Starting phenix.real_space_refine on Sun Jun 22 17:32:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uee_42161/06_2025/8uee_42161.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uee_42161/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8uee_42161/06_2025/8uee_42161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uee_42161/06_2025/8uee_42161.map" model { file = "/net/cci-nas-00/data/ceres_data/8uee_42161/06_2025/8uee_42161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uee_42161/06_2025/8uee_42161.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 23.62, per 1000 atoms: 0.91 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: 6.56 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 3.91 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: 10.29 Time building geometry restraints manager: 7.82 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: 3.960 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: 0.060 Extract box with map and model: 1.170 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 69.160 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.450 ------------------------------------------------------------------------------- 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 : 6.69 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (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 TRP 0.051 0.002 TRP F 340 HIS 0.011 0.001 HIS A 682 PHE 0.012 0.001 PHE L 200 TYR 0.022 0.001 TYR D 662 ARG 0.006 0.001 ARG A 565 Details of bonding type rmsd hydrogen bonds : bond 0.23914 ( 1222) hydrogen bonds : angle 7.05803 ( 3195) covalent geometry : bond 0.00494 (26476) covalent geometry : angle 0.63382 (35905) 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 : 2.733 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: 0.3428 time to fit residues: 248.8746 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 : 2.890 ------------------------------------------------------------------------------- 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 276 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 84 optimal weight: 0.0000 chunk 167 optimal weight: 0.2980 chunk 132 optimal weight: 0.9980 chunk 256 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 12 ASN K 101 HIS K 162 ASN ** K 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 ASN ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.133819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107661 restraints weight = 40232.620| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.55 r_work: 0.3196 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 26479 Z= 0.115 Angle : 0.570 9.816 35905 Z= 0.280 Chirality : 0.043 0.145 3993 Planarity : 0.004 0.039 4597 Dihedral : 8.150 177.360 3668 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.08 % Allowed : 7.09 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 3242 helix: 0.95 (0.15), residues: 1399 sheet: 0.17 (0.24), residues: 469 loop : 0.44 (0.18), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 340 HIS 0.004 0.001 HIS C 613 PHE 0.010 0.001 PHE A 626 TYR 0.034 0.001 TYR C 641 ARG 0.004 0.000 ARG K 37 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 1222) hydrogen bonds : angle 4.83983 ( 3195) covalent geometry : bond 0.00244 (26476) covalent geometry : angle 0.57011 (35905) Misc. bond : bond 0.00148 ( 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 408 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 378 time to evaluate : 2.771 Fit side-chains REVERT: F 41 GLN cc_start: 0.7943 (pm20) cc_final: 0.7234 (tp40) REVERT: F 44 MET cc_start: 0.5488 (mmm) cc_final: 0.5281 (mtp) REVERT: F 59 GLN cc_start: 0.8398 (mm110) cc_final: 0.8156 (tp40) REVERT: F 125 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7417 (mp0) REVERT: F 225 ASN cc_start: 0.8088 (t0) cc_final: 0.7870 (t0) REVERT: H 47 MET cc_start: 0.5828 (ppp) cc_final: 0.5543 (ppp) REVERT: H 65 LEU cc_start: 0.9287 (mt) cc_final: 0.9059 (mt) REVERT: H 227 MET cc_start: 0.7981 (tpp) cc_final: 0.7671 (tpp) REVERT: H 286 ASP cc_start: 0.8556 (t0) cc_final: 0.7879 (m-30) REVERT: I 72 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7030 (tp30) REVERT: I 148 THR cc_start: 0.8674 (p) cc_final: 0.8401 (m) REVERT: I 246 GLN cc_start: 0.8720 (mt0) cc_final: 0.8369 (mt0) REVERT: I 286 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7967 (m-30) REVERT: I 291 LYS cc_start: 0.8725 (tptp) cc_final: 0.8473 (tptp) REVERT: I 299 MET cc_start: 0.8495 (ptp) cc_final: 0.8242 (ptp) REVERT: I 358 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8302 (m) REVERT: I 374 CYS cc_start: 0.6729 (m) cc_final: 0.6321 (m) REVERT: J 132 MET cc_start: 0.8517 (ppp) cc_final: 0.8284 (ptm) REVERT: K 82 MET cc_start: 0.8113 (tpt) cc_final: 0.7549 (tpt) REVERT: K 191 LYS cc_start: 0.8054 (ttpt) cc_final: 0.7770 (ttpt) REVERT: L 25 ASP cc_start: 0.8003 (p0) cc_final: 0.7649 (t0) REVERT: L 136 ILE cc_start: 0.8572 (mm) cc_final: 0.8335 (mm) REVERT: L 334 GLU cc_start: 0.7515 (mp0) cc_final: 0.7285 (pm20) REVERT: M 75 ILE cc_start: 0.9174 (mt) cc_final: 0.8965 (mp) REVERT: M 96 VAL cc_start: 0.8975 (m) cc_final: 0.8755 (p) REVERT: M 270 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8579 (tp30) REVERT: B 536 HIS cc_start: 0.7866 (m170) cc_final: 0.7566 (m-70) REVERT: B 574 GLU cc_start: 0.7439 (tt0) cc_final: 0.7006 (pt0) outliers start: 30 outliers final: 15 residues processed: 396 average time/residue: 0.3410 time to fit residues: 220.7969 Evaluate side-chains 361 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 342 time to evaluate : 2.716 ------------------------------------------------------------------------------- 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 I residue 358 THR 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 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 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 214 optimal weight: 0.3980 chunk 241 optimal weight: 4.9990 chunk 290 optimal weight: 0.9990 chunk 231 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 150 optimal weight: 0.6980 chunk 293 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 99 optimal weight: 0.0980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 ** 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 = 0.3655 r_free = 0.3655 target = 0.133590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107615 restraints weight = 39958.748| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.52 r_work: 0.3199 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26479 Z= 0.103 Angle : 0.528 8.386 35905 Z= 0.254 Chirality : 0.042 0.141 3993 Planarity : 0.004 0.038 4597 Dihedral : 7.428 173.408 3664 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.04 % Allowed : 9.28 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.15), residues: 3242 helix: 1.15 (0.15), residues: 1406 sheet: 0.29 (0.24), residues: 469 loop : 0.55 (0.18), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 340 HIS 0.003 0.001 HIS L 161 PHE 0.008 0.001 PHE H 255 TYR 0.027 0.001 TYR C 641 ARG 0.003 0.000 ARG L 147 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 1222) hydrogen bonds : angle 4.47629 ( 3195) covalent geometry : bond 0.00229 (26476) covalent geometry : angle 0.52765 (35905) Misc. bond : bond 0.00065 ( 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 383 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 354 time to evaluate : 2.981 Fit side-chains REVERT: F 41 GLN cc_start: 0.7828 (pm20) cc_final: 0.7227 (tp40) REVERT: F 59 GLN cc_start: 0.8423 (mm110) cc_final: 0.8154 (tp40) REVERT: F 82 MET cc_start: 0.7399 (mmm) cc_final: 0.6421 (tmm) REVERT: F 132 MET cc_start: 0.8504 (ppp) cc_final: 0.8184 (tmm) REVERT: F 225 ASN cc_start: 0.8075 (t0) cc_final: 0.7815 (t0) REVERT: F 340 TRP cc_start: 0.8291 (t60) cc_final: 0.7907 (t60) REVERT: H 227 MET cc_start: 0.7952 (tpp) cc_final: 0.7648 (tpp) REVERT: H 237 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8314 (mt-10) REVERT: H 286 ASP cc_start: 0.8530 (t0) cc_final: 0.7884 (m-30) REVERT: H 326 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7899 (tttm) REVERT: I 44 MET cc_start: 0.8342 (mtp) cc_final: 0.8088 (mtm) REVERT: I 72 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7632 (tt0) REVERT: I 286 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: I 291 LYS cc_start: 0.8760 (tptp) cc_final: 0.8501 (tptp) REVERT: I 299 MET cc_start: 0.8587 (ptp) cc_final: 0.8306 (ptp) REVERT: I 374 CYS cc_start: 0.6783 (m) cc_final: 0.6405 (m) REVERT: J 132 MET cc_start: 0.8573 (ppp) cc_final: 0.8293 (ptm) REVERT: K 123 MET cc_start: 0.8800 (mmt) cc_final: 0.8534 (mmm) REVERT: K 191 LYS cc_start: 0.8007 (ttpt) cc_final: 0.7651 (ttpt) REVERT: L 25 ASP cc_start: 0.7980 (p0) cc_final: 0.7656 (t0) REVERT: L 118 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7320 (tppp) REVERT: L 136 ILE cc_start: 0.8538 (mm) cc_final: 0.8308 (mm) REVERT: L 334 GLU cc_start: 0.7540 (mp0) cc_final: 0.7297 (pm20) REVERT: M 75 ILE cc_start: 0.9166 (mt) cc_final: 0.8947 (mp) REVERT: M 270 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8542 (tp30) REVERT: B 536 HIS cc_start: 0.7913 (m170) cc_final: 0.7609 (m-70) REVERT: B 574 GLU cc_start: 0.7395 (tt0) cc_final: 0.6907 (pt0) REVERT: C 598 GLU cc_start: 0.7245 (pm20) cc_final: 0.7001 (pm20) REVERT: A 648 ASP cc_start: 0.7680 (m-30) cc_final: 0.7414 (m-30) REVERT: A 675 ILE cc_start: 0.8686 (mm) cc_final: 0.8144 (mm) outliers start: 29 outliers final: 16 residues processed: 374 average time/residue: 0.3405 time to fit residues: 210.1251 Evaluate side-chains 360 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 340 time to evaluate : 2.731 ------------------------------------------------------------------------------- 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 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 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 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 118 LYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 298 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 306 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 271 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 149 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 M 40 HIS ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.128020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.102256 restraints weight = 40992.327| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.41 r_work: 0.3121 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26479 Z= 0.223 Angle : 0.626 7.755 35905 Z= 0.311 Chirality : 0.047 0.155 3993 Planarity : 0.004 0.039 4597 