Starting phenix.real_space_refine on Fri Dec 8 15:36:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6av9_7007/12_2023/6av9_7007_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6av9_7007/12_2023/6av9_7007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6av9_7007/12_2023/6av9_7007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6av9_7007/12_2023/6av9_7007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6av9_7007/12_2023/6av9_7007_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6av9_7007/12_2023/6av9_7007_updated.pdb" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 0.007 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 60 5.16 5 C 5469 2.51 5 N 1458 2.21 5 O 1680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 117": "OE1" <-> "OE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8673 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2864 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'SME:plan-1': 2, 'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2864 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'SME:plan-1': 2, 'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2864 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'SME:plan-1': 2, 'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.92, per 1000 atoms: 0.57 Number of scatterers: 8673 At special positions: 0 Unit cell: (79.116, 93.69, 135.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 6 15.00 O 1680 8.00 N 1458 7.00 C 5469 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: 3.72 Conformation dependent library (CDL) restraints added in 1.7 seconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2034 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 9 sheets defined 34.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.980A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 122 removed outlier: 5.480A pdb=" N THR C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 145 removed outlier: 3.951A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.771A pdb=" N THR C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 215 removed outlier: 3.971A pdb=" N GLU C 214 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 231 removed outlier: 3.646A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 261 Proline residue: C 258 - end of helix removed outlier: 4.677A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 254 through 261' Processing helix chain 'C' and resid 274 through 282 removed outlier: 3.700A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.554A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP C 292 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 319 Processing helix chain 'C' and resid 338 through 346 removed outlier: 3.917A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 Processing helix chain 'C' and resid 367 through 370 removed outlier: 3.736A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 370' Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.980A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 removed outlier: 5.480A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 145 removed outlier: 3.950A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.771A pdb=" N THR A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.972A pdb=" N GLU A 214 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 231 removed outlier: 3.647A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 Proline residue: A 258 - end of helix removed outlier: 4.677A pdb=" N LEU A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 261' Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.700A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.554A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP A 292 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR A 294 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 338 through 346 removed outlier: 3.916A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 367 through 370 removed outlier: 3.736A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 370' Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 79 through 90 removed outlier: 3.979A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 removed outlier: 5.479A pdb=" N THR B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 145 removed outlier: 3.951A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.771A pdb=" N THR B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.972A pdb=" N GLU B 214 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 231 removed outlier: 3.646A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 Proline residue: B 258 - end of helix removed outlier: 4.677A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 254 through 261' Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.700A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.553A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP B 292 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B 294 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 319 Processing helix chain 'B' and resid 338 through 346 removed outlier: 3.917A pdb=" N GLY B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 367 through 370 removed outlier: 3.735A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 370' Processing sheet with id= A, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.737A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'C' and resid 160 through 162 removed outlier: 3.591A pdb=" N THR C 160 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.738A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= F, first strand: chain 'A' and resid 160 through 162 removed outlier: 3.591A pdb=" N THR A 160 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.737A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= I, first strand: chain 'B' and resid 160 through 162 removed outlier: 3.591A pdb=" N THR B 160 " --> pdb=" O LEU B 178 " (cutoff:3.500A) 189 hydrogen bonds defined for protein. 