Starting phenix.real_space_refine on Mon Feb 19 22:50:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uee_42161/02_2024/8uee_42161_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uee_42161/02_2024/8uee_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uee_42161/02_2024/8uee_42161.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uee_42161/02_2024/8uee_42161.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uee_42161/02_2024/8uee_42161_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uee_42161/02_2024/8uee_42161_updated.pdb" } 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 Residue "F PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 195": "OE1" <-> "OE2" Residue "H ASP 286": "OD1" <-> "OD2" Residue "I ASP 157": "OD1" <-> "OD2" Residue "I PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 207": "OE1" <-> "OE2" Residue "J TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 286": "OD1" <-> "OD2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K ASP 222": "OD1" <-> "OD2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 276": "OE1" <-> "OE2" Residue "M TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 195": "OE1" <-> "OE2" Residue "M GLU 224": "OE1" <-> "OE2" Residue "M ASP 244": "OD1" <-> "OD2" Residue "M GLU 361": "OE1" <-> "OE2" Residue "M GLU 364": "OE1" <-> "OE2" Residue "B PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 569": "OD1" <-> "OD2" Residue "C PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 574": "OE1" <-> "OE2" Residue "C GLU 629": "OE1" <-> "OE2" Residue "D GLU 598": "OE1" <-> "OE2" Residue "A ASP 557": "OD1" <-> "OD2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A GLU 638": "OE1" <-> "OE2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 679": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 13.32, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 9.86 Conformation dependent library (CDL) restraints added in 4.4 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... running ksdssp... Secondary structure from input PDB file: 178 helices and 30 sheets defined 45.4% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.89 Creating SS restraints... Processing helix chain 'F' and resid 55 through 60 removed outlier: 3.577A pdb=" N SER F 60 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 79 through 90 Processing helix chain 'F' and resid 113 through 125 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 144 Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 196 removed outlier: 4.011A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 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 223 through 232 Processing helix chain 'F' and resid 252 through 261 removed outlier: 3.706A pdb=" N ARG F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N CYS F 257 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 287 through 296 removed outlier: 3.675A pdb=" N ARG F 290 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LYS F 291 " --> pdb=" O ASP F 288 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP F 292 " --> pdb=" O ILE F 289 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR F 294 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 305 Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 335 through 348 removed outlier: 5.778A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY F 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 354 removed outlier: 4.025A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 351 through 354' Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 367 through 373 removed outlier: 4.065A pdb=" N LYS F 373 " --> pdb=" O VAL F 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 79 through 91 Processing helix chain 'H' and resid 113 through 124 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 144 Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 182 through 195 removed outlier: 4.423A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU H 195 " --> pdb=" O LYS H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 216 removed outlier: 3.548A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 252 through 256 removed outlier: 3.509A pdb=" N PHE H 255 " --> pdb=" O ASN H 252 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG H 256 " --> pdb=" O GLU H 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 252 through 256' Processing helix chain 'H' and resid 258 through 261 Processing helix chain 'H' and resid 264 through 267 Processing helix chain 'H' and resid 274 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 287 through 295 removed outlier: 3.705A pdb=" N ARG H 290 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS H 291 " --> pdb=" O ASP H 288 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR H 294 " --> pdb=" O LYS H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 309 through 320 Processing helix chain 'H' and resid 335 through 348 removed outlier: 5.524A pdb=" N VAL H 339 " --> pdb=" O LYS H 336 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA H 347 " --> pdb=" O SER H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 354 removed outlier: 3.675A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 351 through 354' Processing helix chain 'H' and resid 359 through 365 Processing helix chain 'H' and resid 367 through 373 removed outlier: 4.216A pdb=" N LYS H 373 " --> pdb=" O VAL H 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 60 No H-bonds generated for 'chain 'I' and resid 57 through 60' Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 79 through 91 Processing helix chain 'I' and resid 98 through 100 No H-bonds generated for 'chain 'I' and resid 98 through 100' Processing helix chain 'I' and resid 113 through 125 Processing helix chain 'I' and resid 137 through 145 Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 182 through 196 removed outlier: 3.776A pdb=" N THR I 194 " --> pdb=" O MET I 190 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU I 195 " --> pdb=" O LYS I 191 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG I 196 " --> pdb=" O ILE I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 216 Processing helix chain 'I' and resid 223 through 232 Processing helix chain 'I' and resid 252 through 256 removed outlier: 3.934A pdb=" N ARG I 256 " --> pdb=" O GLU I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 261 Processing helix chain 'I' and resid 264 through 267 Processing helix chain 'I' and resid 274 through 283 Processing helix chain 'I' and resid 287 through 296 removed outlier: 3.633A pdb=" N ARG I 290 " --> pdb=" O ILE I 287 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS I 291 " --> pdb=" O ASP I 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN I 296 " --> pdb=" O LEU I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 305 Processing helix chain 'I' and resid 309 through 320 Processing helix chain 'I' and resid 335 through 346 removed outlier: 5.591A pdb=" N VAL I 339 " --> pdb=" O LYS I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 352 No H-bonds generated for 'chain 'I' and resid 350 through 352' Processing helix chain 'I' and resid 359 through 373 removed outlier: 3.556A pdb=" N GLU I 364 " --> pdb=" O GLN I 360 " (cutoff:3.500A) Proline residue: I 367 - end of helix removed outlier: 5.105A pdb=" N VAL I 370 " --> pdb=" O GLY I 366 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N HIS I 371 " --> pdb=" O PRO I 367 " (cutoff:3.500A) 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 60 Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'J' and