0.549 8.136 35905 Z= 0.266 Chirality : 0.043 0.147 3993 Planarity : 0.004 0.039 4597 Dihedral : 7.511 172.970 3663 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.22 % Allowed : 10.04 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.15), residues: 3242 helix: 1.12 (0.15), residues: 1399 sheet: 0.20 (0.24), residues: 469 loop : 0.41 (0.18), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 565 TYR 0.027 0.001 TYR C 641 PHE 0.009 0.001 PHE I 200 TRP 0.018 0.002 TRP F 340 HIS 0.004 0.001 HIS J 161 Details of bonding type rmsd covalent geometry : bond 0.00298 (26476) covalent geometry : angle 0.54852 (35905) hydrogen bonds : bond 0.03568 ( 1222) hydrogen bonds : angle 4.52398 ( 3195) Misc. bond : bond 0.00108 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 346 time to evaluate : 1.115 Fit side-chains REVERT: F 41 GLN cc_start: 0.7941 (pm20) cc_final: 0.7247 (tp40) REVERT: F 59 GLN cc_start: 0.8461 (mm110) cc_final: 0.8195 (tp40) REVERT: F 125 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7465 (mp0) REVERT: F 216 LEU cc_start: 0.8233 (mt) cc_final: 0.8018 (mp) REVERT: F 222 ASP cc_start: 0.8045 (t0) cc_final: 0.7612 (t0) REVERT: F 225 ASN cc_start: 0.8045 (t0) cc_final: 0.7807 (t0) REVERT: F 340 TRP cc_start: 0.8418 (t60) cc_final: 0.8012 (t60) REVERT: H 227 MET cc_start: 0.8011 (tpp) cc_final: 0.7714 (tpp) REVERT: H 326 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7901 (tttm) REVERT: I 44 MET cc_start: 0.8337 (mtp) cc_final: 0.8061 (mtm) REVERT: I 72 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: I 119 MET cc_start: 0.8214 (ttm) cc_final: 0.7979 (mtm) REVERT: I 143 TYR cc_start: 0.7581 (m-80) cc_final: 0.6914 (m-80) REVERT: I 286 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8135 (m-30) REVERT: I 374 CYS cc_start: 0.6808 (m) cc_final: 0.6485 (m) REVERT: J 132 MET cc_start: 0.8605 (ppp) cc_final: 0.8339 (ptm) REVERT: K 123 MET cc_start: 0.8912 (mmt) cc_final: 0.8656 (mmm) REVERT: K 191 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7823 (ttpt) REVERT: K 227 MET cc_start: 0.7824 (mmm) cc_final: 0.7429 (mmm) REVERT: L 25 ASP cc_start: 0.8019 (p0) cc_final: 0.7698 (t0) REVERT: L 136 ILE cc_start: 0.8536 (mm) cc_final: 0.8320 (mm) REVERT: L 236 LEU cc_start: 0.8318 (mp) cc_final: 0.8079 (mp) REVERT: L 340 TRP cc_start: 0.8831 (t60) cc_final: 0.8325 (t60) REVERT: M 270 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8554 (tp30) REVERT: B 536 HIS cc_start: 0.7909 (m170) cc_final: 0.7590 (m-70) REVERT: B 574 GLU cc_start: 0.7398 (tt0) cc_final: 0.6898 (pt0) REVERT: A 648 ASP cc_start: 0.7683 (m-30) cc_final: 0.7415 (m-30) REVERT: A 675 ILE cc_start: 0.8701 (mm) cc_final: 0.8168 (mm) outliers start: 34 outliers final: 20 residues processed: 370 average time/residue: 0.1678 time to fit residues: 102.5159 Evaluate side-chains 361 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 338 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 651 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 209 optimal weight: 6.9990 chunk 321 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 269 optimal weight: 3.9990 chunk 150 optimal weight: 0.1980 chunk 256 optimal weight: 4.9990 chunk 306 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 ASN I 12 ASN I 162 ASN J 12 ASN K 101 HIS K 162 ASN M 88 HIS ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.127300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.101573 restraints weight = 40838.452| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.40 r_work: 0.3113 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 26479 Z= 0.239 Angle : 0.631 8.010 35905 Z= 0.313 Chirality : 0.047 0.166 3993 Planarity : 0.004 0.039 4597 Dihedral : 7.513 169.926 3662 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.80 % Allowed : 11.41 