450 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: 2.29 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1449 1.30 - 1.43: 2214 1.43 - 1.55: 5085 1.55 - 1.68: 9 1.68 - 1.81: 108 Bond restraints: 8865 Sorted by residual: bond pdb=" CG HIC A 73 " pdb=" CD2 HIC A 73 " ideal model delta sigma weight residual 1.369 1.305 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" CG HIC C 73 " pdb=" CD2 HIC C 73 " ideal model delta sigma weight residual 1.369 1.307 0.062 2.00e-02 2.50e+03 9.72e+00 bond pdb=" CG HIC B 73 " pdb=" CD2 HIC B 73 " ideal model delta sigma weight residual 1.369 1.307 0.062 2.00e-02 2.50e+03 9.61e+00 bond pdb=" C HIC B 73 " pdb=" O HIC B 73 " ideal model delta sigma weight residual 1.231 1.169 0.062 2.00e-02 2.50e+03 9.57e+00 bond pdb=" C HIC C 73 " pdb=" O HIC C 73 " ideal model delta sigma weight residual 1.231 1.170 0.061 2.00e-02 2.50e+03 9.40e+00 ... (remaining 8860 not shown) Histogram of bond angle deviations from ideal: 98.81 - 106.13: 328 106.13 - 113.44: 4945 113.44 - 120.76: 3907 120.76 - 128.08: 2767 128.08 - 135.40: 95 Bond angle restraints: 12042 Sorted by residual: angle pdb=" N LYS B 118 " pdb=" CA LYS B 118 " pdb=" C LYS B 118 " ideal model delta sigma weight residual 111.82 104.11 7.71 1.16e+00 7.43e-01 4.41e+01 angle pdb=" N LYS C 118 " pdb=" CA LYS C 118 " pdb=" C LYS C 118 " ideal model delta sigma weight residual 111.82 104.15 7.67 1.16e+00 7.43e-01 4.37e+01 angle pdb=" N LYS A 118 " pdb=" CA LYS A 118 " pdb=" C LYS A 118 " ideal model delta sigma weight residual 111.82 104.16 7.66 1.16e+00 7.43e-01 4.36e+01 angle pdb=" C ALA C 131 " pdb=" CA ALA C 131 " pdb=" CB ALA C 131 " ideal model delta sigma weight residual 115.89 108.76 7.13 1.32e+00 5.74e-01 2.92e+01 angle pdb=" C ALA B 131 " pdb=" CA ALA B 131 " pdb=" CB ALA B 131 " ideal model delta sigma weight residual 115.89 108.77 7.12 1.32e+00 5.74e-01 2.91e+01 ... (remaining 12037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 5097 21.63 - 43.26: 165 43.26 - 64.89: 39 64.89 - 86.53: 9 86.53 - 108.16: 6 Dihedral angle restraints: 5316 sinusoidal: 2136 harmonic: 3180 Sorted by residual: dihedral pdb=" O2A ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PA ADP B 801 " pdb=" PB ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 48.16 -108.16 1 2.00e+01 2.50e-03 3.15e+01 dihedral pdb=" O2A ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PA ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 48.15 -108.15 1 2.00e+01 2.50e-03 3.15e+01 dihedral pdb=" O2A ADP C 801 " pdb=" O3A ADP C 801 " pdb=" PA ADP C 801 " pdb=" PB ADP C 801 " ideal model delta sinusoidal sigma weight residual -60.00 48.14 -108.14 1 2.00e+01 2.50e-03 3.15e+01 ... (remaining 5313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 696 0.041 - 0.082: 421 0.082 - 0.124: 158 0.124 - 0.165: 43 0.165 - 0.206: 23 Chirality restraints: 1341 Sorted by residual: chirality pdb=" CA PHE C 223 " pdb=" N PHE C 223 " pdb=" C PHE C 223 " pdb=" CB PHE C 223 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PHE A 223 " pdb=" N PHE A 223 " pdb=" C PHE A 223 " pdb=" CB PHE A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PHE B 223 " pdb=" N PHE B 223 " pdb=" C PHE B 223 " pdb=" CB PHE B 223 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1338 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 101 " 0.051 5.00e-02 4.00e+02 7.79e-02 9.70e+00 pdb=" N PRO B 102 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 101 " -0.051 5.00e-02 4.00e+02 7.78e-02 9.68e+00 pdb=" N PRO C 102 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 101 " 0.051 5.00e-02 4.00e+02 7.76e-02 9.64e+00 pdb=" N PRO A 102 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.042 5.00e-02 4.00e+02 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 129 2.52 - 3.11: 8123 3.11 - 3.71: 13903 3.71 - 4.30: 20116 4.30 - 4.90: 31070 Nonbonded interactions: 73341 Sorted by model distance: nonbonded pdb=" NZ LYS A 113 " pdb=" NH2 ARG A 116 " model vdw 1.920 3.200 nonbonded pdb=" NZ LYS C 113 " pdb=" NH2 ARG C 116 " model vdw 1.920 3.200 nonbonded pdb=" NZ LYS B 113 " pdb=" NH2 ARG B 116 " model vdw 1.920 3.200 nonbonded pdb=" OG1 THR A 358 " pdb=" OE1 GLU A 361 " model vdw 2.071 2.440 nonbonded pdb=" OG1 THR C 358 " pdb=" OE1 GLU C 361 " model vdw 2.072 2.440 ... (remaining 73336 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=0.00 max=1.00 mean=0.94 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.150 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: 0.000 Extract box with map and model: 1.300 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 26.660 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.008 0.076 8865 Z= 0.531 Angle : 1.112 8.475 12042 Z= 0.591 Chirality : 0.062 0.206 1341 Planarity : 0.007 0.078 1536 Dihedral : 12.768 108.157 3282 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 32.37 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.83 % Favored : 86.80 % Rotamer: Outliers : 0.33 % Allowed : 2.93 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.62 (0.20), residues: 1068 helix: -4.23 (0.16), residues: 300 sheet: -2.44 (0.38), residues: 141 loop : -2.68 (0.21), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 86 HIS 0.007 0.003 HIS A 101 PHE 0.022 0.002 PHE B 262 TYR 0.024 0.004 TYR B 337 ARG 0.006 0.001 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 247 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 250 average time/residue: 0.1926 time to fit residues: 67.1137 Evaluate side-chains 144 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1105 time to fit residues: 1.8710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 27 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 87 HIS ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 ASN A 87 HIS ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN B 49 GLN B 87 HIS ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8865 Z= 0.197 Angle : 0.828 7.351 12042 Z= 0.404 Chirality : 0.050 0.172 1341 Planarity : 0.005 0.054 1536 Dihedral : 10.985 122.114 1245 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 3.15 % Allowed : 10.97 % Favored : 85.88 % 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: -3.64 (0.22), residues: 1068 helix: -2.65 (0.22), residues: 342 sheet: -2.32 (0.32), residues: 201 loop : -2.20 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 356 HIS 0.009 0.002 HIS B 101 PHE 0.024 0.002 PHE C 352 TYR 0.015 0.001 TYR B 218 ARG 0.003 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 200 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 219 average time/residue: 0.1667 time to fit residues: 53.7575 Evaluate side-chains 173 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1971 time to fit residues: 4.6374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 314 GLN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8865 Z= 0.258 Angle : 0.811 11.670 12042 Z= 0.385 Chirality : 0.049 0.187 1341 Planarity : 0.005 0.046 1536 Dihedral : 10.595 125.942 1245 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.14 % Favored : 88.86 % Rotamer: Outliers : 3.69 % Allowed : 15.20 % Favored : 81.11 % 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: -3.26 (0.23), residues: 1068 helix: -2.27 (0.23), residues: 351 sheet: -2.11 (0.31), residues: 201 loop : -2.00 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 356 HIS 0.015 0.002 HIS B 101 PHE 0.014 0.002 PHE A 223 TYR 0.018 0.002 TYR B 218 ARG 0.004 0.001 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 156 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 13 residues processed: 181 average time/residue: 0.1625 time to fit residues: 44.0999 Evaluate side-chains 145 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1171 time to fit residues: 3.7459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.0970 chunk 73 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 98 optimal weight: 0.0370 chunk 104 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 128 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8865 Z= 0.182 Angle : 0.774 10.695 12042 Z= 0.359 Chirality : 0.047 0.191 1341 Planarity : 0.004 0.042 1536 Dihedral : 10.144 129.181 1245 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.67 % Favored : 89.14 % Rotamer: Outliers : 1.85 % Allowed : 21.28 % Favored : 76.87 % 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: -2.87 (0.23), residues: 1068 helix: -1.66 (0.25), residues: 348 sheet: -1.92 (0.33), residues: 207 loop : -1.98 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 356 HIS 0.018 0.002 HIS B 101 PHE 0.008 0.001 PHE A 223 TYR 0.017 0.001 TYR C 218 ARG 0.002 0.000 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 168 average time/residue: 0.1825 time to fit residues: 45.2846 Evaluate side-chains 147 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0865 time to fit residues: 2.3864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 77 optimal weight: 0.0030 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 93 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 overall best weight: 6.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 GLN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8865 Z= 0.349 Angle : 0.852 9.609 12042 Z= 0.405 Chirality : 0.050 0.200 1341 Planarity : 0.005 0.044 1536 Dihedral : 10.417 128.791 1245 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.08 % Favored : 87.45 % Rotamer: Outliers : 4.89 % Allowed : 20.30 % Favored : 74.81 % 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: -2.93 (0.24), residues: 1068 helix: -1.59 (0.26), residues: 357 sheet: -1.92 (0.33), residues: 207 loop : -2.14 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 356 HIS 0.023 0.003 HIS C 101 PHE 0.015 0.002 PHE A 223 TYR 0.021 0.002 TYR B 218 ARG 0.003 0.001 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 140 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 19 residues processed: 170 average time/residue: 0.1658 time to fit residues: 42.1189 Evaluate side-chains 148 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1045 time to fit residues: 4.7602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 0.0040 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 0.031 8865 Z= 0.184 Angle : 0.781 10.574 12042 Z= 0.360 Chirality : 0.046 0.200 1341 Planarity : 0.004 0.043 1536 Dihedral : 9.863 129.334 1245 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.05 % Favored : 88.76 % Rotamer: Outliers : 2.06 % Allowed : 21.28 % Favored : 76.66 % 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: -2.45 (0.25), residues: 1068 helix: -1.14 (0.27), residues: 357 sheet: -1.24 (0.40), residues: 156 loop : -2.08 