resid 79 through 91 Processing helix chain 'J' and resid 98 through 100 No H-bonds generated for 'chain 'J' and resid 98 through 100' Processing helix chain 'J' and resid 113 through 125 Processing helix chain 'J' and resid 137 through 145 removed outlier: 4.177A pdb=" N SER J 145 " --> pdb=" O SER J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 182 through 196 removed outlier: 4.026A pdb=" N THR J 194 " --> pdb=" O MET J 190 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU J 195 " --> pdb=" O LYS J 191 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG J 196 " --> pdb=" O ILE J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 216 Processing helix chain 'J' and resid 223 through 232 Processing helix chain 'J' and resid 252 through 256 removed outlier: 3.806A pdb=" N ARG J 256 " --> pdb=" O GLU J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 261 Processing helix chain 'J' and resid 264 through 267 Processing helix chain 'J' and resid 274 through 284 Processing helix chain 'J' and resid 290 through 294 Processing helix chain 'J' and resid 302 through 305 Processing helix chain 'J' and resid 309 through 320 Processing helix chain 'J' and resid 338 through 348 Processing helix chain 'J' and resid 359 through 365 Processing helix chain 'J' and resid 367 through 372 removed outlier: 3.577A pdb=" N VAL J 370 " --> pdb=" O PRO J 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 60 removed outlier: 3.923A pdb=" N SER K 60 " --> pdb=" O GLU K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 79 through 91 Processing helix chain 'K' and resid 98 through 100 No H-bonds generated for 'chain 'K' and resid 98 through 100' Processing helix chain 'K' and resid 113 through 125 Processing helix chain 'K' and resid 137 through 144 removed outlier: 3.512A pdb=" N LEU K 142 " --> pdb=" O ALA K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 174 No H-bonds generated for 'chain 'K' and resid 172 through 174' Processing helix chain 'K' and resid 182 through 195 removed outlier: 3.754A pdb=" N THR K 194 " --> pdb=" O MET K 190 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLU K 195 " --> pdb=" O LYS K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 216 removed outlier: 3.735A pdb=" N ILE K 208 " --> pdb=" O ALA K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 232 Processing helix chain 'K' and resid 252 through 256 removed outlier: 3.648A pdb=" N ARG K 256 " --> pdb=" O GLU K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 261 Processing helix chain 'K' and resid 264 through 267 Processing helix chain 'K' and resid 274 through 283 Processing helix chain 'K' and resid 290 through 296 Processing helix chain 'K' and resid 302 through 304 No H-bonds generated for 'chain 'K' and resid 302 through 304' Processing helix chain 'K' and resid 309 through 318 Processing helix chain 'K' and resid 335 through 348 removed outlier: 5.395A pdb=" N VAL K 339 " --> pdb=" O LYS K 336 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP K 340 " --> pdb=" O TYR K 337 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA K 347 " --> pdb=" O SER K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 352 No H-bonds generated for 'chain 'K' and resid 350 through 352' Processing helix chain 'K' and resid 359 through 373 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) Proline residue: K 367 - end of helix removed outlier: 5.225A pdb=" N VAL K 370 " --> pdb=" O GLY K 366 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS K 371 " --> pdb=" O PRO K 367 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG K 372 " --> pdb=" O SER K 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 79 through 91 Processing helix chain 'L' and resid 98 through 100 No H-bonds generated for 'chain 'L' and resid 98 through 100' Processing helix chain 'L' and resid 113 through 125 Processing helix chain 'L' and resid 137 through 144 removed outlier: 3.534A pdb=" N TYR L 143 " --> pdb=" O VAL L 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 174 No H-bonds generated for 'chain 'L' and resid 172 through 174' Processing helix chain 'L' and resid 182 through 196 removed outlier: 3.882A pdb=" N THR L 194 " --> pdb=" O MET L 190 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU L 195 " --> pdb=" O LYS L 191 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG L 196 " --> pdb=" O ILE L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 216 Processing helix chain 'L' and resid 223 through 230 Processing helix chain 'L' and resid 252 through 261 removed outlier: 3.877A pdb=" N ARG L 256 " --> pdb=" O GLU L 253 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS L 257 " --> pdb=" O ARG L 254 " (cutoff:3.500A) Proline residue: L 258 - end of helix Processing helix chain 'L' and resid 264 through 267 Processing helix chain 'L' and resid 274 through 284 Processing helix chain 'L' and resid 290 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 302 through 305 Processing helix chain 'L' and resid 309 through 320 Processing helix chain 'L' and resid 335 through 348 removed outlier: 3.632A pdb=" N SER L 338 " --> pdb=" O ARG L 335 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL L 339 " --> pdb=" O LYS L 336 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP L 340 " --> pdb=" O TYR L 337 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA L 347 " --> pdb=" O SER L 344 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 354 removed outlier: 3.599A pdb=" N GLN L 354 " --> pdb=" O THR L 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 351 through 354' Processing helix chain 'L' and resid 359 through 365 Processing helix chain 'L' and resid 367 through 373 removed outlier: 3.580A pdb=" N LYS L 373 " --> pdb=" O VAL L 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 60 Processing helix chain 'M' and resid 62 through 64 No H-bonds generated for 'chain 'M' and resid 62 through 64' Processing helix chain 'M' and resid 79 through 91 Processing helix chain 'M' and resid 98 through 100 No H-bonds generated for 'chain 'M' and resid 98 through 100' Processing helix chain 'M' and resid 113 through 125 Processing helix chain 'M' and resid 137 through 144 Processing helix chain 'M' and resid 172 through 174 No H-bonds generated for 'chain 'M' and resid 172 through 174' Processing helix chain 'M' and resid 182 through 196 removed outlier: 4.019A pdb=" N THR M 194 " --> pdb=" O MET M 190 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU M 195 " --> pdb=" O LYS M 191 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG M 196 " --> pdb=" O ILE M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 216 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 223 through 232 Processing helix chain 'M' and resid 252 through 256 removed outlier: 3.605A pdb=" N ARG M 256 " --> pdb=" O GLU M 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 261 Processing helix chain 'M' and resid 264 through 267 Processing helix chain 'M' and resid 274 through 283 Processing helix chain 'M' and resid 287 through 296 removed outlier: 3.768A pdb=" N ARG M 290 " --> pdb=" O ILE M 287 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LYS M 291 " --> pdb=" O ASP M 288 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP M 292 " --> pdb=" O ILE M 289 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR M 294 " --> pdb=" O LYS M 291 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN M 296 " --> pdb=" O LEU M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 302 