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.15), residues: 3242 helix: 1.07 (0.15), residues: 1378 sheet: -0.22 (0.24), residues: 462 loop : 0.13 (0.17), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 95 TYR 0.026 0.002 TYR C 641 PHE 0.015 0.002 PHE H 375 TRP 0.014 0.002 TRP J 356 HIS 0.006 0.001 HIS J 161 Details of bonding type rmsd covalent geometry : bond 0.00558 (26476) covalent geometry : angle 0.63107 (35905) hydrogen bonds : bond 0.04103 ( 1222) hydrogen bonds : angle 4.70293 ( 3195) Misc. bond : bond 0.00060 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 335 time to evaluate : 0.989 Fit side-chains REVERT: F 216 LEU cc_start: 0.8286 (mt) cc_final: 0.8030 (mp) REVERT: F 222 ASP cc_start: 0.8208 (t0) cc_final: 0.7669 (t0) REVERT: F 225 ASN cc_start: 0.8203 (t0) cc_final: 0.7976 (t0) REVERT: F 269 MET cc_start: 0.9009 (ttm) cc_final: 0.8743 (mtp) REVERT: F 340 TRP cc_start: 0.8592 (t60) cc_final: 0.8077 (t60) REVERT: H 41 GLN cc_start: 0.7187 (tp-100) cc_final: 0.6945 (pt0) REVERT: H 221 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8467 (tt) REVERT: H 227 MET cc_start: 0.8159 (tpp) cc_final: 0.7861 (tpp) REVERT: I 44 MET cc_start: 0.8524 (mtp) cc_final: 0.8289 (mtm) REVERT: I 72 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: I 286 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8400 (m-30) REVERT: I 358 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8528 (m) REVERT: I 374 CYS cc_start: 0.7198 (m) cc_final: 0.6892 (m) REVERT: K 77 THR cc_start: 0.8979 (m) cc_final: 0.8646 (p) REVERT: K 123 MET cc_start: 0.8950 (mmt) cc_final: 0.8693 (mmm) REVERT: K 191 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7956 (ttpt) REVERT: L 25 ASP cc_start: 0.8300 (p0) cc_final: 0.7853 (t0) REVERT: L 83 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7509 (tm-30) REVERT: L 340 TRP cc_start: 0.8983 (t60) cc_final: 0.8442 (t60) REVERT: M 270 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8424 (tp30) REVERT: B 536 HIS cc_start: 0.7817 (m170) cc_final: 0.7449 (m-70) REVERT: B 574 GLU cc_start: 0.7344 (tt0) cc_final: 0.6802 (pt0) REVERT: D 666 LEU cc_start: 0.7851 (tp) cc_final: 0.6989 (pt) REVERT: A 638 GLU cc_start: 0.6775 (pm20) cc_final: 0.6334 (tm-30) REVERT: A 648 ASP cc_start: 0.7818 (m-30) cc_final: 0.7487 (m-30) REVERT: A 675 ILE cc_start: 0.8474 (mm) cc_final: 0.7903 (mm) outliers start: 50 outliers final: 35 residues processed: 368 average time/residue: 0.1403 time to fit residues: 85.9841 Evaluate side-chains 350 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 310 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain I residue 297 ASN Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 639 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 288 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 250 optimal weight: 0.0020 chunk 73 optimal weight: 0.5980 chunk 179 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 217 optimal weight: 0.0270 chunk 204 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 overall best weight: 0.7048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 ASN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 ASN J 41 GLN K 101 HIS K 162 ASN M 12 ASN ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.104857 restraints weight = 40300.770| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.39 r_work: 0.3165 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26479 Z= 0.106 Angle : 0.541 7.367 35905 Z= 0.262 Chirality : 0.043 0.140 3993 Planarity : 0.004 0.037 4597 Dihedral : 7.199 164.388 3662 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.84 % Allowed : 12.52 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.15), residues: 3242 helix: 1.28 (0.15), residues: 1378 sheet: -0.17 (0.23), residues: 462 loop : 0.29 (0.17), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 