Starting phenix.real_space_refine on Thu Mar 14 13:24:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm3_13511/03_2024/7pm3_13511_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm3_13511/03_2024/7pm3_13511.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm3_13511/03_2024/7pm3_13511_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm3_13511/03_2024/7pm3_13511_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm3_13511/03_2024/7pm3_13511_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm3_13511/03_2024/7pm3_13511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm3_13511/03_2024/7pm3_13511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm3_13511/03_2024/7pm3_13511_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm3_13511/03_2024/7pm3_13511_updated.pdb" } resolution = 3.1 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= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Br 3 7.06 5 P 9 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 5649 2.51 5 N 1494 2.21 5 O 1719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B ASP 187": "OD1" <-> "OD2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C ASP 187": "OD1" <-> "OD2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D ASP 187": "OD1" <-> "OD2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8940 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" 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: "C" 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: "D" 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: 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: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 127 Unusual residues: {' MG': 1, '9UE': 2, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.26, per 1000 atoms: 0.59 Number of scatterers: 8940 At special positions: 0 Unit cell: (89.1, 90.2, 136.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 3 34.99 S 63 16.00 P 9 15.00 Mg 3 11.99 O 1719 8.00 N 1494 7.00 C 5649 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=0, symmetry=0 Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.7 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 15 sheets defined 42.0% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 113 through 125 removed outlier: 3.556A pdb=" N MET B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.671A pdb=" N TYR B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.509A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 253 through 262 Proline residue: B 258 - end of helix removed outlier: 4.695A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 4.208A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.577A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.014A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 4.340A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.500A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.575A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.648A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 253 through 262 Proline residue: C 258 - end of helix removed outlier: 4.758A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 294 removed outlier: 4.175A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.572A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.020A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 4.372A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 113 through 125 removed outlier: 3.551A pdb=" N MET D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.648A pdb=" N TYR D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 232 removed outlier: 3.556A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 253 through 262 Proline residue: D 258 - end of helix removed outlier: 4.727A pdb=" N LEU D 261 " --> pdb=" O CYS D 257 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 4.270A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 removed outlier: 3.533A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 