Dihedral : 7.349 163.606 3662 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.58 % Allowed : 11.08 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 3242 helix: 1.10 (0.15), residues: 1385 sheet: -0.17 (0.24), residues: 462 loop : 0.23 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 656 HIS 0.006 0.001 HIS J 161 PHE 0.016 0.002 PHE K 124 TYR 0.024 0.002 TYR C 641 ARG 0.006 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 1222) hydrogen bonds : angle 4.64502 ( 3195) covalent geometry : bond 0.00525 (26476) covalent geometry : angle 0.62621 (35905) Misc. bond : bond 0.00057 ( 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 390 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 346 time to evaluate : 2.841 Fit side-chains REVERT: F 125 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7427 (mp0) REVERT: F 216 LEU cc_start: 0.8289 (mt) cc_final: 0.8023 (mp) REVERT: F 222 ASP cc_start: 0.8101 (t0) cc_final: 0.7609 (t0) REVERT: F 225 ASN cc_start: 0.8145 (t0) cc_final: 0.7902 (t0) REVERT: F 269 MET cc_start: 0.9038 (ttm) cc_final: 0.8734 (mtp) REVERT: F 340 TRP cc_start: 0.8532 (t60) cc_final: 0.8076 (t60) REVERT: H 41 GLN cc_start: 0.7178 (tp-100) cc_final: 0.6887 (pt0) REVERT: H 221 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8464 (tt) REVERT: H 227 MET cc_start: 0.8078 (tpp) cc_final: 0.7820 (tpp) REVERT: H 269 MET cc_start: 0.8872 (mtt) cc_final: 0.8568 (mmt) REVERT: H 305 MET cc_start: 0.8203 (mmm) cc_final: 0.7917 (mmm) REVERT: I 44 MET cc_start: 0.8401 (mtp) cc_final: 0.8157 (mtm) REVERT: I 72 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: I 286 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8130 (m-30) REVERT: I 291 LYS cc_start: 0.8835 (tptp) cc_final: 0.8432 (tptt) REVERT: I 374 CYS cc_start: 0.6922 (m) cc_final: 0.6597 (m) REVERT: J 180 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8826 (tp) REVERT: K 12 ASN cc_start: 0.8808 (p0) cc_final: 0.8589 (p0) REVERT: K 77 THR cc_start: 0.8926 (m) cc_final: 0.8580 (p) REVERT: K 82 MET cc_start: 0.8371 (tpt) cc_final: 0.7803 (tpt) REVERT: K 191 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7849 (ttpt) REVERT: L 25 ASP cc_start: 0.8104 (p0) cc_final: 0.7800 (t0) REVERT: L 83 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7510 (tm-30) REVERT: L 136 ILE cc_start: 0.8485 (mm) cc_final: 0.8259 (mm) REVERT: L 305 MET cc_start: 0.8758 (mmm) cc_final: 0.8551 (mmm) REVERT: L 334 GLU cc_start: 0.7640 (mp0) cc_final: 0.7330 (pm20) REVERT: L 340 TRP cc_start: 0.8927 (t60) cc_final: 0.8416 (t60) REVERT: M 270 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8563 (tp30) REVERT: B 536 HIS cc_start: 0.7809 (m170) cc_final: 0.7482 (m-70) REVERT: B 574 GLU cc_start: 0.7328 (tt0) cc_final: 0.6833 (pt0) REVERT: C 598 GLU cc_start: 0.7218 (pm20) cc_final: 0.6992 (pm20) REVERT: D 666 LEU cc_start: 0.7715 (tp) cc_final: 0.6962 (pt) REVERT: A 638 GLU cc_start: 0.6811 (pm20) cc_final: 0.6347 (tm-30) REVERT: A 648 ASP cc_start: 0.7871 (m-30) cc_final: 0.7530 (m-30) REVERT: A 675 ILE cc_start: 0.8571 (mm) cc_final: 0.8013 (mm) outliers start: 44 outliers final: 31 residues processed: 376 average time/residue: 0.3491 time to fit residues: 218.1409 Evaluate side-chains 353 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 317 time to evaluate : 3.395 ------------------------------------------------------------------------------- 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 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 299 MET Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 180 LEU 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 201 VAL 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 360 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 291 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 106 optimal weight: 0.0670 chunk 246 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 321 optimal weight: 4.9990 chunk 300 optimal weight: 8.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- 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 J 12 ASN K 101 HIS K 162 ASN M 12 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 = 0.3602 r_free = 0.3602 target = 0.129312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.103314 restraints weight = 40696.586| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.52 r_work: 0.3138 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26479 Z= 0.142 Angle : 0.559 8.995 35905 Z= 0.272 Chirality : 0.044 0.148 3993 Planarity : 0.004 0.036 4597 Dihedral : 7.056 154.532 3662 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.91 % Allowed : 12.13 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.15), residues: 3242 helix: 1.25 (0.15), residues: 1378 sheet: -0.06 (0.23), residues: 469 loop : 0.30 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 340 HIS 0.005 0.001 HIS K 161 PHE 0.010 0.001 PHE I 31 TYR 0.016 0.001 TYR C 641 ARG 0.004 0.000 ARG D 551 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 1222) hydrogen bonds : angle 4.43016 ( 3195) covalent geometry : bond 0.00332 (26476) covalent geometry : angle 0.55874 (35905) Misc. bond : bond 0.00039 ( 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 395 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 342 time to evaluate : 2.779 Fit side-chains REVERT: F 125 