95 TYR 0.030 0.001 TYR C 641 PHE 0.011 0.001 PHE H 375 TRP 0.013 0.001 TRP F 340 HIS 0.005 0.001 HIS K 161 Details of bonding type rmsd covalent geometry : bond 0.00238 (26476) covalent geometry : angle 0.54054 (35905) hydrogen bonds : bond 0.03068 ( 1222) hydrogen bonds : angle 4.36585 ( 3195) Misc. bond : bond 0.00033 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 349 time to evaluate : 1.058 Fit side-chains REVERT: F 125 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7375 (mp0) REVERT: F 216 LEU cc_start: 0.8202 (mt) cc_final: 0.7918 (mp) REVERT: F 222 ASP cc_start: 0.8048 (t0) cc_final: 0.7534 (t0) REVERT: F 313 MET cc_start: 0.8995 (tpp) cc_final: 0.8758 (mmm) REVERT: H 221 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8476 (tt) REVERT: H 227 MET cc_start: 0.8093 (tpp) cc_final: 0.7807 (tpp) REVERT: H 237 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8375 (mt-10) REVERT: I 44 MET cc_start: 0.8385 (mtp) cc_final: 0.8111 (mtm) REVERT: I 72 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: I 269 MET cc_start: 0.8789 (mtm) cc_final: 0.8501 (mtm) REVERT: I 286 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.8005 (m-30) REVERT: I 358 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8352 (m) REVERT: K 77 THR cc_start: 0.8961 (m) cc_final: 0.8617 (p) REVERT: K 123 MET cc_start: 0.8857 (mmt) cc_final: 0.8565 (mmm) REVERT: K 132 MET cc_start: 0.9174 (ttp) cc_final: 0.8906 (ttp) REVERT: K 191 LYS cc_start: 0.8135 (ttpt) cc_final: 0.7836 (ttpt) REVERT: L 25 ASP cc_start: 0.8168 (p0) cc_final: 0.7786 (t0) REVERT: L 83 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7292 (tt0) REVERT: L 236 LEU cc_start: 0.8393 (mp) cc_final: 0.8149 (mp) REVERT: L 340 TRP cc_start: 0.8897 (t60) cc_final: 0.8398 (t60) REVERT: M 82 MET cc_start: 0.7776 (tpp) cc_final: 0.7359 (tpt) REVERT: M 92 ASN cc_start: 0.8806 (m-40) cc_final: 0.8239 (m-40) REVERT: M 270 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8589 (tp30) REVERT: B 536 HIS cc_start: 0.7843 (m170) cc_final: 0.7478 (m-70) REVERT: B 574 GLU cc_start: 0.7292 (tt0) cc_final: 0.6820 (pt0) REVERT: C 598 GLU cc_start: 0.7317 (pm20) cc_final: 0.7064 (pm20) REVERT: A 648 ASP cc_start: 0.7999 (m-30) cc_final: 0.7651 (m-30) REVERT: A 675 ILE cc_start: 0.8590 (mm) cc_final: 0.8050 (mm) outliers start: 51 outliers final: 32 residues processed: 385 average time/residue: 0.1562 time to fit residues: 100.8915 Evaluate side-chains 354 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 317 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain M residue 360 GLN Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 598 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 250 optimal weight: 0.1980 chunk 298 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 178 optimal weight: 0.0980 chunk 136 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 chunk 241 optimal weight: 4.9990 chunk 311 optimal weight: 9.9990 chunk 228 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 ASN I 12 ASN J 12 ASN K 101 HIS K 162 ASN A 523 ASN A 615 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.129974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104102 restraints weight = 40634.247| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.49 r_work: 0.3151 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26479 Z= 0.126 Angle : 0.548 9.417 35905 Z= 0.264 Chirality : 0.043 0.189 3993 Planarity : 0.004 0.035 4597 Dihedral : 6.898 156.148 3662 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.05 % Allowed : 13.06 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.15), residues: 3242 helix: 1.34 (0.15), residues: 1378 sheet: -0.18 (0.23), residues: 462 loop : 0.32 (0.17), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 551 TYR 0.033 0.001 TYR C 641 PHE 0.009 