Starting phenix.real_space_refine on Mon Mar 11 16:42:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6av9_7007/03_2024/6av9_7007_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6av9_7007/03_2024/6av9_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_7007/03_2024/6av9_7007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6av9_7007/03_2024/6av9_7007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6av9_7007/03_2024/6av9_7007_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6av9_7007/03_2024/6av9_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.04, per 1000 atoms: 0.58 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: 3.66 Conformation dependent library (CDL) restraints added in 2.2 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: 1.90 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: 2.25 Time building geometry restraints manager: 3.89 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: 0.010 Normalize map: mean=0, sd=1: 0.280 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: 1.440 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.780 Find NCS groups from input model: 0.510 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.230 ------------------------------------------------------------------------------- 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 : 0.911 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 REVERT: C 133 TYR cc_start: 0.8034 (t80) cc_final: 0.7321 (t80) REVERT: C 325 MET cc_start: 0.9393 (ttp) cc_final: 0.9106 (mtt) REVERT: A 315 LYS cc_start: 0.8188 (tttm) cc_final: 0.7616 (ttmm) REVERT: B 325 MET cc_start: 0.9368 (ttp) cc_final: 0.9120 (mtt) outliers start: 3 outliers final: 3 residues processed: 250 average time/residue: 0.1826 time to fit residues: 63.6603 Evaluate side-chains 145 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 224 GLU 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: 0.6980 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8865 Z= 0.194 Angle : 0.825 7.620 12042 Z= 0.402 Chirality : 0.050 0.172 1341 Planarity : 0.005 0.054 1536 Dihedral : 12.059 122.271 1254 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 2.93 % Allowed : 11.40 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.22), residues: 1068 helix: -2.62 (0.22), residues: 342 sheet: -2.33 (0.32), residues: 201 loop : -2.21 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 356 HIS 0.005 0.001 HIS B 101 PHE 0.024 0.002 PHE C 352 TYR 0.016 0.001 TYR B 218 ARG 0.003 0.000 ARG A 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 235 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 208 time to evaluate : 1.019 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: C 355 MET cc_start: 0.8432 (tpt) cc_final: 0.8169 (tmm) REVERT: A 133 TYR cc_start: 0.7715 (t80) cc_final: 0.7158 (t80) REVERT: B 79 TRP cc_start: 0.8583 (m100) cc_final: 0.8205 (m100) REVERT: B 133 TYR cc_start: 0.7700 (t80) cc_final: 0.7364 (t80) REVERT: B 355 MET cc_start: 0.8700 (tpp) cc_final: 0.8406 (tpp) outliers start: 27 outliers final: 10 residues processed: 223 average time/residue: 0.1670 time to fit residues: 54.3924 Evaluate side-chains 165 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 155 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 216 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 0.0770 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.0040 chunk 106 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 overall best weight: 1.7954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN B 371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8865 Z= 0.187 Angle : 0.782 12.509 12042 Z= 0.367 Chirality : 0.047 0.186 1341 Planarity : 0.004 0.044 1536 Dihedral : 10.334 127.848 1245 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 4.67 % Allowed : 14.01 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.23), residues: 1068 helix: -2.01 (0.24), residues: 351 sheet: -2.09 (0.31), residues: 201 loop : -1.88 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 356 HIS 0.013 0.002 HIS A 101 PHE 0.013 0.001 PHE C 352 TYR 0.016 0.001 TYR C 218 ARG 0.003 0.000 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 208 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 165 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 TYR cc_start: 0.7589 (t80) cc_final: 0.7290 (t80) REVERT: C 325 MET cc_start: 0.9220 (ttp) cc_final: 0.8809 (mtt) REVERT: C 355 MET cc_start: 0.8508 (tpt) cc_final: 0.8259 (tpp) REVERT: B 221 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8448 (tt) REVERT: B 313 MET cc_start: 0.8743 (mtm) cc_final: 0.8297 (ttp) REVERT: B 325 MET cc_start: 0.9247 (ttp) cc_final: 0.8827 (mtm) outliers start: 43 outliers final: 22 residues processed: 191 average time/residue: 0.1749 time to fit residues: 48.1915 Evaluate side-chains 168 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 145 