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7462 (mp0) REVERT: F 216 LEU cc_start: 0.8379 (mt) cc_final: 0.8100 (mp) REVERT: F 222 ASP cc_start: 0.8056 (t0) cc_final: 0.7583 (t0) REVERT: F 313 MET cc_start: 0.9053 (tpp) cc_final: 0.8808 (mmm) REVERT: H 221 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8514 (tt) REVERT: H 227 MET cc_start: 0.8079 (tpp) cc_final: 0.7873 (tpp) REVERT: H 269 MET cc_start: 0.8872 (mtt) cc_final: 0.8529 (mmt) REVERT: H 305 MET cc_start: 0.8157 (mmm) cc_final: 0.7905 (mmm) REVERT: I 44 MET cc_start: 0.8383 (mtp) cc_final: 0.8120 (mtm) REVERT: I 72 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: I 286 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8084 (m-30) REVERT: I 299 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8330 (ptp) REVERT: I 358 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8423 (m) REVERT: K 12 ASN cc_start: 0.8835 (p0) cc_final: 0.8573 (p0) REVERT: K 77 THR cc_start: 0.8965 (m) cc_final: 0.8636 (p) REVERT: K 82 MET cc_start: 0.8361 (tpt) cc_final: 0.7768 (tpt) REVERT: K 123 MET cc_start: 0.8876 (mmt) cc_final: 0.8619 (mmm) REVERT: K 132 MET cc_start: 0.9162 (ttp) cc_final: 0.8895 (ttp) REVERT: K 191 LYS cc_start: 0.8203 (ttpt) cc_final: 0.7908 (ttpt) REVERT: L 25 ASP cc_start: 0.8169 (p0) cc_final: 0.7842 (t0) REVERT: L 83 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7362 (tt0) REVERT: L 136 ILE cc_start: 0.8491 (mm) cc_final: 0.8263 (mm) REVERT: L 340 TRP cc_start: 0.8890 (t60) cc_final: 0.8436 (t60) REVERT: M 82 MET cc_start: 0.7768 (tpp) cc_final: 0.7476 (tpt) REVERT: M 92 ASN cc_start: 0.8877 (m-40) cc_final: 0.8278 (m-40) REVERT: M 270 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8384 (tp30) REVERT: B 536 HIS cc_start: 0.7904 (m170) cc_final: 0.7554 (m-70) REVERT: B 574 GLU cc_start: 0.7303 (tt0) cc_final: 0.6845 (pt0) REVERT: C 598 GLU cc_start: 0.7261 (pm20) cc_final: 0.7036 (pm20) REVERT: D 666 LEU cc_start: 0.7678 (tp) cc_final: 0.6934 (pt) REVERT: A 648 ASP cc_start: 0.7993 (m-30) cc_final: 0.7645 (m-30) REVERT: A 675 ILE cc_start: 0.8625 (mm) cc_final: 0.8088 (mm) outliers start: 53 outliers final: 32 residues processed: 376 average time/residue: 0.3300 time to fit residues: 207.7392 Evaluate side-chains 359 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 321 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 248 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 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 299 MET Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 30 VAL 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 299 MET 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 116 ARG 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 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 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 244 optimal weight: 7.9990 chunk 87 optimal weight: 0.5980 chunk 242 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 218 optimal weight: 0.8980 chunk 240 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 J 41 GLN K 101 HIS K 162 ASN M 12 ASN ** M 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.130719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.104796 restraints weight = 40555.575| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.53 r_work: 0.3158 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26479 Z= 0.109 Angle : 0.537 8.315 35905 Z= 0.258 Chirality : 0.043 0.141 3993 Planarity : 0.003 0.036 4597 Dihedral : 6.670 146.881 3662 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.84 % Allowed : 12.85 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.15), residues: 3242 helix: 1.39 (0.15), residues: 1378 sheet: -0.03 (0.23), residues: 469 loop : 0.40 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 656 HIS 0.006 0.001 HIS M 101 PHE 0.008 0.001 PHE H 255 TYR 0.017 0.001 TYR C 641 ARG 0.004 0.000 ARG D 551 Details of bonding type rmsd hydrogen bonds : bond 0.02942 ( 1222) hydrogen bonds : angle 4.26905 ( 3195) covalent geometry : bond 0.00250 (26476) covalent geometry : angle 0.53716 (35905) Misc. bond : bond 0.00036 ( 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 399 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 348 time to evaluate : 2.734 Fit side-chains REVERT: F 125 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7492 (mp0) REVERT: F 216 LEU cc_start: 0.8324 (mt) cc_final: 0.8026 (mp) REVERT: F 222 ASP cc_start: 0.8019 (t0) cc_final: 0.7543 (t0) REVERT: H 221 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8510 (tt) REVERT: H 227 MET cc_start: 0.8116 (tpp) cc_final: 0.7859 (tpp) REVERT: H 237 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8375 (mt-10) REVERT: H 286 ASP cc_start: 0.8645 (t0) cc_final: 0.7947 (m-30) REVERT: H 305 MET cc_start: 0.8122 (mmm) cc_final: 0.7892 (mmm) REVERT: I 44 MET cc_start: 0.8338 (mtp) cc_final: 0.8082 (mtm) REVERT: I 72 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: I 269 MET cc_start: 0.8845 (mtm) cc_final: 0.8555 (mtm) REVERT: I 286 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: I 299 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8202 (ptp) REVERT: I 358 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8353 (m) REVERT: J 180 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8917 (tp) REVERT: K 77 