through 305 Processing helix chain 'M' and resid 309 through 320 Processing helix chain 'M' and resid 335 through 348 removed outlier: 5.236A pdb=" N VAL M 339 " --> pdb=" O LYS M 336 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA M 347 " --> pdb=" O SER M 344 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 354 removed outlier: 3.783A pdb=" N GLN M 354 " --> pdb=" O THR M 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 351 through 354' Processing helix chain 'M' and resid 359 through 365 Processing helix chain 'M' and resid 367 through 371 removed outlier: 3.607A pdb=" N VAL M 370 " --> pdb=" O PRO M 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.552A pdb=" N HIS B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 532 through 536' Processing helix chain 'B' and resid 542 through 554 Processing helix chain 'B' and resid 562 through 575 Processing helix chain 'B' and resid 580 through 589 removed outlier: 3.655A pdb=" N GLN B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 611 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) Processing helix chain 'B' and resid 616 through 629 Processing helix chain 'B' and resid 641 through 650 Processing helix chain 'B' and resid 655 through 658 removed outlier: 3.902A pdb=" N ALA B 658 " --> pdb=" O SER B 655 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 655 through 658' Processing helix chain 'C' and resid 532 through 535 No H-bonds generated for 'chain 'C' and resid 532 through 535' Processing helix chain 'C' and resid 542 through 554 Processing helix chain 'C' and resid 562 through 575 Processing helix chain 'C' and resid 580 through 589 Processing helix chain 'C' and resid 593 through 595 No H-bonds generated for 'chain 'C' and resid 593 through 595' Processing helix chain 'C' and resid 597 through 610 Processing helix chain 'C' and resid 616 through 629 Processing helix chain 'C' and resid 641 through 650 removed outlier: 3.526A pdb=" N VAL C 646 " --> pdb=" O VAL C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 657 No H-bonds generated for 'chain 'C' and resid 655 through 657' Processing helix chain 'C' and resid 677 through 681 removed outlier: 3.604A pdb=" N LEU C 681 " --> pdb=" O THR C 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 677 through 681' Processing helix chain 'D' and resid 534 through 536 No H-bonds generated for 'chain 'D' and resid 534 through 536' Processing helix chain 'D' and resid 544 through 553 Processing helix chain 'D' and resid 562 through 575 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 581 through 590 removed outlier: 3.540A pdb=" N GLN D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 595 No H-bonds generated for 'chain 'D' and resid 593 through 595' Processing helix chain 'D' and resid 597 through 611 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 616 through 628 Processing helix chain 'D' and resid 641 through 650 Processing helix chain 'D' and resid 655 through 657 No H-bonds generated for 'chain 'D' and resid 655 through 657' Processing helix chain 'D' and resid 677 through 681 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 562 through 575 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 580 through 589 Processing helix chain 'A' and resid 593 through 595 No H-bonds generated for 'chain 'A' and resid 593 through 595' Processing helix chain 'A' and resid 597 through 611 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) Processing helix chain 'A' and resid 616 through 629 Processing helix chain 'A' and resid 642 through 650 removed outlier: 3.578A pdb=" N VAL A 646 " --> pdb=" O VAL A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 658 No H-bonds generated for 'chain 'A' and resid 656 through 658' Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing sheet with id= A, first strand: chain 'F' and resid 132 through 136 removed outlier: 6.897A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE F 31 " --> pdb=" O VAL F 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 35 through 38 removed outlier: 3.647A pdb=" N ARG F 37 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.367A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'H' and resid 132 through 136 removed outlier: 7.017A pdb=" N THR H 103 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ALA H 135 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (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) removed outlier: 3.565A pdb=" N PHE H 31 " --> pdb=" O VAL H 17 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 34 through 38 Processing sheet with id= G, first strand: chain 'H' and resid 297 through 300 removed outlier: 6.253A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N SER H 300 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU H 153 " --> pdb=" O SER H 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'I' and resid 8 through 12 Processing sheet with id= J, first strand: chain 'I' and resid 52 through 54 Processing sheet with id= K, first strand: chain 'I' and resid 105 through 107 Processing sheet with id= L, first strand: chain 'I' and resid 297 through 300 removed outlier: 6.156A pdb=" N ILE I 151 " --> pdb=" O VAL I 298 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N SER I 300 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU I 153 " --> pdb=" O SER I 300 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 238 through 241 Processing sheet with id= N, first strand: chain 'J' and resid 132 through 136 removed outlier: 6.770A pdb=" N THR J 103 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ALA J 135 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU J 105 " --> pdb=" O ALA J 135 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU J 8 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N THR J 106 " --> pdb=" O LEU J 8 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N CYS J 10 " --> pdb=" O THR J 106 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE J 31 " --> pdb=" O VAL J 17 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 35 through 38 removed outlier: 3.552A pdb=" N ARG J 37 " --> pdb=" O THR J 66 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 297 through 300 removed outlier: 6.287A pdb=" N ILE J 151 " --> pdb=" O VAL J 298 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N SER J 300 " --> pdb=" O ILE J 151 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU J 153 " --> pdb=" O SER J 300 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 238 through 241 Processing sheet with id= R, first strand: chain 'K' and resid 132 through 136 removed outlier: 7.113A pdb=" N THR K 103 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ALA K 135 " --> pdb=" O THR K 103 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU K 105 " --> pdb=" O ALA K 135 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N CYS K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 52 through 54 Processing sheet with id= T, first strand: chain 'K' and resid 297 through 300 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) Processing sheet with id= U, first strand: chain 'K' and resid 238 through 241 Processing sheet with id= V, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.502A pdb=" N PHE L 31 " --> pdb=" O VAL L 17 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 35 through 38 Processing sheet with id= X, first strand: chain 'L' and resid 103 through 107 removed outlier: 3.539A pdb=" N TYR L 133 " --> pdb=" O THR L 103 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 160 through 165 Processing sheet with id= Z, first strand: chain 'L' and resid 238 through 241 Processing sheet with id= AA, first strand: chain 'M' and resid 132 through 136 removed outlier: 7.078A pdb=" N THR M 103 " --> pdb=" O TYR M 133 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N ALA M 135 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU M 105 " --> pdb=" O ALA M 135 " (cutoff:3.500A) 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= AB, first strand: chain 'M' and resid 34 through 38 Processing sheet with id= AC, first strand: chain 'M' and resid 297 through 300 removed outlier: 6.281A pdb=" N ILE M 151 " --> pdb=" O VAL M 298 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N SER M 300 " --> pdb=" O ILE M 151 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU M 153 " --> pdb=" O SER M 300 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 238 through 241 917 hydrogen bonds defined for protein. 