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 280 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8865 Z= 0.211 Angle : 0.766 10.921 12042 Z= 0.358 Chirality : 0.047 0.191 1341 Planarity : 0.004 0.040 1536 Dihedral : 10.200 130.711 1245 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 4.89 % Allowed : 19.65 % 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: -2.68 (0.24), residues: 1068 helix: -1.63 (0.26), residues: 333 sheet: -1.89 (0.32), residues: 207 loop : -1.74 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 356 HIS 0.015 0.002 HIS B 101 PHE 0.011 0.002 PHE C 223 TYR 0.017 0.001 TYR B 218 ARG 0.003 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 200 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 155 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: C 324 THR cc_start: 0.8683 (p) cc_final: 0.8429 (t) REVERT: A 119 MET cc_start: 0.8910 (tmm) cc_final: 0.8643 (tmm) REVERT: A 313 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8422 (ttp) REVERT: A 354 GLN cc_start: 0.8403 (pp30) cc_final: 0.8171 (pp30) REVERT: B 221 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8502 (tt) REVERT: B 313 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8357 (ttp) REVERT: B 325 MET cc_start: 0.9146 (ttp) cc_final: 0.8794 (mtt) REVERT: B 362 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7322 (m-80) outliers start: 45 outliers final: 26 residues processed: 184 average time/residue: 0.1696 time to fit residues: 45.7046 Evaluate side-chains 176 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 362 TYR 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: 10.0000 chunk 1 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 overall best weight: 7.1390 ------------------------------------------------------------------------------- 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 ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 ASN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS B 12 ASN ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 8865 Z= 0.377 Angle : 0.838 9.651 12042 Z= 0.401 Chirality : 0.051 0.202 1341 Planarity : 0.005 0.043 1536 Dihedral : 10.431 127.453 1245 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.99 % Favored : 87.55 % Rotamer: Outliers : 6.30 % Allowed : 18.68 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.24), residues: 1068 helix: -1.66 (0.26), residues: 357 sheet: -1.48 (0.35), residues: 186 loop : -2.07 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 356 HIS 0.022 0.003 HIS C 101 PHE 0.015 0.002 PHE A 223 TYR 0.021 0.002 TYR A 218 ARG 0.004 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 192 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 134 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 236 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8619 (pp) REVERT: C 325 MET cc_start: 0.9229 (ttp) cc_final: 0.8881 (mtt) REVERT: C 354 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.8006 (pp30) REVERT: C 362 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: A 313 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8434 (ttp) REVERT: A 327 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8196 (pt) REVERT: B 221 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8490 (tt) REVERT: B 236 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8644 (pp) REVERT: B 313 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8593 (ttp) REVERT: B 325 MET cc_start: 0.9157 (ttp) cc_final: 0.8890 (mtt) REVERT: B 362 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7617 (m-80) outliers start: 58 outliers final: 28 residues processed: 174 average time/residue: 0.1992 time to fit residues: 49.7308 Evaluate side-chains 165 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 128 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 362 TYR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 362 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 30.0000 chunk 94 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** 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: 0.7937 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8865 Z= 0.291 Angle : 0.802 9.951 12042 Z= 0.376 Chirality : 0.048 0.198 1341 Planarity : 0.005 0.047 1536 Dihedral : 10.183 128.528 1245 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.52 % Favored : 88.20 % Rotamer: Outliers : 6.73 % Allowed : 18.89 % Favored : 74.38 % 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: -2.69 (0.24), residues: 1068 helix: -1.43 (0.26), residues: 357 sheet: -1.36 (0.36), residues: 186 loop : -2.17 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 356 HIS 0.013 0.002 HIS C 101 PHE 0.014 0.002 PHE C 352 TYR 0.020 0.002 TYR A 218 ARG 0.003 0.000 ARG A 290 *********************** 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 208 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 146 time