THR cc_start: 0.8965 (m) cc_final: 0.8634 (p) REVERT: K 123 MET cc_start: 0.8843 (mmt) cc_final: 0.8579 (mmm) REVERT: K 132 MET cc_start: 0.9129 (ttp) cc_final: 0.8818 (ttp) REVERT: K 191 LYS cc_start: 0.8186 (ttpt) cc_final: 0.7886 (ttpt) REVERT: L 25 ASP cc_start: 0.8177 (p0) cc_final: 0.7816 (t0) REVERT: L 83 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7354 (tt0) REVERT: L 136 ILE cc_start: 0.8453 (mm) cc_final: 0.8212 (mm) REVERT: L 334 GLU cc_start: 0.7119 (pm20) cc_final: 0.6904 (pp20) REVERT: L 340 TRP cc_start: 0.8882 (t60) cc_final: 0.8420 (t60) REVERT: M 82 MET cc_start: 0.7696 (tpp) cc_final: 0.7488 (tpt) REVERT: M 92 ASN cc_start: 0.8905 (m-40) cc_final: 0.8276 (m-40) REVERT: M 270 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8375 (tp30) REVERT: B 536 HIS cc_start: 0.7904 (m170) cc_final: 0.7551 (m-70) REVERT: B 574 GLU cc_start: 0.7284 (tt0) cc_final: 0.6847 (pt0) REVERT: B 640 ASP cc_start: 0.7353 (p0) cc_final: 0.6697 (p0) REVERT: C 537 SER cc_start: 0.8997 (t) cc_final: 0.8616 (t) REVERT: C 598 GLU cc_start: 0.7264 (pm20) cc_final: 0.7023 (pm20) REVERT: A 648 ASP cc_start: 0.8086 (m-30) cc_final: 0.7756 (m-30) REVERT: A 675 ILE cc_start: 0.8639 (mm) cc_final: 0.8108 (mm) outliers start: 51 outliers final: 35 residues processed: 379 average time/residue: 0.3223 time to fit residues: 205.1389 Evaluate side-chains 364 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 322 time to evaluate : 3.033 ------------------------------------------------------------------------------- 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 86 TRP Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 248 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 299 MET 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 30 VAL 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 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 B residue 528 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 C residue 532 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 12 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 174 optimal weight: 0.5980 chunk 259 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 313 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 218 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 314 optimal weight: 8.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 ** M 101 HIS ** 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 = 0.3606 r_free = 0.3606 target = 0.129664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104132 restraints weight = 40881.513| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.41 r_work: 0.3150 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2106 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= 0.146 Angle : 0.560 10.388 35905 Z= 0.269 Chirality : 0.044 0.179 3993 Planarity : 0.004 0.034 4597 Dihedral : 6.545 143.042 3662 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.80 % Allowed : 13.24 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.15), residues: 3242 helix: 1.40 (0.15), residues: 1378 sheet: -0.07 (0.23), residues: 469 loop : 0.37 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 656 HIS 0.006 0.001 HIS H 101 PHE 0.009 0.001 PHE K 124 TYR 0.016 0.001 TYR C 641 ARG 0.004 0.000 ARG C 543 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 1222) hydrogen bonds : angle 4.30585 ( 3195) covalent geometry : bond 0.00345 (26476) covalent geometry : angle 0.56012 (35905) Misc. bond : bond 0.00046 ( 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 382 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 332 time to evaluate : 3.408 Fit side-chains REVERT: F 216 LEU cc_start: 0.8215 (mt) cc_final: 0.7903 (mp) REVERT: F 222 ASP cc_start: 0.8051 (t0) cc_final: 0.7543 (t0) REVERT: H 221 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8488 (tt) REVERT: H 227 MET cc_start: 0.8056 (tpp) cc_final: 0.7823 (tpp) REVERT: H 237 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8368 (mt-10) REVERT: I 44 MET cc_start: 0.8389 (mtp) cc_final: 0.8133 (mtm) REVERT: I 72 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7583 (mt-10) REVERT: I 269 MET cc_start: 0.8770 (mtm) cc_final: 0.8482 (mtm) REVERT: I 286 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: I 299 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8217 (ptp) REVERT: I 358 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8389 (m) REVERT: K 12 ASN cc_start: 0.8833 (p0) cc_final: 0.8579 (p0) REVERT: K 77 THR cc_start: 0.8955 (m) cc_final: 0.8611 (p) REVERT: K 123 MET cc_start: 0.8835 (mmt) cc_final: 0.8577 (mmm) REVERT: K 132 MET cc_start: 0.9161 (ttp) cc_final: 0.8787 (ttp) REVERT: K 191 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7828 (ttpt) REVERT: K 328 LYS cc_start: 0.8294 (mttp) cc_final: 0.7552 (tttm) REVERT: L 25 ASP cc_start: 0.8194 (p0) cc_final: 0.7845 (t0) REVERT: L 83 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7329 (tt0) REVERT: L 136 ILE cc_start: 0.8399 (mm) cc_final: 0.8153 (mm) REVERT: L 334 GLU cc_start: 0.7146 (pm20) cc_final: 0.6892 (pp20) REVERT: L 340 TRP cc_start: 0.8924 (t60) cc_final: 0.8438 (t60) REVERT: L 364 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8495 (tp30) REVERT: M 270 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8377 (tp30) REVERT: B 536 HIS cc_start: 0.7838 (m170) cc_final: 0.7482 (m-70) REVERT: B 574 GLU cc_start: 0.7268 (tt0) cc_final: 0.6828 (pt0) REVERT: B 640 ASP cc_start: 0.7260 (p0) cc_final: 0.6558 (p0) REVERT: C 537 SER cc_start: 0.8940 (t) cc_final: 0.8573 (t) REVERT: A 640 ASP cc_start: 0.7485 (t0) cc_final: 0.6504 (p0) REVERT: A 648 ASP cc_start: 0.8065 (m-30) cc_final: 0.7735 (m-30) REVERT: A 675 ILE cc_start: 0.8607 (mm) cc_final: 0.8077 (mm) outliers start: 50 outliers final: 39 residues processed: 366 average time/residue: 0.3728 time to fit residues: 229.9163 Evaluate side-chains 369 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 324 time to evaluate : 2.839 ------------------------------------------------------------------------------- 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 270 GLU Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 30 VAL 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 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 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 633 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain D residue 639 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 176 optimal weight: 3.9990 chunk 286 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 275 optimal weight: 0.0010 chunk 184 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 157 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- 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 M 12 ASN ** M 101 HIS ** 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 = 0.130402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104949 restraints weight = 40681.139| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.39 r_work: 0.3166 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26479 Z= 0.116 Angle : 0.547 10.160 35905 Z= 0.262 Chirality : 0.043 0.140 3993 Planarity : 0.003 0.035 4597 Dihedral : 6.401 137.243 3662 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.16 % Allowed : 13.28 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.15), residues: 3242 helix: 1.46 (0.15), residues: 1378 sheet: -0.05 (0.23), residues: 469 loop : 0.44 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 656 HIS 0.006 0.001 HIS K 161 PHE 0.010 0.001 PHE B 540 TYR 0.015 0.001 TYR C 641 ARG 0.003 0.000 ARG D 551 Details of bonding type rmsd hydrogen bonds : bond 0.02926 ( 1222) hydrogen bonds : angle 4.22940 ( 3195) covalent geometry : bond 0.00269 (26476) covalent geometry : angle 0.54715 (35905) Misc. bond : bond 0.00041 ( 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 395 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 335 time to evaluate : 2.743 Fit side-chains REVERT: F 125 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7467 (mp0) REVERT: F 216 LEU cc_start: 0.8223 (mt) cc_final: 0.7892 (mp) REVERT: F 222 ASP cc_start: 0.8058 (t0) cc_final: 0.7564 (t0) REVERT: F 313 MET cc_start: 0.8998 (tpp) cc_final: 0.8753 (mmm) REVERT: H 221 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8494 (tt) REVERT: H 227 MET cc_start: 0.8117 (tpp) cc_final: 0.7828 (tpp) REVERT: H 237 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8363 (mt-10) REVERT: I 72 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7636 (mt-10) REVERT: I 269 MET cc_start: 0.8744 (mtm) cc_final: 0.8446 (mtm) REVERT: I 286 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7971 (m-30) REVERT: I 299 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8214 (ptp) REVERT: I 358 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8373 (m) REVERT: K 12 ASN cc_start: 0.8823 (p0) cc_final: 0.8560 (p0) REVERT: K 77 THR cc_start: 0.8962 (m) cc_final: 0.8624 (p) REVERT: K 132 MET cc_start: 0.9150 (ttp) cc_final: 0.8770 (ttp) REVERT: K 191 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7827 (ttpt) REVERT: K 227 MET cc_start: 0.7808 (mmm) cc_final: 0.7230 (mmm) REVERT: K 328 LYS cc_start: 0.8253 (mttp) cc_final: 0.7532 (tttm) REVERT: L 25 ASP cc_start: 0.8187 (p0) cc_final: 0.7826 (t0) REVERT: L 83 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7403 (tt0) REVERT: L 136 ILE cc_start: 0.8385 (mm) cc_final: 0.8138 (mm) REVERT: L 334 GLU cc_start: 0.7224 (pm20) cc_final: 0.6938 (pp20) REVERT: L 340 TRP cc_start: 0.8905 (t60) cc_final: 0.8422 (t60) REVERT: L 364 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8482 (tp30) REVERT: M 92 ASN cc_start: 0.8847 (m-40) cc_final: 0.8175 (m-40) REVERT: M 270 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8379 (tp30) REVERT: B 536 HIS cc_start: 0.7900 (m170) cc_final: 0.7544 (m-70) REVERT: B 574 GLU cc_start: 0.7251 (tt0) cc_final: 0.6820 (pt0) REVERT: B 640 ASP cc_start: 0.7232 (p0) cc_final: 0.6548 (p0) REVERT: C 537 SER cc_start: 0.8942 (t) cc_final: 0.8570 (t) REVERT: A 640 ASP cc_start: 0.7487 (t0) cc_final: 0.6517 (p0) REVERT: A 648 ASP cc_start: 0.8119 (m-30) cc_final: 0.7784 (m-30) REVERT: A 675 ILE cc_start: 0.8616 (mm) cc_final: 0.8094 (mm) outliers start: 60 outliers final: 43 residues processed: 372 average time/residue: 0.3282 time to fit residues: 204.8428 Evaluate side-chains 377 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 328 time to evaluate : 2.676 ------------------------------------------------------------------------------- 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 103 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 349 