Starting phenix.real_space_refine (version: dev) on Sat Feb 18 23:09:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm3_13511/02_2023/7pm3_13511_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm3_13511/02_2023/7pm3_13511.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm3_13511/02_2023/7pm3_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_13511/02_2023/7pm3_13511_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm3_13511/02_2023/7pm3_13511_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm3_13511/02_2023/7pm3_13511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm3_13511/02_2023/7pm3_13511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm3_13511/02_2023/7pm3_13511_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm3_13511/02_2023/7pm3_13511_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 5.78, per 1000 atoms: 0.65 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: 3.64 Conformation dependent library (CDL) restraints added in 1.4 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: 0.96 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: 2.70 Time building geometry restraints manager: 3.78 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: 5268 32.15 - 64.31: 108 64.31 - 96.46: 12 96.46 - 128.61: 12 128.61 - 160.76: 9 Dihedral angle restraints: 5409 sinusoidal: 2193 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 5406 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 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. 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: 4.480 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: 8.720 Check model and map are aligned: 0.140 Process input model: 27.070 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.090 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: 44.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 : 17.190 160.764 3351 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 % 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 *********************** 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 : 1.078 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2359 time to fit residues: 49.9001 Evaluate side-chains 73 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7788 ------------------------------------------------------------------------------- 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: 1.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.0570 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 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: 0.6098 ------------------------------------------------------------------------------- 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: 0.8272 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 9138 Z= 0.242 Angle : 1.290 46.705 12414 Z= 0.493 Chirality : 0.050 0.294 1371 Planarity : 0.006 0.058 1578 Dihedral : 15.325 179.249 1263 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.21 % 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: 0.74 (0.25), residues: 1098 helix: 0.01 (0.24), residues: 441 sheet: 0.51 (0.33), residues: 225 loop : 1.36 (0.32), residues: 432 *********************** 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 : 1.018 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 78 average time/residue: 0.1664 time to fit residues: 20.4296 Evaluate side-chains 72 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2740 ------------------------------------------------------------------------------- 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: 1.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 0.0870 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- 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: 0.8366 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 9138 Z= 0.311 Angle : 1.276 47.390 12414 Z= 0.486 Chirality : 0.049 0.286 1371 Planarity : 0.005 0.054 1578 Dihedral : 14.437 179.036 1263 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer Outliers : 0.85 % 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: 1.02 (0.26), residues: 1098 helix: 0.44 (0.25), residues: 438 sheet: 0.58 (0.33), residues: 225 loop : 1.31 (0.32), residues: 435 *********************** 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 83 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 1.109 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 82 average time/residue: 0.2021 time to fit residues: 24.3214 Evaluate side-chains 69 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0847 time to fit residues: 1.7480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN D 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 9138 Z= 0.248 Angle : 1.235 47.542 12414 Z= 0.460 Chirality : 0.047 0.251 1371 Planarity : 0.005 0.049 1578 Dihedral : 14.080 175.207 1263 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1098 helix: 0.54 (0.25), residues: 441 sheet: 0.63 (0.34), residues: 225 loop : 1.29 (0.32), residues: 432 *********************** 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: 6 poor density : 71 time to evaluate : 1.119 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 76 average time/residue: 0.1871 time to fit residues: 21.9274 Evaluate side-chains 72 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0916 time to fit residues: 2.2749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.8430 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.061 9138 Z= 0.494 Angle : 1.311 47.720 12414 Z= 0.510 Chirality : 0.053 0.293 1371 Planarity : 0.006 0.055 1578 Dihedral : 14.656 178.554 1263 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.26), residues: 1098 helix: 0.34 (0.25), residues: 435 sheet: 0.52 (0.35), residues: 225 loop : 0.98 (0.32), residues: 438 *********************** 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 72 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.954 