to evaluate : 0.964 Fit side-chains REVERT: C 119 MET cc_start: 0.9035 (tmm) cc_final: 0.8812 (tmm) REVERT: C 324 THR cc_start: 0.8762 (p) cc_final: 0.8511 (t) REVERT: C 325 MET cc_start: 0.9179 (ttp) cc_final: 0.8869 (mtt) REVERT: C 362 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: A 313 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8461 (ttp) REVERT: A 327 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7988 (pt) REVERT: B 221 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8491 (tt) REVERT: B 236 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8622 (pp) REVERT: B 299 MET cc_start: 0.8156 (ttt) cc_final: 0.7899 (ttt) REVERT: B 313 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8401 (ttp) REVERT: B 362 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.7623 (m-80) outliers start: 62 outliers final: 38 residues processed: 187 average time/residue: 0.1728 time to fit residues: 46.7482 Evaluate side-chains 177 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 132 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 362 TYR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 362 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.0070 chunk 11 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 overall best weight: 1.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7871 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8865 Z= 0.188 Angle : 0.770 10.393 12042 Z= 0.356 Chirality : 0.046 0.190 1341 Planarity : 0.004 0.044 1536 Dihedral : 9.744 130.069 1245 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.61 % Favored : 88.20 % Rotamer: Outliers : 4.02 % Allowed : 21.82 % Favored : 74.16 % 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: -1.08 (0.27), residues: 357 sheet: -1.35 (0.37), residues: 186 loop : -2.03 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 356 HIS 0.026 0.002 HIS B 101 PHE 0.014 0.001 PHE B 352 TYR 0.017 0.001 TYR B 218 ARG 0.002 0.000 ARG A 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 187 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 1.024 Fit side-chains REVERT: C 76 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8403 (pt) REVERT: C 324 THR cc_start: 0.8724 (p) cc_final: 0.8451 (t) REVERT: C 325 MET cc_start: 0.9139 (ttp) cc_final: 0.8800 (mtt) REVERT: A 313 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8539 (ttp) REVERT: A 327 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7995 (pt) REVERT: B 119 MET cc_start: 0.8853 (tmm) cc_final: 0.8604 (tmm) REVERT: B 236 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8630 (pp) REVERT: B 313 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8394 (ttp) REVERT: B 362 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.7478 (m-80) outliers start: 37 outliers final: 25 residues processed: 173 average time/residue: 0.1851 time to fit residues: 47.2520 Evaluate side-chains 166 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 362 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 0.0980 chunk 81 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7908 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8865 Z= 0.254 Angle : 0.807 11.960 12042 Z= 0.377 Chirality : 0.048 0.195 1341 Planarity : 0.005 0.044 1536 Dihedral : 9.875 130.994 1245 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.14 % Favored : 88.58 % Rotamer: Outliers : 5.21 % Allowed : 21.82 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.25), residues: 1068 helix: -1.17 (0.27), residues: 366 sheet: -1.23 (0.37), residues: 183 loop : -1.97 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 356 HIS 0.021 0.002 HIS B 101 PHE 0.033 0.002 PHE B 352 TYR 0.020 0.002 TYR C 218 ARG 0.002 0.000 ARG C 290 *********************** 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 189 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 141 time to evaluate : 0.987 Fit side-chains REVERT: C 324 THR cc_start: 0.8752 (p) cc_final: 0.8485 (t) REVERT: C 325 MET cc_start: 0.9010 (ttp) cc_final: 0.8791 (mtt) REVERT: C 354 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8024 (pp30) REVERT: C 362 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: A 313 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8452 (ttp) REVERT: A 327 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7850 (pt) REVERT: B 119 MET cc_start: 0.8830 (tmm) cc_final: 0.8588 (tmm) REVERT: B 236 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8639 (pp) REVERT: B 299 MET cc_start: 0.8064 (ttt) cc_final: 0.7860 (ttt) REVERT: B 313 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8606 (ttp) REVERT: B 362 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7618 (m-80) outliers start: 48 outliers final: 32 residues processed: 172 average time/residue: 0.1646 time to fit residues: 41.5026 Evaluate side-chains 171 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 362 