LEU 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 305 MET Chi-restraints excluded: chain H residue 320 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 270 GLU Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain I residue 299 MET 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 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 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 12 ASN 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 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 C residue 633 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain D residue 609 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 192 optimal weight: 3.9990 chunk 318 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 249 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 220 optimal weight: 7.9990 chunk 206 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 L 59 GLN ** M 101 HIS ** 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 = 0.3613 r_free = 0.3613 target = 0.130245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.104775 restraints weight = 40800.099| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.40 r_work: 0.3160 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2233 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= 0.132 Angle : 0.560 11.540 35905 Z= 0.268 Chirality : 0.043 0.237 3993 Planarity : 0.004 0.034 4597 Dihedral : 6.357 135.498 3662 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.98 % Allowed : 13.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.15), residues: 3242 helix: 1.45 (0.15), residues: 1378 sheet: -0.07 (0.23), residues: 469 loop : 0.43 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 656 HIS 0.005 0.001 HIS K 161 PHE 0.011 0.001 PHE B 540 TYR 0.015 0.001 TYR C 641 ARG 0.003 0.000 ARG D 551 Details of bonding type rmsd hydrogen bonds : bond 0.02998 ( 1222) hydrogen bonds : angle 4.23277 ( 3195) covalent geometry : bond 0.00309 (26476) covalent geometry : angle 0.56029 (35905) Misc. bond : bond 0.00036 ( 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 381 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 326 time to evaluate : 3.014 Fit side-chains REVERT: F 125 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7393 (mp0) REVERT: F 216 LEU cc_start: 0.8213 (mt) cc_final: 0.7886 (mp) REVERT: F 222 ASP cc_start: 0.8082 (t0) cc_final: 0.7588 (t0) REVERT: H 221 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8542 (tt) REVERT: H 227 MET cc_start: 0.8064 (tpp) cc_final: 0.7828 (tpp) REVERT: H 237 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8368 (mt-10) REVERT: I 44 MET cc_start: 0.8371 (mtp) cc_final: 0.8107 (mtm) REVERT: I 72 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: I 269 MET cc_start: 0.8750 (mtm) cc_final: 0.8435 (mtm) REVERT: I 286 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: I 299 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8259 (ptp) REVERT: I 358 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8388 (m) REVERT: J 47 MET cc_start: 0.7845 (mmm) cc_final: 0.7389 (mmm) REVERT: K 12 ASN cc_start: 0.8826 (p0) cc_final: 0.8574 (p0) REVERT: K 77 THR cc_start: 0.8957 (m) cc_final: 0.8625 (p) REVERT: K 132 MET cc_start: 0.9154 (ttp) cc_final: 0.8754 (ttp) REVERT: K 191 LYS cc_start: 0.8104 (ttpt) cc_final: 0.7824 (ttpt) REVERT: K 227 MET cc_start: 0.7833 (mmm) cc_final: 0.7215 (mmm) REVERT: K 328 LYS cc_start: 0.8257 (mttp) cc_final: 0.7523 (tttm) REVERT: L 25 ASP cc_start: 0.8115 (p0) cc_final: 0.7785 (t0) REVERT: L 136 ILE cc_start: 0.8381 (mm) cc_final: 0.8134 (mm) REVERT: L 340 TRP cc_start: 0.8923 (t60) cc_final: 0.8442 (t60) REVERT: L 364 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8503 (tp30) REVERT: M 270 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8383 (tp30) REVERT: B 536 HIS cc_start: 0.7841 (m170) cc_final: 0.7487 (m-70) REVERT: B 574 GLU cc_start: 0.7245 (tt0) cc_final: 0.6820 (pt0) REVERT: C 537 SER cc_start: 0.8946 (t) cc_final: 0.8575 (t) REVERT: A 648 ASP cc_start: 0.8009 (m-30) cc_final: 0.7640 (m-30) REVERT: A 675 ILE cc_start: 0.8632 (mm) cc_final: 0.8101 (mm) outliers start: 55 outliers final: 41 residues processed: 362 average time/residue: 0.3290 time to fit residues: 197.8553 Evaluate side-chains 365 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 318 time to evaluate : 2.739 ------------------------------------------------------------------------------- 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 103 THR 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 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 299 MET 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 24 ASP Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 122 ILE 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 B residue 528 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 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 609 VAL 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 200 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 198 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 157 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ** M 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 ASN 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 = 0.130255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104393 