348 removed outlier: 4.607A pdb=" N VAL D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TRP D 340 " --> pdb=" O LYS D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 354 removed outlier: 4.355A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 371 Processing sheet with id= A, first strand: chain 'B' and resid 8 through 12 Processing sheet with id= B, first strand: chain 'B' and resid 52 through 54 Processing sheet with id= C, first strand: chain 'B' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.692A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= F, first strand: chain 'C' and resid 8 through 12 Processing sheet with id= G, first strand: chain 'C' and resid 52 through 54 Processing sheet with id= H, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= I, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.675A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= K, first strand: chain 'D' and resid 8 through 12 Processing sheet with id= L, first strand: chain 'D' and resid 52 through 54 Processing sheet with id= M, first strand: chain 'D' and resid 103 through 107 Processing sheet with id= N, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.602A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 238 through 241 326 hydrogen bonds defined for protein. 825 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: 2.72 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2371 1.33 - 1.47: 2623 1.47 - 1.60: 4021 1.60 - 1.73: 9 1.73 - 1.86: 114 Bond restraints: 9138 Sorted by residual: bond pdb=" C4 9UE D 405 " pdb=" C5 9UE D 405 " ideal model delta sigma weight residual 0.880 1.498 -0.618 2.00e-02 2.50e+03 9.53e+02 bond pdb=" C4 9UE C 401 " pdb=" C5 9UE C 401 " ideal model delta sigma weight residual 0.880 1.497 -0.617 2.00e-02 2.50e+03 9.52e+02 bond pdb=" C4 9UE D 401 " pdb=" C5 9UE D 401 " ideal model delta sigma weight residual 0.880 1.497 -0.617 2.00e-02 2.50e+03 9.51e+02 bond pdb=" C11 9UE C 401 " pdb=" C12 9UE C 401 " ideal model delta sigma weight residual 2.064 1.518 0.546 2.00e-02 2.50e+03 7.45e+02 bond pdb=" C11 9UE D 401 " pdb=" C12 9UE D 401 " ideal model delta sigma weight residual 2.064 1.519 0.545 2.00e-02 2.50e+03 7.42e+02 ... (remaining 9133 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.82: 373 106.82 - 114.32: 5219 114.32 - 121.82: 4968 121.82 - 129.33: 1785 129.33 - 136.83: 69 Bond angle restraints: 12414 Sorted by residual: angle pdb=" C20 9UE D 405 " pdb=" C21 9UE D 405 " pdb=" C28 9UE D 405 " ideal model delta sigma weight residual 73.46 132.34 -58.88 3.00e+00 1.11e-01 3.85e+02 angle pdb=" C20 9UE C 401 " pdb=" C21 9UE C 401 " pdb=" C28 9UE C 401 " ideal model delta sigma weight residual 73.46 132.33 -58.87 3.00e+00 1.11e-01 3.85e+02 angle pdb=" C20 9UE D 401 " pdb=" C21 9UE D 401 " pdb=" C28 9UE D 401 " ideal model delta sigma weight residual 73.46 131.68 -58.22 3.00e+00 1.11e-01 3.77e+02 angle pdb=" C20 9UE D 405 " pdb=" C21 9UE D 405 " pdb=" C22 9UE D 405 " ideal model delta sigma weight residual 176.54 122.24 54.30 3.00e+00 1.11e-01 3.28e+02 angle pdb=" C20 9UE C 401 " pdb=" C21 9UE C 401 " pdb=" C22 9UE C 401 " ideal model delta sigma weight residual 176.54 122.24 54.30 3.00e+00 1.11e-01 3.28e+02 ... (remaining 12409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.15: 5280 32.15 - 64.31: 111 64.31 - 96.46: 18 96.46 - 128.61: 21 128.61 - 160.76: 15 Dihedral angle restraints: 5445 sinusoidal: 2229 harmonic: 3216 Sorted by residual: dihedral pdb=" O1B ADP D 402 " pdb=" O3A ADP D 402 " pdb=" PB ADP D 402 " pdb=" PA ADP D 402 " ideal model delta sinusoidal sigma weight residual 300.00 168.79 131.21 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" O1B ADP C 402 " pdb=" O3A ADP C 402 " pdb=" PB ADP C 402 " pdb=" PA ADP C 402 " ideal model delta sinusoidal sigma weight residual 300.00 168.84 131.16 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 168.95 131.05 1 2.00e+01 2.50e-03 3.98e+01 ... (remaining 