2307 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: 8.14 Time building geometry restraints manager: 10.57 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: 96.35 - 104.34: 535 104.34 - 112.33: 13556 112.33 - 120.32: 11470 120.32 - 128.31: 10146 128.31 - 136.30: 198 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: 111 2.49 - 3.10: 18695 3.10 - 3.70: 38395 3.70 - 4.30: 57459 4.30 - 4.90: 95216 Nonbonded interactions: 209876 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 209871 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.160 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 65.660 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.710 ------------------------------------------------------------------------------- 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 : 0.005 0.070 26476 Z= 0.319 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 *********************** 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 fitting. rotamer outliers: 12 poor density : 436 time to evaluate : 2.826 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: 0.3381 time to fit residues: 243.2086 Evaluate side-chains 348 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 344 time to evaluate : 3.310 ------------------------------------------------------------------------------- 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: 1.9990 chunk 137 optimal weight: 0.9990 chunk 84 optimal weight: 0.2980 chunk 167 optimal weight: 0.0070 chunk 132 optimal weight: 0.6980 chunk 256 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 HIS K 101 HIS K 162 ASN L 225 ASN C 645 ASN ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 26476 Z= 0.149 Angle : 0.539 8.533 35905 Z= 0.259 Chirality : 0.042 0.141 3993 Planarity : 0.004 0.039 4597 Dihedral : 8.099 171.930 3668 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.97 % Allowed : 6.98 % Favored : 92.05 % 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: 0.50 (0.15), residues: 3242 helix: 0.65 (0.14), residues: 1409 sheet: 0.07 (0.23), residues: 483 loop : 0.30 (0.18), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 340 HIS 0.004 0.001 HIS L 173 PHE 0.012 0.001 PHE A 626 TYR 0.033 0.001 TYR C 641 ARG 0.004 0.000 ARG K 37 *********************** 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 395 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 368 time to evaluate : 2.927 Fit side-chains REVERT: F 41 GLN cc_start: 0.7976 (pm20) cc_final: 0.7217 (tp40) REVERT: F 107 GLU cc_start: 0.8177 (tt0) cc_final: 0.7820 (pt0) REVERT: F 225 ASN cc_start: 0.7978 (t0) cc_final: 0.7755 (t0) REVERT: F 372 ARG cc_start: 0.8132 (ttm110) cc_final: 0.7872 (ptp-110) REVERT: H 47 MET cc_start: 0.5681 (ppp) cc_final: 0.5456 (ppp) REVERT: H 224 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7796 (mp0) REVERT: H 227 MET cc_start: 0.7982 (tpp) cc_final: 0.7660 (tpp) REVERT: I 148 THR cc_start: 0.8726 (p) cc_final: 0.8420 (m) REVERT: I 286 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: I 374 CYS cc_start: 0.7041 (m) cc_final: 0.6627 (m) REVERT: J 155 SER cc_start: 0.9261 (t) cc_final: 0.9031 (t) REVERT: K 191 LYS cc_start: 0.8030 (ttpt) cc_final: 0.7750 (ttpt) REVERT: L 25 ASP cc_start: 0.7989 (p0) cc_final: 0.7607 (t0) REVERT: M 75 ILE cc_start: 0.9229 (mt) cc_final: 0.9018 (mp) REVERT: M 96 VAL cc_start: 0.9060 (m) cc_final: 0.8852 (p) REVERT: B 536 HIS cc_start: 0.7726 (m170) cc_final: 0.7435 (m-70) REVERT: B 574 GLU cc_start: 0.7332 (tt0) cc_final: 0.6992 (pt0) outliers start: 27 outliers final: 20 residues processed: 384 average time/residue: 0.3568 time to fit residues: 225.1879 Evaluate side-chains 365 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 344 time to evaluate : 3.015 ------------------------------------------------------------------------------- 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 100 GLU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 653 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 165 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 297 optimal weight: 1.9990 chunk 321 optimal weight: 0.9980 chunk 264 optimal weight: 10.0000 chunk 295 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 26476 Z= 0.297 Angle : 0.581 7.148 35905 Z= 0.283 Chirality : 0.045 0.152 3993 Planarity : 0.004 0.041 4597 Dihedral : 7.549 164.777 3664 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.40 % Allowed : 9.68 % Favored : 88.92 % 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: 0.36 (0.15), residues: 3242 helix: 0.57 (0.14), residues: 1416 sheet: -0.09 (0.24), residues: 448 loop : 0.20 (0.18), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 340 HIS 0.007 0.001 HIS K 161 PHE 0.013 0.001 PHE H 375 TYR 0.026 0.001 TYR C 641 ARG 0.004 0.000 ARG I 256 *********************** 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 386 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 347 time to evaluate : 2.822 Fit side-chains REVERT: F 41 GLN cc_start: 0.8017 (pm20) cc_final: 0.7238 (tp40) REVERT: F 216 LEU cc_start: 0.8511 (mt) cc_final: 0.8237 (mp) REVERT: F 225 ASN cc_start: 0.8083 (t0) cc_final: 0.7841 (t0) REVERT: F 340 TRP cc_start: 0.8566 (t60) cc_final: 0.8066 (t60) REVERT: F 372 ARG cc_start: 0.8218 (ttm110) cc_final: 0.7778 (ttm-80) REVERT: H 224 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7917 (mp0) REVERT: H 227 MET cc_start: 0.8037 (tpp) cc_final: 0.7756 (tpp) REVERT: H 269 MET cc_start: 0.9005 (mtt) cc_final: 0.8672 (mmt) REVERT: H 305 MET cc_start: 0.8343 (mmm) cc_final: 0.8005 (mmm) REVERT: H 326 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7918 (tttm) REVERT: I 72 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: I 119 MET cc_start: 0.8338 (ttm) cc_final: 0.8107 (mtm) REVERT: I 143 TYR cc_start: 0.7861 (m-10) cc_final: 0.7275 (m-80) REVERT: I 148 THR cc_start: 0.8798 (p) cc_final: 0.8580 (m) REVERT: I 286 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: I 374 CYS cc_start: 0.7159 (m) cc_final: 0.6843 (m) REVERT: J 155 SER cc_start: 0.9293 (t) cc_final: 0.9071 (t) REVERT: K 82 MET cc_start: 0.8208 (tpt) cc_final: 0.7724 (tpt) REVERT: K 123 MET cc_start: 0.9018 (mmt) cc_final: 0.8808 (mmm) REVERT: K 191 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7919 (ttpt) REVERT: L 25 ASP cc_start: 0.8171 (p0) cc_final: 0.7799 (t0) REVERT: L 83 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7229 (tm-30) REVERT: L 269 MET cc_start: 0.9050 (mtp) cc_final: 0.8716 (mtt) REVERT: L 334 GLU cc_start: 0.7423 (pm20) cc_final: 0.6951 (pm20) REVERT: M 113 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7385 (mmtt) REVERT: M 270 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8674 (tp30) REVERT: B 536 HIS cc_start: 0.7684 (m170) cc_final: 0.7363 (m-70) REVERT: B 574 GLU cc_start: 0.7270 (tt0) cc_final: 0.6707 (pt0) REVERT: B 640 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.6604 (p0) REVERT: A 638 GLU cc_start: 0.6815 (pm20) cc_final: 0.6347 (tm-30) REVERT: A 648 ASP cc_start: 0.7632 (m-30) cc_final: 0.7365 (m-30) REVERT: A 675 ILE cc_start: 0.8630 (mm) cc_final: 0.8071 (mm) outliers start: 39 outliers final: 28 residues processed: 370 average time/residue: 0.3453 time to fit residues: 207.1380 Evaluate side-chains 356 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 324 time to evaluate : 2.643 ------------------------------------------------------------------------------- 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 374 CYS Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 346 LEU 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 B residue 640 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 653 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 8.9990 chunk 223 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 141 optimal weight: 0.0070 chunk 199 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 chunk 316 optimal weight: 0.0370 chunk 155 optimal weight: 1.9990 chunk 282 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- 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 ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26476 Z= 0.143 Angle : 0.506 6.876 35905 Z= 0.239 Chirality : 0.042 0.135 3993 Planarity : 0.003 0.036 4597 Dihedral : 7.121 159.140 3663 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.08 % Allowed : 11.19 % Favored : 87.73 % 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: 0.60 (0.15), residues: 3242 helix: 0.81 (0.15), residues: 1395 sheet: -0.04 (0.24), residues: 448 loop : 0.33 (0.18), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 340 HIS 0.004 0.001 HIS L 173 PHE 0.009 0.001 PHE M 255 TYR 0.019 0.001 TYR C 641 ARG 0.004 0.000 ARG C 543 *********************** 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 384 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 354 time to evaluate : 3.348 Fit side-chains REVERT: F 41 GLN cc_start: 0.7938 (pm20) cc_final: 0.7251 (tp40) REVERT: F 216 LEU cc_start: 0.8457 (mt) cc_final: 0.8152 (mp) REVERT: F 225 ASN cc_start: 0.7978 (t0) cc_final: 0.7725 (t0) REVERT: F 340 TRP cc_start: 0.8436 (t60) cc_final: 0.8074 (t60) REVERT: F 372 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7630 (ptp-110) REVERT: H 184 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8292 (m-30) REVERT: H 221 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8353 (tt) REVERT: H 224 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7864 (mp0) REVERT: H 227 MET cc_start: 0.8075 (tpp) cc_final: 0.7727 (tpp) REVERT: H 286 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8546 (m-30) REVERT: H 305 MET cc_start: 0.8364 (mmm) cc_final: 0.8065 (mmm) REVERT: I 72 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: I 119 MET cc_start: 0.8260 (ttm) cc_final: 0.8008 (mtm) REVERT: I 143 TYR cc_start: 0.7865 (m-80) cc_final: 0.7285 (m-80) REVERT: I 286 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: I 288 ASP cc_start: 0.8213 (t70) cc_final: 0.7808 (t0) REVERT: I 374 CYS cc_start: 0.7187 (m) cc_final: 0.6957 (m) REVERT: J 155 SER cc_start: 0.9251 (t) cc_final: 0.9006 (t) REVERT: K 123 MET cc_start: 0.8947 (mmt) cc_final: 0.8725 (mmm) REVERT: K 191 LYS cc_start: 0.8182 (ttpt) cc_final: 0.7890 (ttpt) REVERT: L 25 ASP cc_start: 0.8085 (p0) cc_final: 0.7777 (t0) REVERT: L 83 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7216 (tm-30) REVERT: M 270 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8713 (tp30) REVERT: B 536 HIS cc_start: 0.7719 (m170) cc_final: 0.7398 (m-70) REVERT: B 574 GLU cc_start: 0.7148 (tt0) cc_final: 0.6627 (pt0) REVERT: B 640 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.6618 (p0) REVERT: C 535 MET cc_start: 0.7573 (mmt) cc_final: 0.7255 (mtt) REVERT: D 683 MET cc_start: 0.7253 (ptm) cc_final: 0.6988 (ptm) REVERT: A 648 ASP cc_start: 0.7752 (m-30) cc_final: 0.7409 (m-30) REVERT: A 675 ILE cc_start: 0.8622 (mm) cc_final: 0.8081 (mm) outliers start: 30 outliers final: 14 residues processed: 372 average time/residue: 0.3321 time to fit residues: 203.6534 Evaluate side-chains 352 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 331 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 374 CYS Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain I residue 297 ASN Chi-restraints excluded: chain K residue 190 MET 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 B residue 640 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain A residue 653 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 235 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 269 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 283 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 M 88 HIS ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26476 Z= 0.279 Angle : 0.568 7.432 35905 Z= 0.274 Chirality : 0.045 0.147 3993 Planarity : 0.004 0.036 4597 Dihedral : 7.039 152.702 3662 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.94 % Allowed : 12.16 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.40 (0.15), residues: 3242 helix: 0.66 (0.15), residues: 1416 sheet: -0.14 (0.24), residues: 448 loop : 0.19 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 356 HIS 0.005 0.001 HIS H 161 PHE 0.012 0.001 PHE H 375 TYR 0.022 0.001 TYR J 133 ARG 0.005 0.000 ARG F 95 *********************** 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 391 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 337 time to evaluate : 3.643 Fit side-chains revert: symmetry clash REVERT: F 41 GLN cc_start: 0.7971 (pm20) cc_final: 0.7258 (tp40) REVERT: F 216 LEU cc_start: 0.8483 (mt) cc_final: 0.8147 (mp) REVERT: F 225 ASN cc_start: 0.8040 (t0) cc_final: 0.7788 (t0) REVERT: F 340 TRP cc_start: 0.8646 (t60) cc_final: 0.8090 (t60) REVERT: H 184 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8442 (m-30) REVERT: H 221 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8442 (tt) REVERT: H 224 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7946 (mp0) REVERT: H 227 MET cc_start: 0.8157 (tpp) cc_final: 0.7819 (tpp) REVERT: H 269 MET cc_start: 0.9061 (mtt) cc_final: 0.8766 (mmt) REVERT: H 286 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8579 (m-30) REVERT: H 305 MET cc_start: 0.8417 (mmm) cc_final: 0.8125 (mmm) REVERT: I 72 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: I 119 MET cc_start: 0.8319 (ttm) cc_final: 0.8108 (mtm) REVERT: I 143 TYR cc_start: 0.8354 (m-80) cc_final: 0.7462 (m-80) REVERT: I 286 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: I 288 ASP cc_start: 0.8289 (t70) cc_final: 0.7807 (t0) REVERT: I 374 CYS cc_start: 0.7294 (m) cc_final: 0.7004 (m) REVERT: J 155 SER cc_start: 0.9259 (t) cc_final: 0.9023 (t) REVERT: K 82 MET cc_start: 0.8176 (tpt) cc_final: 0.7700 (tpt) REVERT: K 123 MET cc_start: 0.8986 (mmt) cc_final: 0.8776 (mmm) REVERT: K 191 LYS cc_start: 0.8251 (ttpt) cc_final: 0.7997 (ttpt) REVERT: L 25 ASP cc_start: 0.8176 (p0) cc_final: 0.7876 (t0) REVERT: L 83 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7443 (tt0) REVERT: L 334 GLU cc_start: 0.7496 (pm20) cc_final: 0.7131 (pm20) REVERT: M 270 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8671 (tp30) REVERT: B 