Starting phenix.real_space_refine (version: dev) on Sat Feb 18 07:18:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eje_31160/02_2023/7eje_31160_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eje_31160/02_2023/7eje_31160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eje_31160/02_2023/7eje_31160.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eje_31160/02_2023/7eje_31160.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eje_31160/02_2023/7eje_31160_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eje_31160/02_2023/7eje_31160_updated.pdb" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "C ARG 235": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 7602 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2379 Classifications: {'peptide': 311} Link IDs: {'CIS': 3, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "B" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2379 Classifications: {'peptide': 311} Link IDs: {'CIS': 3, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "C" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2379 Classifications: {'peptide': 311} Link IDs: {'CIS': 3, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ANP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.80, per 1000 atoms: 0.63 Number of scatterers: 7602 At special positions: 0 Unit cell: (107.092, 75.748, 114.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 27 15.00 Mg 3 11.99 O 1515 8.00 N 1341 7.00 C 4677 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 6 sheets defined 42.9% alpha, 10.9% beta 8 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 25 through 28 Processing helix chain 'A' and resid 35 through 44 removed outlier: 4.121A pdb=" N GLU A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 68 through 81 Processing helix chain 'A' and resid 89 through 96 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 133 through 145 removed outlier: 4.939A pdb=" N GLN A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 198 through 211 removed outlier: 3.589A pdb=" N GLN A 206 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.710A pdb=" N THR A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 259 removed outlier: 3.962A pdb=" N ARG A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.740A pdb=" N ALA A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 35 through 44 removed outlier: 4.119A pdb=" N GLU B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 68 through 81 Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 133 through 145 removed outlier: 4.940A pdb=" N GLN B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 168 through 178 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.711A pdb=" N THR B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 259 removed outlier: 3.961A pdb=" N ARG B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.740A pdb=" N ALA B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 28 Processing helix chain 'C' and resid 35 through 44 removed outlier: 4.119A pdb=" N GLU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 68 through 81 Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 133 through 145 removed outlier: 4.938A pdb=" N GLN C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 168 through 178 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 226 through 231 removed outlier: 3.711A pdb=" N THR C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 259 removed outlier: 3.960A pdb=" N ARG C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.742A pdb=" N ALA C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 122 through 126 removed outlier: 7.258A pdb=" N VAL A 263 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N MET A 125 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE A 265 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N VAL A 264 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU A 219 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N THR A 266 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL A 221 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LYS A 156 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 219 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET A 158 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL A 221 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE A 160 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ALA A 190 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASP A 161 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA A 192 " --> pdb=" O ASP A 161 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 299 through 304 Processing sheet with id= C, first strand: chain 'B' and resid 122 through 126 removed outlier: 7.257A pdb=" N VAL B 263 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N MET B 125 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE B 265 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL B 264 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU B 219 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR B 266 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL B 221 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LYS B 156 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU B 219 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET B 158 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL B 221 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE B 160 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA B 190 " --> pdb=" O TYR B 159 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASP B 161 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA B 192 " --> pdb=" O ASP B 161 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 299 through 304 Processing sheet with id= E, first strand: chain 'C' and resid 122 through 126 removed outlier: 7.258A pdb=" N VAL C 263 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N MET C 125 