restraints weight = 40678.019| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.51 r_work: 0.3150 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26479 Z= 0.130 Angle : 0.563 12.960 35905 Z= 0.268 Chirality : 0.043 0.217 3993 Planarity : 0.004 0.036 4597 Dihedral : 6.311 132.620 3662 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.87 % Allowed : 13.67 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.15), residues: 3242 helix: 1.44 (0.15), residues: 1385 sheet: -0.07 (0.23), residues: 469 loop : 0.45 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 656 HIS 0.004 0.001 HIS J 161 PHE 0.018 0.001 PHE B 540 TYR 0.016 0.001 TYR C 641 ARG 0.005 0.000 ARG C 543 Details of bonding type rmsd hydrogen bonds : bond 0.02990 ( 1222) hydrogen bonds : angle 4.22086 ( 3195) covalent geometry : bond 0.00305 (26476) covalent geometry : angle 0.56347 (35905) Misc. bond : bond 0.00040 ( 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 376 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 324 time to evaluate : 2.762 Fit side-chains REVERT: F 125 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7608 (mp0) REVERT: F 216 LEU cc_start: 0.8318 (mt) cc_final: 0.8000 (mp) REVERT: F 222 ASP cc_start: 0.8058 (t0) cc_final: 0.7604 (t0) REVERT: H 221 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8581 (tt) REVERT: H 227 MET cc_start: 0.8087 (tpp) cc_final: 0.7863 (tpp) REVERT: H 237 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8360 (mt-10) REVERT: I 44 MET cc_start: 0.8349 (mtp) cc_final: 0.8082 (mtm) REVERT: I 72 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: I 269 MET cc_start: 0.8792 (mtm) cc_final: 0.8487 (mtm) REVERT: I 286 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: I 299 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8265 (ptp) REVERT: I 358 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8413 (m) REVERT: J 47 MET cc_start: 0.7963 (mmm) cc_final: 0.7491 (mmm) REVERT: K 12 ASN cc_start: 0.8846 (p0) cc_final: 0.8569 (p0) REVERT: K 77 THR cc_start: 0.8977 (m) cc_final: 0.8659 (p) REVERT: K 132 MET cc_start: 0.9136 (ttp) cc_final: 0.8758 (ttp) REVERT: K 328 LYS cc_start: 0.8318 (mttp) cc_final: 0.7638 (tttm) REVERT: L 25 ASP cc_start: 0.8103 (p0) cc_final: 0.7807 (t0) REVERT: L 136 ILE cc_start: 0.8439 (mm) cc_final: 0.8211 (mm) REVERT: L 340 TRP cc_start: 0.8921 (t60) cc_final: 0.8476 (t60) REVERT: L 364 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8488 (tp30) REVERT: M 270 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8411 (tp30) REVERT: B 536 HIS cc_start: 0.7898 (m170) cc_final: 0.7556 (m-70) REVERT: B 541 ASP cc_start: 0.6734 (OUTLIER) cc_final: 0.6468 (m-30) REVERT: B 574 GLU cc_start: 0.7244 (tt0) cc_final: 0.6851 (pt0) REVERT: C 537 SER cc_start: 0.8990 (t) cc_final: 0.8621 (t) REVERT: A 648 ASP cc_start: 0.8080 (m-30) cc_final: 0.7691 (m-30) REVERT: A 675 ILE cc_start: 0.8681 (mm) cc_final: 0.8165 (mm) outliers start: 52 outliers final: 43 residues processed: 357 average time/residue: 0.3188 time to fit residues: 190.2815 Evaluate side-chains 368 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 318 time to evaluate : 2.761 ------------------------------------------------------------------------------- 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 103 THR 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 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 270 GLU Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain I residue 299 MET 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 24 ASP Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 122 ILE 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 190 MET 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 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 541 ASP 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 609 VAL 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 31 optimal weight: 4.9990 chunk 201 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 255 optimal weight: 0.4980 chunk 217 optimal weight: 0.9980 chunk 295 optimal weight: 8.9990 chunk 301 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.130576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105188 restraints weight = 40658.814| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.38 r_work: 0.3167 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2317 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= 0.112 Angle : 0.553 12.495 35905 Z= 0.263 Chirality : 0.043 0.191 3993 Planarity : 0.003 0.036 4597 Dihedral : 6.264 130.797 3662 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.80 % Allowed : 13.85 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 3242 helix: 1.47 (0.15), residues: 1385 sheet: -0.04 (0.23), residues: 469 loop : 0.48 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 656 HIS 0.005 0.001 HIS M 101 PHE 0.017 0.001 PHE B 540 TYR 0.016 0.001 TYR C 641 ARG 0.004 0.000 ARG C 543 Details of bonding type rmsd hydrogen bonds : bond 0.02876 ( 1222) hydrogen bonds : angle 4.18171 ( 3195) covalent geometry : bond 0.00258 (26476) covalent geometry : angle 0.55267 (35905) Misc. bond : bond 0.00035 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11421.59 seconds wall clock time: 199 minutes 44.70 seconds (11984.70 seconds total)