536 HIS cc_start: 0.7756 (m170) cc_final: 0.7426 (m-70) REVERT: B 640 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.6554 (p0) REVERT: C 537 SER cc_start: 0.9031 (t) cc_final: 0.8712 (t) REVERT: D 666 LEU cc_start: 0.7748 (tp) cc_final: 0.7029 (pt) REVERT: D 683 MET cc_start: 0.7292 (ptm) cc_final: 0.7071 (ptm) REVERT: A 648 ASP cc_start: 0.7877 (m-30) cc_final: 0.7461 (m-30) REVERT: A 675 ILE cc_start: 0.8645 (mm) cc_final: 0.8090 (mm) outliers start: 54 outliers final: 37 residues processed: 373 average time/residue: 0.3387 time to fit residues: 207.7714 Evaluate side-chains 371 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 327 time to evaluate : 2.886 ------------------------------------------------------------------------------- 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 107 GLU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 374 CYS Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain I residue 297 ASN 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 212 ILE Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain M residue 360 GLN Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 653 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 106 optimal weight: 0.8980 chunk 284 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 316 optimal weight: 20.0000 chunk 262 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 41 GLN K 101 HIS K 173 HIS L 40 HIS ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 26476 Z= 0.402 Angle : 0.646 8.883 35905 Z= 0.318 Chirality : 0.048 0.161 3993 Planarity : 0.004 0.043 4597 Dihedral : 7.314 155.419 3662 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.41 % Allowed : 13.03 % 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: 0.00 (0.15), residues: 3242 helix: 0.39 (0.14), residues: 1412 sheet: -0.40 (0.24), residues: 448 loop : -0.07 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 340 HIS 0.006 0.001 HIS J 161 PHE 0.017 0.002 PHE C 520 TYR 0.034 0.002 TYR C 641 ARG 0.010 0.001 ARG D 628 *********************** 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 394 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 327 time to evaluate : 3.024 Fit side-chains REVERT: F 57 GLU cc_start: 0.8600 (tp30) cc_final: 0.8256 (tp30) REVERT: F 216 LEU cc_start: 0.8507 (mt) cc_final: 0.8171 (mp) REVERT: F 225 ASN cc_start: 0.8087 (t0) cc_final: 0.7844 (t0) REVERT: H 184 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8472 (m-30) REVERT: H 221 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8585 (tt) REVERT: H 286 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8551 (m-30) REVERT: H 305 MET cc_start: 0.8433 (mmm) cc_final: 0.8191 (mmm) REVERT: I 72 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7557 (mt-10) REVERT: I 78 ASN cc_start: 0.8612 (t0) cc_final: 0.8387 (t0) REVERT: I 286 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: I 374 CYS cc_start: 0.7356 (m) cc_final: 0.7051 (m) REVERT: J 291 LYS cc_start: 0.8474 (ttpp) cc_final: 0.8130 (tptt) REVERT: K 82 MET cc_start: 0.8313 (tpt) cc_final: 0.7762 (tpt) REVERT: K 286 ASP cc_start: 0.8277 (m-30) cc_final: 0.8031 (m-30) REVERT: K 328 LYS cc_start: 0.8479 (mttp) cc_final: 0.7524 (ptmm) REVERT: L 25 ASP cc_start: 0.8267 (p0) cc_final: 0.8065 (t0) REVERT: L 83 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7348 (tt0) REVERT: L 334 GLU cc_start: 0.7405 (pm20) cc_final: 0.7187 (pm20) REVERT: M 253 GLU cc_start: 0.8093 (mp0) cc_final: 0.7756 (mp0) REVERT: M 270 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8407 (tp30) REVERT: B 536 HIS cc_start: 0.7689 (m170) cc_final: 0.7336 (m-70) REVERT: B 640 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.6608 (p0) REVERT: B 665 TYR cc_start: 0.7438 (m-80) cc_final: 0.7108 (m-80) REVERT: C 535 MET cc_start: 0.7638 (mmt) cc_final: 0.7305 (mtt) REVERT: C 537 SER cc_start: 0.9068 (t) cc_final: 0.8760 (t) REVERT: C 662 TYR cc_start: 0.7079 (m-80) cc_final: 0.6748 (m-80) REVERT: D 666 LEU cc_start: 0.7854 (tp) cc_final: 0.7135 (pt) REVERT: A 648 ASP cc_start: 0.8066 (m-30) cc_final: 0.7658 (m-30) REVERT: A 675 ILE cc_start: 0.8718 (mm) cc_final: 0.8189 (mt) outliers start: 67 outliers final: 44 residues processed: 374 average time/residue: 0.3332 time to fit residues: 205.7131 Evaluate side-chains 367 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 316 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 374 CYS Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 270 GLU Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain I residue 297 ASN Chi-restraints excluded: chain I residue 370 VAL 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 89 THR Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain M residue 360 GLN Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 653 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 305 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 266 optimal weight: 6.9990 chunk 176 optimal weight: 0.7980 chunk 315 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 173 HIS ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26476 Z= 0.177 Angle : 0.534 9.396 35905 Z= 0.254 Chirality : 0.043 0.137 3993 Planarity : 0.004 0.037 4597 Dihedral : 6.976 149.776 3662 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.58 % Allowed : 14.29 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3242 helix: 0.66 (0.15), residues: 1416 sheet: -0.23 (0.24), residues: 434 loop : 0.05 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 656 HIS 0.004 0.001 HIS I 371 PHE 0.019 0.001 PHE H 223 TYR 0.033 0.001 TYR C 641 ARG 0.003 0.000 ARG F 95 *********************** 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 390 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 346 time to evaluate : 3.245 Fit side-chains REVERT: F 57 GLU cc_start: 0.8517 (tp30) cc_final: 0.8186 (tp30) REVERT: F 216 LEU cc_start: 0.8462 (mt) cc_final: 0.8095 (mp) REVERT: F 225 ASN cc_start: 0.8005 (t0) cc_final: 0.7751 (t0) REVERT: F 338 SER cc_start: 0.9413 (m) cc_final: 0.9151 (t) REVERT: H 184 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8354 (m-30) REVERT: H 221 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8594 (tt) REVERT: H 227 MET cc_start: 0.8256 (tpp) cc_final: 0.7648 (tpp) REVERT: H 286 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8005 (m-30) REVERT: H 305 MET cc_start: 0.8404 (mmm) cc_final: 0.8175 (mmm) REVERT: I 72 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: I 286 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7935 (m-30) REVERT: I 288 ASP cc_start: 0.8201 (t70) cc_final: 0.7812 (t0) REVERT: I 374 CYS cc_start: 0.7443 (m) cc_final: 0.7110 (m) REVERT: J 155 SER cc_start: 0.9291 (t) cc_final: 0.9071 (t) REVERT: K 82 MET cc_start: 0.8089 (tpt) cc_final: 0.7586 (tpt) REVERT: K 328 LYS cc_start: 0.8397 (mttp) cc_final: 0.7690 (tttm) REVERT: L 83 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7454 (tt0) REVERT: L 121 GLN cc_start: 0.7870 (tt0) cc_final: 0.7629 (tt0) REVERT: L 334 GLU cc_start: 0.7340 (pm20) cc_final: 0.7127 (pm20) REVERT: L 364 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8486 (tp30) REVERT: M 253 GLU cc_start: 0.8038 (mp0) cc_final: 0.7673 (mp0) REVERT: M 270 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8472 (tp30) REVERT: B 536 HIS cc_start: 0.7695 (m170) cc_final: 0.7346 (m-70) REVERT: B 640 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.6560 (p0) REVERT: B 663 GLU cc_start: 0.7604 (tp30) cc_final: 0.7282 (tt0) REVERT: B 665 TYR cc_start: 0.7308 (m-80) cc_final: 