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.1694 time to fit residues: 18.7976 Evaluate side-chains 64 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0942 time to fit residues: 2.1249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0050 chunk 107 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 12 optimal weight: 0.0020 chunk 61 optimal weight: 0.7980 overall best weight: 0.3802 ------------------------------------------------------------------------------- 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: 0.8350 moved from start: 0.4100 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= 0.172 Angle : 1.223 47.574 12414 Z= 0.450 Chirality : 0.045 0.237 1371 Planarity : 0.005 0.047 1578 Dihedral : 13.917 174.831 1263 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 0.53 % 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: 0.94 (0.26), residues: 1098 helix: 0.47 (0.25), residues: 444 sheet: 0.83 (0.35), residues: 219 loop : 0.97 (0.32), residues: 435 *********************** 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 76 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 1.083 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 75 average time/residue: 0.1780 time to fit residues: 20.4909 Evaluate side-chains 66 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0848 time to fit residues: 1.6910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 0.0040 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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: 0.8350 moved from start: 0.4198 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= 0.187 Angle : 1.220 47.443 12414 Z= 0.448 Chirality : 0.045 0.249 1371 Planarity : 0.005 0.046 1578 Dihedral : 13.778 174.722 1263 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 0.53 % 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: 1.06 (0.26), residues: 1098 helix: 0.66 (0.25), residues: 441 sheet: 0.87 (0.34), residues: 219 loop : 0.92 (0.32), residues: 438 *********************** 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 70 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 1.043 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 65 average time/residue: 0.1687 time to fit residues: 17.4288 Evaluate side-chains 64 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1066 time to fit residues: 1.7417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8377 moved from start: 0.4257 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= 0.260 Angle : 1.236 47.530 12414 Z= 0.458 Chirality : 0.046 0.261 1371 Planarity : 0.005 0.045 1578 Dihedral : 13.888 175.153 1263 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 0.53 % 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: 0.93 (0.26), residues: 1098 helix: 0.60 (0.25), residues: 441 sheet: 0.59 (0.36), residues: 201 loop : 0.92 (0.31), residues: 456 *********************** 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 68 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 1.092 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 66 average time/residue: 0.1739 time to fit residues: 18.0764 Evaluate side-chains 65 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0701 time to fit residues: 1.4972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.0370 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 0.1980 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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: 0.8348 moved from start: 0.4326 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= 0.181 Angle : 1.215 47.483 12414 Z= 0.444 Chirality : 0.045 0.251 1371 Planarity : 0.005 0.046 1578 Dihedral : 13.611 173.429 1263 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 0.00 % 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: 1.01 (0.26), residues: 1098 helix: 0.67 (0.26), residues: 441 sheet: 0.62 (0.36), residues: 201 loop : 0.95 (0.31), residues: 456 *********************** 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 63 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1774 time to fit residues: 17.4690 Evaluate side-chains 62 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 chunk 69 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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: 0.8343 moved from start: 0.4386 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= 0.181 Angle : 1.213 47.439 12414 Z= 0.443 Chirality : 0.045 0.254 1371 Planarity : 0.005 0.045 1578 Dihedral : 13.444 172.745 1263 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1098 helix: 0.74 (0.26), residues: 441 sheet: 0.69 (0.36), residues: 201 loop : 1.00 (0.31), residues: 456 ********************** 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 65 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 1.090 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.1762 time to fit residues: 17.7637 Evaluate side-chains 62 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.0670 chunk 36 optimal weight: 0.6980 chunk 90 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.091220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.078331 restraints weight = 15845.675| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.06 r_work: 0.3075 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4442 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= 0.168 Angle : 1.209 47.411 12414 Z= 0.440 Chirality : 0.044 0.254 1371 Planarity : 0.005 0.046 1578 Dihedral : 13.285 171.781 1263 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 0.11 % 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: 1.15 (0.26), residues: 1098 helix: 0.77 (0.26), residues: 441 sheet: 0.71 (0.36), residues: 201 loop : 1.05 (0.31), residues: 456 =============================================================================== Job complete usr+sys time: 1839.05 seconds wall clock time: 34 minutes 53.68 seconds (2093.68 seconds total)