0.001 PHE I 31 TRP 0.014 0.001 TRP A 656 HIS 0.006 0.001 HIS K 161 Details of bonding type rmsd covalent geometry : bond 0.00295 (26476) covalent geometry : angle 0.54827 (35905) hydrogen bonds : bond 0.03072 ( 1222) hydrogen bonds : angle 4.31815 ( 3195) Misc. bond : bond 0.00045 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 329 time to evaluate : 1.266 Fit side-chains REVERT: F 125 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7446 (mp0) REVERT: F 216 LEU cc_start: 0.8280 (mt) cc_final: 0.7960 (mp) REVERT: F 222 ASP cc_start: 0.8040 (t0) cc_final: 0.7543 (t0) REVERT: H 221 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8527 (tt) REVERT: H 237 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8394 (mt-10) REVERT: I 44 MET cc_start: 0.8362 (mtp) cc_final: 0.8106 (mtm) REVERT: I 72 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7594 (mt-10) REVERT: I 269 MET cc_start: 0.8813 (mtm) cc_final: 0.8519 (mtm) REVERT: I 286 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: I 358 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8353 (m) REVERT: K 77 THR cc_start: 0.8968 (m) cc_final: 0.8628 (p) REVERT: K 123 MET cc_start: 0.8865 (mmt) cc_final: 0.8590 (mmm) REVERT: K 132 MET cc_start: 0.9123 (ttp) cc_final: 0.8815 (ttp) REVERT: K 191 LYS cc_start: 0.8190 (ttpt) cc_final: 0.7877 (ttpt) REVERT: L 25 ASP cc_start: 0.8177 (p0) cc_final: 0.7798 (t0) REVERT: L 83 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7359 (tt0) REVERT: L 340 TRP cc_start: 0.8901 (t60) cc_final: 0.8422 (t60) REVERT: M 82 MET cc_start: 0.7820 (tpp) cc_final: 0.7433 (tpt) REVERT: M 270 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8418 (tp30) REVERT: B 536 HIS cc_start: 0.7924 (m170) cc_final: 0.7542 (m-70) REVERT: B 574 GLU cc_start: 0.7303 (tt0) cc_final: 0.6842 (pt0) REVERT: B 665 TYR cc_start: 0.7304 (m-80) cc_final: 0.6931 (m-80) REVERT: C 537 SER cc_start: 0.8988 (t) cc_final: 0.8602 (t) REVERT: A 640 ASP cc_start: 0.7497 (t0) cc_final: 0.6494 (p0) REVERT: A 648 ASP cc_start: 0.8047 (m-30) cc_final: 0.7709 (m-30) REVERT: A 675 ILE cc_start: 0.8645 (mm) cc_final: 0.8121 (mm) outliers start: 57 outliers final: 42 residues processed: 369 average time/residue: 0.1452 time to fit residues: 89.7575 Evaluate side-chains 362 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 315 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain M residue 360 GLN Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 639 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 252 optimal weight: 0.9980 chunk 278 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 169 optimal weight: 0.0980 chunk 19 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 HIS H 12 ASN H 162 ASN I 162 ASN J 12 ASN K 101 HIS K 162 ASN L 40 HIS D 684 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.100163 restraints weight = 41060.110| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.39 r_work: 0.3095 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 26479 Z= 0.273 Angle : 0.670 9.002 35905 Z= 0.333 Chirality : 0.048 0.169 3993 Planarity : 0.004 0.037 4597 Dihedral : 7.008 156.592 3662 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.45 % Allowed : 13.06 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.15), residues: 3242 helix: 1.08 (0.15), residues: 1378 sheet: -0.41 (0.23), residues: 462 loop : -0.00 (0.17), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 256 TYR 0.029 0.002 TYR C 641 PHE 0.023 0.002 PHE H 223 TRP 0.018 0.002 TRP A 656 HIS 0.008 0.001 HIS K 161 Details of bonding type rmsd covalent geometry : bond 0.00643 (26476) covalent geometry : angle 0.67019 (35905) hydrogen bonds : bond 0.04176 ( 1222) hydrogen bonds : angle 4.70057 ( 3195) Misc. bond : bond 0.00053 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 318 time to evaluate : 0.953 Fit side-chains REVERT: F 216 LEU cc_start: 0.8306 (mt) cc_final: 0.8016 (mp) REVERT: F 222 ASP cc_start: 0.8162 (t0) cc_final: 0.7668 (t0) REVERT: H 221 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8661 (tt) REVERT: I 72 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7656 (mt-10) REVERT: I 78 ASN cc_start: 0.8446 (t0) cc_final: 0.8199 (t0) REVERT: I 286 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8139 (m-30) REVERT: I 358 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8473 (m) REVERT: J 180 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8877 (tp) REVERT: J 291 LYS cc_start: 0.8413 (ttpp) cc_final: 0.8070 (tptt) REVERT: K 12 ASN cc_start: 0.8891 (p0) cc_final: 0.8599 (p0) REVERT: K 82 MET cc_start: 0.8305 (tpt) cc_final: 0.7746 (tpt) REVERT: K 123 MET cc_start: 0.8897 (mmt) cc_final: 0.8643 (mmm) REVERT: K 126 THR cc_start: 0.8751 (m) cc_final: 0.8412 (p) REVERT: K 132 MET cc_start: 0.9146 (ttp) cc_final: 0.8831 (ttp) REVERT: K 328 LYS cc_start: 0.8381 (mttp) cc_final: 0.7511 (ptmm) REVERT: L 25 ASP cc_start: 0.8231 (p0) cc_final: 0.7932 (t0) REVERT: L 83 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7346 (tt0) REVERT: L 340 TRP cc_start: 0.8990 (t60) cc_final: 0.8502 (t60) REVERT: M 270 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8399 (tp30) REVERT: B 536 HIS cc_start: 0.7802 (m170) cc_final: 0.7433 (m-70) REVERT: B 574 GLU cc_start: 0.7261 (tt0) cc_final: 0.6815 (pt0) REVERT: B 665 TYR cc_start: 0.7376 (m-80) cc_final: 0.7033 (m-80) REVERT: C 537 SER cc_start: 0.9004 (t) cc_final: 0.8662 (t) REVERT: D 538 MET cc_start: 0.8157 (ttm) cc_final: 0.7927 (ttp) REVERT: D 666 LEU cc_start: 0.7749 (tp) cc_final: 0.7024 (pt) REVERT: A 648 ASP cc_start: 0.8094 (m-30) cc_final: 0.7737 (m-30) REVERT: A 675 ILE cc_start: 0.8678 (mm) cc_final: 0.8173 (mt) outliers start: 68 outliers final: 53 residues processed: 366 average time/residue: 0.1558 time to fit residues: 94.3895 Evaluate side-chains 365 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 306 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 244 ASP Chi-restraints excluded: chain I residue 270 GLU Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain M residue 360 GLN Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain D residue 555 GLU Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 639 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 236 optimal weight: 1.9990 chunk 294 optimal weight: 0.0570 chunk 169 optimal weight: 0.2980 chunk 121 optimal weight: 0.3980 chunk 238 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 226 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 202 optimal weight: 3.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 12 ASN H 162 ASN J 12 ASN K 41 GLN K 101 HIS K 162 ASN L 59 GLN D 684 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.130747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105215 restraints weight = 40298.257| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.51 r_work: 0.3165 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 26479 Z= 0.094 Angle : 0.550 12.385 35905 Z= 0.264 Chirality : 0.042 0.139 3993 Planarity : 0.004 0.040 4597 Dihedral : 6.602 145.508 3662 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.66 % Allowed : 14.11 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.15), residues: 3242 helix: 1.35 (0.15), residues: 1378 sheet: -0.17 (0.23), residues: 469 loop : 0.30 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 543 TYR 0.029 0.001 TYR C 641 PHE 0.030 0.001 PHE H 223 TRP 0.017 0.001 TRP A 656 HIS 0.008 0.001 HIS K 161 Details of bonding type rmsd covalent geometry : bond 0.00204 (26476) covalent geometry : angle 0.54998 (35905) hydrogen bonds : bond 0.02777 ( 1222) hydrogen bonds : angle 4.25768 ( 3195) Misc. bond : bond 