TYR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 362 TYR 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: 0.9990 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8865 Z= 0.208 Angle : 0.793 12.572 12042 Z= 0.366 Chirality : 0.047 0.192 1341 Planarity : 0.004 0.042 1536 Dihedral : 9.685 130.637 1245 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.61 % Favored : 88.11 % Rotamer: Outliers : 4.67 % Allowed : 21.82 % Favored : 73.51 % 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: -2.23 (0.25), residues: 1068 helix: -1.03 (0.27), residues: 354 sheet: -1.24 (0.38), residues: 186 loop : -1.84 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 356 HIS 0.019 0.002 HIS B 101 PHE 0.036 0.002 PHE B 352 TYR 0.018 0.001 TYR B 218 ARG 0.002 0.000 ARG B 183 *********************** 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 184 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 141 time to evaluate : 1.078 Fit side-chains REVERT: C 324 THR cc_start: 0.8714 (p) cc_final: 0.8448 (t) REVERT: C 325 MET cc_start: 0.9016 (ttp) cc_final: 0.8775 (mtt) REVERT: A 313 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8418 (ttp) REVERT: A 325 MET cc_start: 0.8983 (ptm) cc_final: 0.8680 (ttp) REVERT: B 82 MET cc_start: 0.8113 (tpt) cc_final: 0.7766 (tmm) REVERT: B 119 MET cc_start: 0.8762 (tmm) cc_final: 0.8552 (tmm) REVERT: B 236 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8652 (pp) REVERT: B 299 MET cc_start: 0.7961 (ttt) cc_final: 0.7750 (ttt) REVERT: B 313 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8456 (ttp) REVERT: B 362 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7495 (m-80) outliers start: 43 outliers final: 37 residues processed: 165 average time/residue: 0.1668 time to fit residues: 40.5827 Evaluate side-chains 175 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 134 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 362 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7908 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8865 Z= 0.261 Angle : 0.803 9.558 12042 Z= 0.375 Chirality : 0.048 0.193 1341 Planarity : 0.005 0.043 1536 Dihedral : 9.834 131.168 1245 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.96 % Favored : 88.76 % Rotamer: Outliers : 5.43 % Allowed : 21.28 % Favored : 73.29 % 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: -2.25 (0.25), residues: 1068 helix: -1.12 (0.27), residues: 354 sheet: -1.24 (0.38), residues: 186 loop : -1.81 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 356 HIS 0.018 0.002 HIS B 101 PHE 0.036 0.002 PHE B 352 TYR 0.021 0.002 TYR A 218 ARG 0.003 0.000 ARG A 290 ********************** 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 188 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 138 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: C 105 LEU cc_start: 0.8569 (tt) cc_final: 0.8345 (mp) REVERT: C 324 THR cc_start: 0.8732 (p) cc_final: 0.8469 (t) REVERT: C 354 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8106 (pp30) REVERT: A 82 MET cc_start: 0.8044 (tpt) cc_final: 0.7227 (tmm) REVERT: A 313 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8509 (ttp) REVERT: B 236 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8648 (pp) REVERT: B 299 MET cc_start: 0.8055 (ttt) cc_final: 0.7840 (ttt) REVERT: B 313 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8495 (ttp) REVERT: B 362 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.7658 (m-80) outliers start: 50 outliers final: 39 residues processed: 171 average time/residue: 0.1641 time to fit residues: 41.3315 Evaluate side-chains 175 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 131 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 362 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.091227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.081366 restraints weight = 23983.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.083412 restraints weight = 12050.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.084791 restraints weight = 7270.048| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8865 Z= 0.261 Angle : 0.805 9.342 12042 Z= 0.377 Chirality : 0.047 0.193 1341 Planarity : 0.005 0.043 1536 Dihedral : 9.828 130.800 1245 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.52 % Favored : 88.20 % Rotamer: Outliers : 5.54 % Allowed : 21.82 % Favored : 72.64 % 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: -2.26 (0.25), residues: 1068 helix: -1.15 (0.27), residues: 354 sheet: -1.21 (0.38), residues: 186 loop : -1.80 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 356 HIS 0.017 0.002 HIS B 101 PHE 0.035 0.002 PHE B 352 TYR 0.020 0.002 TYR A 218 ARG 0.003 0.000 ARG A 290 =============================================================================== Job complete usr+sys time: 1711.06 seconds wall clock time: 32 minutes 17.28 seconds (1937.28 seconds total)