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 356 HIS 0.014 0.002 HIS C 101 PHE 0.012 0.001 PHE B 223 TYR 0.020 0.001 TYR B 362 ARG 0.002 0.000 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 1.069 Fit side-chains outliers start: 19 outliers final: 6 residues processed: 166 average time/residue: 0.1736 time to fit residues: 42.9178 Evaluate side-chains 143 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0874 time to fit residues: 2.3551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 76 optimal weight: 30.0000 chunk 87 optimal weight: 0.1980 chunk 58 optimal weight: 9.9990 chunk 104 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8865 Z= 0.235 Angle : 0.795 9.771 12042 Z= 0.371 Chirality : 0.047 0.192 1341 Planarity : 0.004 0.041 1536 Dihedral : 9.838 131.250 1245 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.80 % Favored : 87.92 % Rotamer: Outliers : 1.52 % Allowed : 23.13 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.25), residues: 1068 helix: -1.01 (0.28), residues: 357 sheet: -1.36 (0.37), residues: 186 loop : -2.04 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 356 HIS 0.028 0.003 HIS B 101 PHE 0.033 0.002 PHE B 352 TYR 0.025 0.002 TYR B 362 ARG 0.002 0.000 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 1.095 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 146 average time/residue: 0.1610 time to fit residues: 35.5254 Evaluate side-chains 141 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0901 time to fit residues: 2.8460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8865 Z= 0.291 Angle : 0.824 10.415 12042 Z= 0.386 Chirality : 0.049 0.197 1341 Planarity : 0.005 0.042 1536 Dihedral : 9.963 130.610 1245 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.61 % Favored : 88.11 % Rotamer: Outliers : 2.28 % Allowed : 21.93 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.53 (0.24), residues: 1068 helix: -1.23 (0.26), residues: 363 sheet: -1.34 (0.37), residues: 186 loop : -2.09 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 356 HIS 0.022 0.002 HIS B 101 PHE 0.033 0.002 PHE B 352 TYR 0.021 0.002 TYR A 218 ARG 0.003 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 0.933 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 146 average time/residue: 0.1638 time to fit residues: 36.1940 Evaluate side-chains 145 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0879 time to fit residues: 3.5460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8865 Z= 0.200 Angle : 0.793 8.794 12042 Z= 0.366 Chirality : 0.046 0.192 1341 Planarity : 0.004 0.043 1536 Dihedral : 9.720 129.889 1245 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.33 % Favored : 88.39 % Rotamer: Outliers : 0.87 % Allowed : 22.91 % Favored : 76.22 % 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: -2.26 (0.25), residues: 1068 helix: -0.98 (0.28), residues: 357 sheet: -1.28 (0.38), residues: 186 loop : -1.91 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 356 HIS 0.021 0.002 HIS B 101 PHE 0.035 0.002 PHE B 352 TYR 0.018 0.001 TYR C 218 ARG 0.002 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 1.019 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 148 average time/residue: 0.1776 time to fit residues: 38.7890 Evaluate side-chains 140 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2046 time to fit residues: 2.4832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 48 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 8865 Z= 0.326 Angle : 0.860 10.008 12042 Z= 0.406 Chirality : 0.050 0.197 1341 Planarity : 0.005 0.041 1536 Dihedral : 10.072 130.678 1245 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.80 % Favored : 87.92 % Rotamer: Outliers : 0.98 % Allowed : 23.56 % Favored : 75.46 % 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: -2.47 (0.24), residues: 1068 helix: -1.34 (0.26), residues: 375 sheet: -1.35 (0.38), residues: 186 loop : -1.91 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 86 HIS 0.020 0.002 HIS B 101 PHE 0.036 0.003 PHE B 352 TYR 0.023 0.002 TYR C 218 ARG 0.004 0.001 ARG C 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 1.138 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 142 average time/residue: 0.1697 time to fit residues: 36.2252 Evaluate side-chains 141 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0894 time to fit residues: 2.5782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.090310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.080401 restraints weight = 24369.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.082372 restraints weight = 12471.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.083692 restraints weight = 7618.684| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8865 Z= 0.297 Angle : 0.848 10.096 12042 Z= 0.398 Chirality : 0.049 0.232 1341 Planarity : 0.005 0.043 1536 Dihedral : 10.041 128.815 1245 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.17 % Favored : 87.55 % Rotamer: Outliers : 0.76 % Allowed : 23.34 % Favored : 75.90 % 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: -2.41 (0.25), residues: 1068 helix: -1.25 (0.26), residues: 360 sheet: -1.29 (0.37), residues: 192 loop : -1.92 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 356 HIS 0.018 0.002 HIS B 101 PHE 0.035 0.002 PHE B 352 TYR 0.021 0.002 TYR C 218 ARG 0.003 0.000 ARG A 290 =============================================================================== Job complete usr+sys time: 1713.36 seconds wall clock time: 32 minutes 10.04 seconds (1930.04 seconds total)