0.00022 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 332 time to evaluate : 1.064 Fit side-chains REVERT: F 125 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7555 (mp0) REVERT: F 216 LEU cc_start: 0.8312 (mt) cc_final: 0.8003 (mp) REVERT: F 222 ASP cc_start: 0.8067 (t0) cc_final: 0.7618 (t0) REVERT: H 221 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8661 (tt) REVERT: H 237 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8408 (mt-10) REVERT: I 44 MET cc_start: 0.8334 (mtp) cc_final: 0.8112 (mtm) REVERT: I 72 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: I 269 MET cc_start: 0.8769 (mtm) cc_final: 0.8470 (mtm) REVERT: I 286 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: I 358 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8347 (m) REVERT: J 119 MET cc_start: 0.8467 (mtp) cc_final: 0.8242 (mtm) REVERT: J 180 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8923 (tp) REVERT: K 12 ASN cc_start: 0.8836 (p0) cc_final: 0.8555 (p0) REVERT: K 77 THR cc_start: 0.8994 (m) cc_final: 0.8678 (p) REVERT: K 82 MET cc_start: 0.8190 (tpt) cc_final: 0.7669 (tpt) REVERT: K 123 MET cc_start: 0.8867 (mmt) cc_final: 0.8594 (mmm) REVERT: K 132 MET cc_start: 0.9126 (ttp) cc_final: 0.8812 (ttp) REVERT: K 227 MET cc_start: 0.7772 (mmm) cc_final: 0.7224 (mmm) REVERT: K 328 LYS cc_start: 0.8329 (mttp) cc_final: 0.7639 (tttm) REVERT: L 25 ASP cc_start: 0.8146 (p0) cc_final: 0.7817 (t0) REVERT: L 83 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7227 (tt0) REVERT: L 236 LEU cc_start: 0.8431 (mp) cc_final: 0.8176 (mp) REVERT: L 340 TRP cc_start: 0.8867 (t60) cc_final: 0.8449 (t60) REVERT: L 364 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8514 (tp30) REVERT: M 270 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8380 (tp30) REVERT: B 536 HIS cc_start: 0.7904 (m170) cc_final: 0.7529 (m-70) REVERT: B 574 GLU cc_start: 0.7264 (tt0) cc_final: 0.6862 (pt0) REVERT: B 665 TYR cc_start: 0.7355 (m-80) cc_final: 0.6975 (m-80) REVERT: B 683 MET cc_start: 0.7556 (ptm) cc_final: 0.7276 (ptm) REVERT: C 537 SER cc_start: 0.8980 (t) cc_final: 0.8609 (t) REVERT: A 648 ASP cc_start: 0.8124 (m-30) cc_final: 0.7758 (m-30) REVERT: A 675 ILE cc_start: 0.8672 (mm) cc_final: 0.8154 (mm) outliers start: 46 outliers final: 31 residues processed: 361 average time/residue: 0.1600 time to fit residues: 96.6563 Evaluate side-chains 359 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 322 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 639 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 72 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 298 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 316 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 249 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 323 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 12 ASN H 162 ASN K 101 HIS K 162 ASN D 684 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.126658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101158 restraints weight = 41300.390| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.40 r_work: 0.3108 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26479 Z= 0.231 Angle : 0.632 11.236 35905 Z= 0.310 Chirality : 0.047 0.158 3993 Planarity : 0.004 0.039 4597 Dihedral : 6.734 146.349 3662 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.05 % Allowed : 13.93 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.15), residues: 3242 helix: 1.20 (0.15), residues: 1378 sheet: -0.27 (0.23), residues: 469 loop : 0.11 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 543 TYR 0.027 0.002 TYR C 641 PHE 0.018 0.002 PHE B 540 TRP 0.020 0.002 TRP A 656 HIS 0.007 0.001 HIS J 161 Details of bonding type rmsd covalent geometry : bond 0.00545 (26476) covalent geometry : angle 0.63238 (35905) hydrogen bonds : bond 0.03808 ( 1222) hydrogen bonds : angle 4.52770 ( 3195) Misc. bond : bond 0.00052 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 318 time to evaluate : 0.995 Fit side-chains REVERT: F 125 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7453 (mp0) REVERT: F 216 LEU cc_start: 0.8345 (mt) cc_final: 0.8067 (mp) REVERT: F 222 ASP cc_start: 0.8254 (t0) cc_final: 0.7703 (t0) REVERT: H 221 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8676 (tt) REVERT: I 72 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: I 78 ASN cc_start: 0.8544 (t0) cc_final: 0.8300 (t0) REVERT: I 358 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8495 (m) REVERT: J 180 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8911 (tp) REVERT: J 291 LYS cc_start: 0.8475 (ttpp) cc_final: 0.8064 (tptt) REVERT: K 12 ASN cc_start: 0.8999 (p0) cc_final: 0.8723 (p0) REVERT: K 77 THR cc_start: 0.8984 (m) cc_final: 0.8646 (p) REVERT: K 82 MET cc_start: 0.8342 (tpt) cc_final: 0.7815 (tpt) REVERT: K 123 MET cc_start: 0.8925 (mmt) cc_final: 0.8670 (mmm) REVERT: K 132 MET cc_start: 0.9256 (ttp) cc_final: 0.8915 (ttp) REVERT: K 328 LYS cc_start: 0.8338 (mttp) cc_final: 0.7617 (tttp) REVERT: L 25 ASP cc_start: 0.8436 (p0) cc_final: 0.7979 (t0) REVERT: L 83 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7438 (tt0) REVERT: L 340 TRP cc_start: 0.9023 (t60) cc_final: 0.8537 (t60) REVERT: L 364 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8726 (tp30) REVERT: M 270 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8498 (tp30) REVERT: B 536 HIS cc_start: 0.7838 (m170) cc_final: 0.7444 (m-70) REVERT: B 574 GLU cc_start: 0.7273 (tt0) cc_final: 0.6818 (pt0) REVERT: C 537 SER cc_start: 0.8993 (t) cc_final: 0.8671 (t) REVERT: D 666 LEU cc_start: 0.7729 (tp) cc_final: 0.7002 (pt) REVERT: A 648 ASP cc_start: 0.8018 (m-30) cc_final: 0.7643 (m-30) REVERT: A 675 ILE cc_start: 0.8582 (mm) cc_final: 0.8075 (mt) outliers start: 57 outliers final: 42 residues processed: 358 average time/residue: 0.1481 time to fit residues: 89.0056 Evaluate side-chains 356 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 309 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain H residue 12 ASN Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain D residue 555 GLU Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 639 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 196 optimal weight: 2.9990 chunk 108 optimal weight: 0.0370 chunk 234 optimal weight: 0.9990 chunk 280 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 278 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 275 optimal weight: 0.0870 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 ASN I 162 ASN K 101 HIS K 162 ASN D 684 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.104542 restraints weight = 40603.161| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.52 r_work: 0.3155 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26479 Z= 0.100 Angle : 0.561 12.787 35905 Z= 0.268 Chirality : 0.043 0.142 3993 Planarity : 0.004 0.037 4597 Dihedral : 6.475 136.082 3662 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.37 % Allowed : 14.79 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.15), residues: 3242 helix: 1.36 (0.15), residues: 1385 sheet: -0.19 (0.23), residues: 469 loop : 0.27 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 543 TYR 0.028 0.001 TYR C 641 PHE 0.017 0.001 PHE H 223 TRP 0.019 0.002 TRP A 656 HIS 0.005 0.001 HIS K 161 Details of bonding type rmsd covalent geometry : bond 0.00225 (26476) covalent geometry : angle 0.56097 (35905) hydrogen bonds : bond 0.02848 ( 1222) hydrogen bonds : angle 4.23550 ( 3195) Misc. bond : bond 0.00045 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 332 time to evaluate : 1.058 Fit side-chains REVERT: F 125 