5442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 1332 0.141 - 0.281: 32 0.281 - 0.422: 1 0.422 - 0.563: 0 0.563 - 0.703: 6 Chirality restraints: 1371 Sorted by residual: chirality pdb=" C6 9UE D 401 " pdb=" N 9UE D 401 " pdb=" C29 9UE D 401 " pdb=" C5 9UE D 401 " both_signs ideal model delta sigma weight residual False -2.65 -1.94 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" C6 9UE C 401 " pdb=" N 9UE C 401 " pdb=" C29 9UE C 401 " pdb=" C5 9UE C 401 " both_signs ideal model delta sigma weight residual False -2.65 -1.95 -0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" C6 9UE D 405 " pdb=" N 9UE D 405 " pdb=" C29 9UE D 405 " pdb=" C5 9UE D 405 " both_signs ideal model delta sigma weight residual False -2.65 -1.96 -0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 1368 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 335 " 0.134 9.50e-02 1.11e+02 7.45e-02 2.63e+01 pdb=" NE ARG C 335 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG C 335 " 0.084 2.00e-02 2.50e+03 pdb=" NH1 ARG C 335 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG C 335 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 335 " 0.133 9.50e-02 1.11e+02 7.40e-02 2.63e+01 pdb=" NE ARG D 335 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG D 335 " 0.084 2.00e-02 2.50e+03 pdb=" NH1 ARG D 335 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG D 335 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 335 " 0.133 9.50e-02 1.11e+02 7.39e-02 2.60e+01 pdb=" NE ARG B 335 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG B 335 " 0.083 2.00e-02 2.50e+03 pdb=" NH1 ARG B 335 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG B 335 " -0.023 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 69 2.60 - 3.17: 7575 3.17 - 3.75: 13483 3.75 - 4.32: 19631 4.32 - 4.90: 32283 Nonbonded interactions: 73041 Sorted by model distance: nonbonded pdb=" O3B ADP D 402 " pdb="MG MG D 404 " model vdw 2.019 2.170 nonbonded pdb=" OH TYR C 218 " pdb=" OE2 GLU C 226 " model vdw 2.242 2.440 nonbonded pdb=" OH TYR B 169 " pdb=" OH TYR D 53 " model vdw 2.258 2.440 nonbonded pdb=" NZ LYS B 18 " pdb=" O2B ADP B 401 " model vdw 2.292 2.520 nonbonded pdb=" OG SER B 234 " pdb=" OE1 GLU B 237 " model vdw 2.321 2.440 ... (remaining 73036 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 'B' and resid 5 through 375) selection = (chain 'C' and resid 5 through 375) selection = (chain 'D' and resid 5 through 375) } 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: 1.260 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: 0.010 Extract box with map and model: 6.820 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.080 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.025 0.618 9138 Z= 1.673 Angle : 2.306 58.879 12414 Z= 0.867 Chirality : 0.071 0.703 1371 Planarity : 0.010 0.074 1578 Dihedral : 19.419 160.764 3387 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.98 (0.22), residues: 1098 helix: -1.68 (0.19), residues: 435 sheet: 0.13 (0.31), residues: 207 loop : 0.36 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 79 HIS 0.007 0.001 HIS C 101 PHE 0.021 0.002 PHE D 262 TYR 0.029 0.006 TYR C 53 ARG 0.085 0.019 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: C 47 MET cc_start: 0.6837 (tmm) cc_final: 0.6118 (tmm) REVERT: C 190 MET cc_start: 0.7621 (mtp) cc_final: 0.7396 (mtp) REVERT: C 269 MET cc_start: 0.7419 (mtt) cc_final: 0.7215 (mtm) REVERT: D 190 MET cc_start: 0.7986 (mtp) cc_final: 0.7655 (mtt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2141 time to fit residues: 45.2135 Evaluate side-chains 73 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.0570 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9138 Z= 0.231 Angle : 1.288 47.062 12414 Z= 0.491 Chirality : 0.051 0.319 1371 Planarity : 0.005 0.058 1578 Dihedral : 20.442 177.052 1299 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.21 % Allowed : 3.94 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1098 helix: 0.07 (0.24), residues: 441 sheet: 0.53 (0.33), residues: 225 loop : 1.38 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 356 HIS 0.006 0.001 HIS C 371 PHE 0.022 0.002 PHE C 352 TYR 0.013 0.001 TYR B 143 ARG 0.003 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.786 Fit side-chains REVERT: C 47 MET cc_start: 0.7256 (tmm) cc_final: 0.6842 (tmm) REVERT: C 190 MET cc_start: 0.7856 (mtp) cc_final: 0.7646 (mtp) REVERT: D 47 MET cc_start: 0.7175 (tmm) cc_final: 0.6534 (tmm) REVERT: D 82 MET cc_start: 0.8555 (tpt) cc_final: 0.8332 (mmm) REVERT: D 190 MET cc_start: 0.8129 (mtp) cc_final: 0.7781 (mtt) REVERT: D 227 MET cc_start: 0.7655 (tpt) cc_final: 0.7363 (tpt) outliers start: 2 outliers final: 0 residues processed: 78 average time/residue: 0.1623 time to fit residues: 19.8766 Evaluate side-chains 70 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 0.2980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN C 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9138 Z= 0.240 Angle : 1.251 47.488 12414 Z= 0.468 Chirality : 0.048 0.274 1371 Planarity : 0.005 0.049 1578 Dihedral : 19.402 171.961 1299 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.64 % Allowed : 5.32 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1098 helix: 0.53 (0.25), residues: 438 sheet: 0.62 (0.33), residues: 225 loop : 1.39 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 356 HIS 0.004 0.001 HIS D 173 PHE 0.011 0.001 PHE B 262 TYR 0.011 0.001 TYR B 143 ARG 0.002 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 1.056 Fit side-chains REVERT: B 206 ARG cc_start: 0.7598 (ttm-80) cc_final: 0.7331 (ttt-90) REVERT: B 313 MET cc_start: 0.8732 (mmm) cc_final: 0.8506 (mmm) REVERT: B 354 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7464 (pm20) REVERT: C 269 MET cc_start: 0.7182 (mtm) cc_final: 0.6892 (mtm) REVERT: D 47 MET cc_start: 0.7024 (tmm) cc_final: 0.6460 (tmm) REVERT: D 190 MET cc_start: 0.8095 (mtp) cc_final: 0.7740 (mtt) REVERT: D 305 MET cc_start: 0.8195 (mtp) cc_final: 0.7847 (mtm) outliers start: 6 outliers final: 2 residues processed: 80 average time/residue: 0.1975 time to fit residues: 23.1773 Evaluate side-chains 70 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 305 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 89 optimal weight: 0.4980 chunk 60 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9138 Z= 0.236 Angle : 1.235 47.573 12414 Z= 0.458 Chirality : 0.047 0.276 1371 Planarity : 0.005 0.046 1578 Dihedral : 19.304 171.082 1299 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.75 % Allowed : 6.50 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.26), residues: 1098 helix: 0.69 (0.26), residues: 438 sheet: 0.65 (0.33), residues: 225 loop : 1.38 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 340 HIS 0.003 0.001 HIS B 101 PHE 0.008 0.001 PHE B 255 TYR 0.007 0.001 TYR B 91 ARG 0.002 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.782 Fit side-chains REVERT: B 206 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7259 (ttt180) REVERT: B 313 MET cc_start: 0.8789 (mmm) cc_final: 0.8572 (mmm) REVERT: C 47 MET cc_start: 0.7351 (tmm) cc_final: 0.7124 (tmm) REVERT: D 47 MET cc_start: 0.7066 (tmm) cc_final: 0.6436 (tmm) REVERT: D 190 MET cc_start: 0.8126 (mtp) cc_final: 0.7762 (mtt) REVERT: D 305 MET cc_start: 0.8359 (mtp) cc_final: 0.7786 (mtm) outliers start: 7 outliers final: 5 residues processed: 75 average time/residue: 0.1711 time to fit residues: 19.5504 Evaluate side-chains 73 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 267 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 9138 Z= 0.554 Angle : 1.331 47.979 12414 Z= 0.521 Chirality : 0.054 0.298 1371 Planarity : 0.006 0.054 1578 Dihedral : 19.972 179.158 1299 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.38 % Allowed : 7.56 % Favored : 91.05 % 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: 0.80 (0.26), residues: 1098 helix: 0.32 (0.25), residues: 435 sheet: 0.54 (0.35), residues: 225 loop : 1.07 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP D 356 HIS 0.007 0.002 HIS B 88 PHE 0.020 0.002 PHE C 352 TYR 0.014 0.002 TYR C 306 ARG 0.005 0.001 ARG D 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 1.027 Fit side-chains REVERT: B 354 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7368 (pm20) REVERT: D 47 MET cc_start: 0.7308 (tmm) cc_final: 0.6730 (tmm) REVERT: D 157 ASP cc_start: 0.8070 (t0) cc_final: 0.7721 (t0) REVERT: D 190 MET cc_start: 0.8177 (mtp) cc_final: 0.7826 (mtt) REVERT: D 305 MET cc_start: 0.8348 (mtp) cc_final: 0.7849 (mtm) outliers start: 13 outliers final: 10 residues processed: 78 average time/residue: 0.1568 time to fit residues: 19.2929 Evaluate side-chains 75 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 286 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.0770 chunk 103 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9138 Z= 0.210 Angle : 1.228 47.688 12414 Z= 0.453 Chirality : 0.046 0.285 1371 Planarity : 0.005 0.047 1578 Dihedral : 19.261 171.788 1299 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.28 % Allowed : 8.52 % Favored : 90.20 % 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: 0.97 (0.26), residues: 1098 helix: 0.45 (0.25), residues: 444 sheet: 0.77 (0.35), residues: 219 loop : 1.09 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.003 0.001 HIS B 101 PHE 0.007 0.001 PHE D 31 TYR 0.007 0.001 TYR C 69 ARG 0.002 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.992 Fit side-chains REVERT: D 47 MET cc_start: 0.7106 (tmm) cc_final: 0.6650 (tmm) REVERT: D 190 MET cc_start: 0.8133 (mtp) cc_final: 0.7773 (mtt) REVERT: D 305 MET cc_start: 0.8358 (mtp) cc_final: 0.7777 (mtm) outliers start: 12 outliers final: 9 residues processed: 78 average time/residue: 0.1667 time to fit residues: 20.0059 Evaluate side-chains 73 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 267 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 90 optimal weight: 0.0030 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 overall best weight: 0.4768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9138 Z= 0.192 Angle : 1.219 47.519 12414 Z= 0.447 Chirality : 0.046 0.288 1371 Planarity : 0.005 0.047 1578 Dihedral : 19.106 170.992 1299 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.38 % Allowed : 8.52 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1098 helix: 0.64 (0.25), residues: 441 sheet: 0.83 (0.34), residues: 219 loop : 1.00 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.002 0.001 HIS D 101 PHE 0.007 0.001 PHE C 352 TYR 0.007 0.001 TYR C 133 ARG 0.002 0.000 ARG D 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.988 Fit side-chains REVERT: D 47 MET cc_start: 0.7027 (tmm) cc_final: 0.6505 (tmm) REVERT: D 190 MET cc_start: 0.8124 (mtp) cc_final: 0.7783 (mtt) REVERT: D 305 MET cc_start: 0.8335 (mtp) cc_final: 0.7754 (mtm) outliers start: 13 outliers final: 8 residues processed: 77 average time/residue: 0.1572 time to fit residues: 19.0845 Evaluate side-chains 73 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 267 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 0.0270 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9138 Z= 0.259 Angle : 1.235 47.586 12414 Z= 0.457 Chirality : 0.047 0.300 1371 Planarity : 0.005 0.045 1578 Dihedral : 19.235 173.935 1299 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.06 % Allowed : 8.95 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1098 helix: 0.61 (0.25), residues: 441 sheet: 0.79 (0.34), residues: 219 loop : 0.95 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.003 0.001 HIS B 88 PHE 0.009 0.001 PHE B 352 TYR 0.006 0.001 TYR B 91 ARG 0.002 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 1.079 Fit side-chains REVERT: B 313 MET cc_start: 0.8791 (mmm) cc_final: 0.8508 (mmm) REVERT: C 227 MET cc_start: 0.8121 (tpt) cc_final: 0.7871 (tpt) REVERT: D 44 MET cc_start: 0.1766 (tpp) cc_final: 0.1409 (tmm) REVERT: D 47 MET cc_start: 0.7075 (tmm) cc_final: 0.6506 (tmm) REVERT: D 157 ASP cc_start: 0.8056 (t0) cc_final: 0.7628 (t0) REVERT: D 190 MET cc_start: 0.8151 (mtp) cc_final: 0.7815 (mtt) REVERT: D 305 MET cc_start: 0.8348 (mtp) cc_final: 0.7785 (mtm) outliers start: 10 outliers final: 9 residues processed: 73 average time/residue: 0.1371 time to fit residues: 16.0145 Evaluate side-chains 74 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 267 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.4980 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 0.0770 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 0.0870 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9138 Z= 0.171 Angle : 1.212 47.546 12414 Z= 0.441 Chirality : 0.045 0.290 1371 Planarity : 0.005 0.046 1578 Dihedral : 18.949 176.956 1299 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.06 % Allowed : 9.27 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1098 helix: 0.72 (0.25), residues: 441 sheet: 0.87 (0.34), residues: 219 loop : 0.99 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 340 HIS 0.003 0.001 HIS B 371 PHE 0.008 0.001 PHE C 352 TYR 0.007 0.001 TYR C 133 ARG 0.002 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.905 Fit side-chains REVERT: B 305 MET cc_start: 0.8519 (mtp) cc_final: 0.8233 (mtm) REVERT: D 47 MET cc_start: 0.7067 (tmm) cc_final: 0.6445 (tmm) REVERT: D 190 MET cc_start: 0.8112 (mtp) cc_final: 0.7774 (mtt) REVERT: D 305 MET cc_start: 0.8340 (mtp) cc_final: 0.7767 (mtm) outliers start: 10 outliers final: 9 residues processed: 75 average time/residue: 0.1645 time to fit residues: 19.1964 Evaluate side-chains 75 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 111 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 0.0870 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9138 Z= 0.187 Angle : 1.214 47.511 12414 Z= 0.443 Chirality : 0.045 0.284 1371 Planarity : 0.005 0.046 1578 Dihedral : 18.969 179.231 1299 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.06 % Allowed : 9.69 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1098 helix: 0.77 (0.25), residues: 441 sheet: 0.65 (0.36), residues: 201 loop : 1.04 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 340 HIS 0.002 0.001 HIS B 371 PHE 0.010 0.001 PHE B 352 TYR 0.005 0.001 TYR C 133 ARG 0.001 0.000 ARG D 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 1.032 Fit side-chains REVERT: B 305 MET cc_start: 0.8506 (mtp) cc_final: 0.8215 (mtm) REVERT: C 227 MET cc_start: 0.8099 (tpt) cc_final: 0.7878 (tpt) REVERT: D 47 MET cc_start: 0.7090 (tmm) cc_final: 0.6454 (tmm) REVERT: D 190 MET cc_start: 0.8126 (mtp) cc_final: 0.7792 (mtt) REVERT: D 305 MET cc_start: 0.8332 (mtp) cc_final: 0.7777 (mtm) outliers start: 10 outliers final: 8 residues processed: 75 average time/residue: 0.1608 time to fit residues: 18.9687 Evaluate side-chains 75 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 111 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.0870 chunk 88 optimal weight: 0.0050 chunk 36 optimal weight: 0.0060 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.091732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.078853 restraints weight = 15597.284| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.05 r_work: 0.3088 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9138 Z= 0.155 Angle : 1.210 47.474 12414 Z= 0.439 Chirality : 0.044 0.281 1371 Planarity : 0.005 0.046 1578 Dihedral : 18.806 176.447 1299 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.85 % Allowed : 10.12 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1098 helix: 0.90 (0.26), residues: 435 sheet: 0.74 (0.35), residues: 222 loop : 0.96 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 340 HIS 0.002 0.001 HIS B 371 PHE 0.009 0.001 PHE B 352 TYR 0.006 0.001 TYR C 133 ARG 0.002 0.000 ARG D 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1793.53 seconds wall clock time: 33 minutes 24.53 seconds (2004.53 seconds total)