0.6950 (m-80) REVERT: C 535 MET cc_start: 0.7612 (mmt) cc_final: 0.7276 (mtt) REVERT: C 537 SER cc_start: 0.9038 (t) cc_final: 0.8716 (t) REVERT: C 662 TYR cc_start: 0.6977 (m-80) cc_final: 0.6656 (m-80) REVERT: A 557 ASP cc_start: 0.7841 (t0) cc_final: 0.7304 (t0) REVERT: A 600 LYS cc_start: 0.7815 (mmmm) cc_final: 0.7448 (mmmm) REVERT: A 640 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.6551 (p0) REVERT: A 648 ASP cc_start: 0.8131 (m-30) cc_final: 0.7767 (m-30) REVERT: A 675 ILE cc_start: 0.8691 (mm) cc_final: 0.8131 (mt) outliers start: 44 outliers final: 26 residues processed: 370 average time/residue: 0.3485 time to fit residues: 211.6579 Evaluate side-chains 367 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 333 time to evaluate : 2.512 ------------------------------------------------------------------------------- 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 324 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain 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 M residue 270 GLU Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain M residue 360 GLN Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 571 LEU 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 D residue 642 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 640 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 194 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 286 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 HIS ** M 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 ASN D 684 GLN ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 26476 Z= 0.299 Angle : 0.588 10.163 35905 Z= 0.282 Chirality : 0.045 0.149 3993 Planarity : 0.004 0.037 4597 Dihedral : 6.988 148.571 3662 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.91 % Allowed : 14.14 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3242 helix: 0.59 (0.15), residues: 1416 sheet: -0.28 (0.24), residues: 434 loop : 0.00 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 656 HIS 0.005 0.001 HIS J 161 PHE 0.012 0.001 PHE L 200 TYR 0.033 0.001 TYR C 641 ARG 0.003 0.000 ARG I 256 *********************** 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 385 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 332 time to evaluate : 3.160 Fit side-chains REVERT: F 57 GLU cc_start: 0.8575 (tp30) cc_final: 0.8237 (tp30) REVERT: F 216 LEU cc_start: 0.8456 (mt) cc_final: 0.8090 (mp) REVERT: F 225 ASN cc_start: 0.8066 (t0) cc_final: 0.7833 (t0) REVERT: F 338 SER cc_start: 0.9421 (m) cc_final: 0.9201 (t) REVERT: H 184 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8387 (m-30) REVERT: H 221 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8618 (tt) REVERT: H 227 MET cc_start: 0.8258 (tpp) cc_final: 0.7993 (tpp) REVERT: H 286 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8045 (m-30) REVERT: H 305 MET cc_start: 0.8404 (mmm) cc_final: 0.8173 (mmm) REVERT: I 72 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: I 286 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7985 (m-30) REVERT: I 374 CYS cc_start: 0.7421 (m) cc_final: 0.7124 (m) REVERT: J 155 SER cc_start: 0.9305 (t) cc_final: 0.9087 (t) REVERT: J 291 LYS cc_start: 0.8451 (ttpp) cc_final: 0.8083 (tptt) REVERT: K 82 MET cc_start: 0.8265 (tpt) cc_final: 0.7730 (tpt) REVERT: K 328 LYS cc_start: 0.8428 (mttp) cc_final: 0.7565 (ptmm) REVERT: L 83 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7393 (tt0) REVERT: L 121 GLN cc_start: 0.7873 (tt0) cc_final: 0.7665 (tt0) REVERT: L 334 GLU cc_start: 0.7357 (pm20) cc_final: 0.7151 (pm20) REVERT: L 364 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8510 (tp30) REVERT: M 270 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8509 (tp30) REVERT: B 536 HIS cc_start: 0.7805 (m170) cc_final: 0.7439 (m-70) REVERT: B 640 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.6574 (p0) REVERT: B 663 GLU cc_start: 0.7667 (tp30) cc_final: 0.7325 (tt0) REVERT: B 665 TYR cc_start: 0.7376 (m-80) cc_final: 0.7035 (m-80) REVERT: C 535 MET cc_start: 0.7667 (mmt) cc_final: 0.7345 (mtt) REVERT: C 537 SER cc_start: 0.9050 (t) cc_final: 0.8727 (t) REVERT: C 662 TYR cc_start: 0.7066 (m-80) cc_final: 0.6757 (m-80) REVERT: D 666 LEU cc_start: 0.7762 (tp) cc_final: 0.7129 (pt) REVERT: A 557 ASP cc_start: 0.7861 (t0) cc_final: 0.7269 (t0) REVERT: A 600 LYS cc_start: 0.7845 (mmmm) cc_final: 0.7478 (mmmm) REVERT: A 640 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.6571 (p0) REVERT: A 648 ASP cc_start: 0.8145 (m-30) cc_final: 0.7785 (m-30) REVERT: A 675 ILE cc_start: 0.8732 (mm) cc_final: 0.8196 (mt) outliers start: 53 outliers final: 38 residues processed: 365 average time/residue: 0.3501 time to fit residues: 210.5244 Evaluate side-chains 373 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 327 time to evaluate : 3.074 ------------------------------------------------------------------------------- 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 107 GLU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 244 ASP Chi-restraints excluded: chain I residue 286 ASP 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 278 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 269 MET Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain M residue 360 GLN Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 571 LEU 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 D residue 642 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 640 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 5.9990 chunk 275 optimal weight: 0.0060 chunk 293 optimal weight: 7.9990 chunk 176 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 265 optimal weight: 0.8980 chunk 277 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 HIS ** M 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 684 GLN ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26476 Z= 0.157 Angle : 0.529 11.584 35905 Z= 0.250 Chirality : 0.042 0.138 3993 Planarity : 0.004 0.036 4597 Dihedral : 6.728 142.832 3662 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.51 % Allowed : 14.97 % Favored : 83.52 % 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: 0.44 (0.15), residues: 3242 helix: 0.75 (0.15), residues: 1416 sheet: -0.19 (0.24), residues: 434 loop : 0.15 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 656 HIS 0.003 0.001 HIS I 371 PHE 0.011 0.001 PHE H 375 TYR 0.034 0.001 TYR C 641 ARG 0.003 0.000 ARG F 95 *********************** 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 382 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 340 time to evaluate : 2.807 Fit side-chains REVERT: F 57 GLU cc_start: 0.8517 (tp30) cc_final: 0.8183 (tp30) REVERT: F 216 LEU cc_start: 0.8417 (mt) cc_final: 0.8023 (mp) REVERT: F 225 ASN cc_start: 0.8019 (t0) cc_final: 0.7777 (t0) REVERT: F 355 MET cc_start: 0.8454 (mtp) cc_final: 0.7868 (mtm) REVERT: H 184 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8323 (m-30) REVERT: H 221 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8616 (tt) REVERT: H 227 MET cc_start: 0.8208 (tpp) cc_final: 0.7918 (tpp) REVERT: H 305 MET cc_start: 0.8379 (mmm) cc_final: 0.8155 (mmm) REVERT: I 44 MET cc_start: 0.8482 (mtp) cc_final: 0.8224 (mtm) REVERT: I 72 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: I 286 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: I 374 CYS cc_start: 0.7319 (m) cc_final: 0.7011 (m) REVERT: J 47 MET cc_start: 0.7625 (mmm) cc_final: 0.7233 (mmm) REVERT: J 155 SER cc_start: 0.9291 (t) cc_final: 0.9065 (t) REVERT: K 82 MET cc_start: 0.8074 (tpt) cc_final: 0.7575 (tpt) REVERT: K 328 LYS cc_start: 0.8436 (mttp) cc_final: 0.7757 (tttp) REVERT: K 364 GLU cc_start: 0.8782 (tp30) cc_final: 0.8424 (pt0) REVERT: L 83 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7479 (tt0) REVERT: L 121 GLN cc_start: 0.7843 (tt0) cc_final: 0.7635 (tt0) REVERT: L 334 GLU cc_start: 0.7304 (pm20) cc_final: 0.7034 (pm20) REVERT: L 364 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8487 (tp30) REVERT: M 270 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8491 (tp30) REVERT: B 536 HIS cc_start: 0.7749 (m170) cc_final: 0.7378 (m-70) REVERT: B 640 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.6517 (p0) REVERT: B 663 GLU cc_start: 0.7602 (tp30) cc_final: 0.7297 (tt0) REVERT: B 665 TYR cc_start: 0.7340 (m-80) cc_final: 0.6999 (m-80) REVERT: B 675 ILE cc_start: 0.8147 (mp) cc_final: 0.7900 (mt) REVERT: C 535 MET cc_start: 0.7563 (mmt) cc_final: 0.7217 (mtt) REVERT: C 537 SER cc_start: 0.9047 (t) cc_final: 0.8748 (t) REVERT: C 662 TYR cc_start: 0.6970 (m-80) cc_final: 0.6659 (m-80) REVERT: D 628 ARG cc_start: 0.6732 (tpp80) cc_final: 0.6444 (tpp-160) REVERT: A 557 ASP cc_start: 0.7905 (t0) cc_final: 0.7317 (t0) REVERT: A 600 LYS cc_start: 0.7841 (mmmm) cc_final: 0.7468 (mmmm) REVERT: A 648 ASP cc_start: 0.8080 (m-30) cc_final: 0.7717 (m-30) REVERT: A 675 ILE cc_start: 0.8716 (mm) cc_final: 0.8163 (mt) outliers start: 42 outliers final: 33 residues processed: 365 average time/residue: 0.3412 time to fit residues: 202.2647 Evaluate side-chains 373 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 334 time to evaluate : 2.865 ------------------------------------------------------------------------------- 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 107 GLU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 221 LEU 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 149 THR Chi-restraints excluded: chain I residue 270 GLU Chi-restraints excluded: chain I residue 286 ASP 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 L residue 54 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain M residue 360 GLN Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain A residue 594 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 310 optimal weight: 10.0000 chunk 189 optimal weight: 0.0570 chunk 147 optimal weight: 0.1980 chunk 215 optimal weight: 0.6980 chunk 325 optimal weight: 5.9990 chunk 299 optimal weight: 0.0870 chunk 259 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 159 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- 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 128 ASN M 101 HIS M 246 GLN C 645 ASN ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 : 0.002 0.037 26476 Z= 0.127 Angle : 0.518 12.487 35905 Z= 0.241 Chirality : 0.041 0.137 3993 Planarity : 0.003 0.036 4597 Dihedral : 6.406 132.105 3662 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.22 % Allowed : 15.47 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.16), residues: 3242 helix: 0.70 (0.15), residues: 1444 sheet: -0.09 (0.24), residues: 434 loop : 0.29 (0.18), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 656 HIS 0.013 0.001 HIS M 101 PHE 0.012 0.001 PHE H 375 TYR 0.030 0.001 TYR C 641 ARG 0.008 0.000 ARG H 95 ********************** 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 fitting. rotamer outliers: 34 poor density : 342 time to evaluate : 3.022 Fit side-chains REVERT: F 57 GLU cc_start: 0.8526 (tp30) cc_final: 0.8180 (tp30) REVERT: F 216 LEU cc_start: 0.8412 (mt) cc_final: 0.8029 (mp) REVERT: F 225 ASN cc_start: 0.7967 (t0) cc_final: 0.7730 (t0) REVERT: F 355 MET cc_start: 0.8463 (mtp) cc_final: 0.8049 (mtm) REVERT: H 184 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8235 (m-30) REVERT: H 221 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8635 (tt) REVERT: H 227 MET cc_start: 0.8218 (tpp) cc_final: 0.7928 (tpp) REVERT: H 305 MET cc_start: 0.8361 (mmm) cc_final: 0.8137 (mmm) REVERT: I 72 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: I 269 MET cc_start: 0.8837 (mtm) cc_final: 0.8508 (mtm) REVERT: I 286 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: J 47 MET cc_start: 0.7625 (mmm) cc_final: 0.7174 (mmm) REVERT: J 155 SER cc_start: 0.9286 (t) cc_final: 0.9059 (t) REVERT: K 82 MET cc_start: 0.8013 (tpt) cc_final: 0.7511 (tpt) REVERT: K 328 LYS cc_start: 0.8444 (mttp) cc_final: 0.7790 (tttp) REVERT: K 364 GLU cc_start: 0.8715 (tp30) cc_final: 0.8405 (pt0) REVERT: L 83 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7436 (tt0) REVERT: L 128 ASN cc_start: 0.7968 (m110) cc_final: 0.7631 (t0) REVERT: L 236 LEU cc_start: 0.8346 (mp) cc_final: 0.8120 (mp) REVERT: L 334 GLU cc_start: 0.7298 (pm20) cc_final: 0.7031 (pm20) REVERT: L 364 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8476 (tp30) REVERT: M 270 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8500 (tp30) REVERT: B 536 HIS cc_start: 0.7760 (m170) cc_final: 0.7388 (m-70) REVERT: B 663 GLU cc_start: 0.7563 (tp30) cc_final: 0.7225 (tt0) REVERT: B 665 TYR cc_start: 0.7310 (m-80) cc_final: 0.6821 (m-80) REVERT: B 675 ILE cc_start: 0.8132 (mp) cc_final: 0.7892 (mt) REVERT: C 535 MET cc_start: 0.7527 (mmt) cc_final: 0.7236 (mtt) REVERT: C 537 SER cc_start: 0.9039 (t) cc_final: 0.8745 (t) REVERT: A 557 ASP cc_start: 0.7817 (t0) cc_final: 0.7196 (t0) REVERT: A 600 LYS cc_start: 0.7850 (mmmm) cc_final: 0.7471 (mmmm) REVERT: A 648 ASP cc_start: 0.8037 (m-30) cc_final: 0.7676 (m-30) REVERT: A 675 ILE cc_start: 0.8688 (mm) cc_final: 0.8185 (mm) outliers start: 34 outliers final: 26 residues processed: 360 average time/residue: 0.3538 time to fit residues: 206.2739 Evaluate side-chains 357 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 326 time to evaluate : 3.153 ------------------------------------------------------------------------------- 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 107 GLU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 244 ASP Chi-restraints excluded: chain I residue 270 GLU Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 143 TYR 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 571 LEU Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 651 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 259 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 266 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.0050 chunk 228 optimal weight: 2.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 HIS H 162 ASN ** J 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 HIS D 684 GLN ** 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 = 0.3577 r_free = 0.3577 target = 0.127095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.101685 restraints weight = 41308.406| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.40 r_work: 0.3118 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26476 Z= 0.290 Angle : 0.586 11.929 35905 Z= 0.280 Chirality : 0.045 0.142 3993 Planarity : 0.004 0.035 4597 Dihedral : 6.658 138.788 3662 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.44 % Allowed : 15.47 % Favored : 83.09 % 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: 0.30 (0.15), residues: 3242 helix: 0.52 (0.14), residues: 1462 sheet: -0.14 (0.24), residues: 434 loop : 0.18 (0.18), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 656 HIS 0.008 0.001 HIS M 101 PHE 0.014 0.001 PHE C 520 TYR 0.031 0.001 TYR C 641 ARG 0.007 0.000 ARG H 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5639.79 seconds wall clock time: 103 minutes 55.62 seconds (6235.62 seconds total)