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7504 (mp0) REVERT: F 216 LEU cc_start: 0.8340 (mt) cc_final: 0.8032 (mp) REVERT: F 222 ASP cc_start: 0.8051 (t0) cc_final: 0.7596 (t0) REVERT: F 313 MET cc_start: 0.9051 (tpp) cc_final: 0.8825 (mmm) REVERT: H 221 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8666 (tt) REVERT: H 237 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8471 (mt-10) REVERT: I 72 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: I 269 MET cc_start: 0.8765 (mtm) cc_final: 0.8479 (mtm) REVERT: I 283 MET cc_start: 0.8662 (mmt) cc_final: 0.8462 (mmm) REVERT: I 358 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8429 (p) REVERT: J 47 MET cc_start: 0.7841 (mmm) cc_final: 0.7386 (mmm) REVERT: J 119 MET cc_start: 0.8450 (mtp) cc_final: 0.8236 (mtm) REVERT: J 155 SER cc_start: 0.9235 (t) cc_final: 0.9029 (t) REVERT: J 180 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8949 (tp) REVERT: J 291 LYS cc_start: 0.8343 (ttpp) cc_final: 0.8069 (tptt) REVERT: K 12 ASN cc_start: 0.8842 (p0) cc_final: 0.8550 (p0) REVERT: K 77 THR cc_start: 0.8991 (m) cc_final: 0.8664 (p) REVERT: K 82 MET cc_start: 0.8204 (tpt) cc_final: 0.7647 (tpt) REVERT: K 123 MET cc_start: 0.8868 (mmt) cc_final: 0.8609 (mmm) REVERT: K 132 MET cc_start: 0.9127 (ttp) cc_final: 0.8802 (ttp) REVERT: K 227 MET cc_start: 0.7793 (mmm) cc_final: 0.7284 (mmm) REVERT: K 328 LYS cc_start: 0.8363 (mttp) cc_final: 0.7745 (tttp) REVERT: L 25 ASP cc_start: 0.8095 (p0) cc_final: 0.7796 (t0) REVERT: L 236 LEU cc_start: 0.8448 (mp) cc_final: 0.8183 (mp) REVERT: L 340 TRP cc_start: 0.8911 (t60) cc_final: 0.8479 (t60) REVERT: L 364 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8553 (tp30) REVERT: M 270 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8403 (tp30) REVERT: B 536 HIS cc_start: 0.7916 (m170) cc_final: 0.7548 (m-70) REVERT: B 574 GLU cc_start: 0.7226 (tt0) cc_final: 0.6856 (pt0) REVERT: C 537 SER cc_start: 0.8986 (t) cc_final: 0.8635 (t) REVERT: A 555 GLU cc_start: 0.8008 (tt0) cc_final: 0.7763 (tt0) REVERT: A 638 GLU cc_start: 0.6859 (pm20) cc_final: 0.6408 (tm-30) REVERT: A 648 ASP cc_start: 0.8054 (m-30) cc_final: 0.7669 (m-30) REVERT: A 675 ILE cc_start: 0.8683 (mm) cc_final: 0.8153 (mm) outliers start: 38 outliers final: 33 residues processed: 356 average time/residue: 0.1450 time to fit residues: 86.2895 Evaluate side-chains 360 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 322 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 639 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 189 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 180 optimal weight: 0.0020 chunk 12 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 12 ASN H 162 ASN I 162 ASN K 101 HIS K 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105250 restraints weight = 40657.631| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.39 r_work: 0.3172 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26479 Z= 0.104 Angle : 0.554 12.339 35905 Z= 0.263 Chirality : 0.043 0.236 3993 Planarity : 0.003 0.037 4597 Dihedral : 6.311 130.209 3662 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.48 % Allowed : 14.83 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.15), residues: 3242 helix: 1.38 (0.15), residues: 1392 sheet: -0.13 (0.23), residues: 469 loop : 0.37 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 543 TYR 0.028 0.001 TYR C 641 PHE 0.014 0.001 PHE B 540 TRP 0.019 0.001 TRP A 656 HIS 0.004 0.001 HIS M 371 Details of bonding type rmsd covalent geometry : bond 0.00239 (26476) covalent geometry : angle 0.55422 (35905) hydrogen bonds : bond 0.02787 ( 1222) hydrogen bonds : angle 4.17797 ( 3195) Misc. bond : bond 0.00034 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5794.14 seconds wall clock time: 100 minutes 11.31 seconds (6011.31 seconds total)