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE C 265 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL C 264 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU C 219 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N THR C 266 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL C 221 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS C 156 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU C 219 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N MET C 158 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL C 221 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE C 160 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA C 190 " --> pdb=" O TYR C 159 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASP C 161 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA C 192 " --> pdb=" O ASP C 161 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 299 through 304 232 hydrogen bonds defined for protein. 639 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2393 1.33 - 1.45: 1187 1.45 - 1.57: 4055 1.57 - 1.69: 52 1.69 - 1.81: 63 Bond restraints: 7750 Sorted by residual: bond pdb=" O3A ANP B 401 " pdb=" PB ANP B 401 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" O3A ANP C 403 " pdb=" PB ANP C 403 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" C MET B 158 " pdb=" N TYR B 159 " ideal model delta sigma weight residual 1.332 1.253 0.079 1.31e-02 5.83e+03 3.63e+01 bond pdb=" C MET C 158 " pdb=" N TYR C 159 " ideal model delta sigma weight residual 1.332 1.254 0.078 1.31e-02 5.83e+03 3.51e+01 ... (remaining 7745 not shown) Histogram of bond angle deviations from ideal: 100.24 - 106.70: 312 106.70 - 113.15: 4186 113.15 - 119.60: 2171 119.60 - 126.05: 3772 126.05 - 132.51: 111 Bond angle restraints: 10552 Sorted by residual: angle pdb=" C LYS B 285 " pdb=" N PRO B 286 " pdb=" CA PRO B 286 " ideal model delta sigma weight residual 119.78 126.62 -6.84 1.03e+00 9.43e-01 4.41e+01 angle pdb=" C LYS A 285 " pdb=" N PRO A 286 " pdb=" CA PRO A 286 " ideal model delta sigma weight residual 119.78 126.62 -6.84 1.03e+00 9.43e-01 4.41e+01 angle pdb=" C LYS C 285 " pdb=" N PRO C 286 " pdb=" CA PRO C 286 " ideal model delta sigma weight residual 119.78 126.59 -6.81 1.03e+00 9.43e-01 4.37e+01 angle pdb=" N GLU C 124 " pdb=" CA GLU C 124 " pdb=" C GLU C 124 " ideal model delta sigma weight residual 108.48 118.33 -9.85 1.80e+00 3.09e-01 2.99e+01 angle pdb=" N GLU B 124 " pdb=" CA GLU B 124 " pdb=" C GLU B 124 " ideal model delta sigma weight residual 108.48 118.33 -9.85 1.80e+00 3.09e-01 2.99e+01 ... (remaining 10547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.88: 4431 32.88 - 65.76: 151 65.76 - 98.64: 11 98.64 - 131.51: 0 131.51 - 164.39: 3 Dihedral angle restraints: 4596 sinusoidal: 1935 harmonic: 2661 Sorted by residual: dihedral pdb=" CA ILE B 314 " pdb=" C ILE B 314 " pdb=" N TYR B 315 " pdb=" CA TYR B 315 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ILE A 314 " pdb=" C ILE A 314 " pdb=" N TYR A 315 " pdb=" CA TYR A 315 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ILE C 314 " pdb=" C ILE C 314 " pdb=" N TYR C 315 " pdb=" CA TYR C 315 " ideal model delta harmonic sigma weight residual 180.00 156.45 23.55 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 4593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1004 0.066 - 0.132: 189 0.132 - 0.198: 4 0.198 - 0.265: 3 0.265 - 0.331: 3 Chirality restraints: 1203 Sorted by residual: chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C3' ANP B 401 " pdb=" C2' ANP B 401 " pdb=" C4' ANP B 401 " pdb=" O3' ANP B 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C3' ANP C 403 " pdb=" C2' ANP C 403 " pdb=" C4' ANP C 403 " pdb=" O3' ANP C 403 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 1200 not shown) Planarity restraints: 1296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 158 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C MET B 158 " -0.052 2.00e-02 2.50e+03 pdb=" O MET B 158 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR B 159 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 158 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.02e+00 pdb=" C MET A 158 " -0.052 2.00e-02 2.50e+03 pdb=" O MET A 158 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR A 159 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 158 " 0.014 2.00e-02 2.50e+03 2.96e-02 8.79e+00 pdb=" C MET C 158 " -0.051 2.00e-02 2.50e+03 pdb=" O MET C 158 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR C 159 " 0.018 2.00e-02 2.50e+03 ... (remaining 1293 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 69 2.14 - 2.83: 2662 2.83 - 3.52: 10947 3.52 - 4.21: 18013 4.21 - 4.90: 30197 Nonbonded interactions: 61888 Sorted by model distance: nonbonded pdb=" O ALA B 217 " pdb=" CG1 VAL B 261 " model vdw 1.454 3.460 nonbonded pdb=" O ALA C 217 " pdb=" CG1 VAL C 261 " model vdw 1.454 3.460 nonbonded pdb=" O ALA A 217 " pdb=" CG1 VAL A 261 " model vdw 1.454 3.460 nonbonded pdb=" CG2 VAL C 270 " pdb=" CG2 ILE C 287 " model vdw 1.579 3.880 nonbonded pdb=" CG2 VAL A 270 " pdb=" CG2 ILE A 287 " model vdw 1.579 3.880 ... (remaining 61883 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' and resid 22 through 336) selection = (chain 'B' and resid 22 through 336) selection = (chain 'C' and resid 22 through 336) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 27 5.49 5 Mg 3 5.21 5 S 39 5.16 5 C 4677 2.51 5 N 1341 2.21 5 O 1515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.430 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: 4.310 Check model and map are aligned: 0.110 Process input model: 25.740 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 : 0.009 0.148 7750 Z= 0.549 Angle : 1.297 15.821 10552 Z= 0.838 Chirality : 0.052 0.331 1203 Planarity : 0.005 0.047 1296 Dihedral : 15.125 164.392 2892 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 41.99 Ramachandran Plot: Outliers : 2.28 % Allowed : 4.89 % Favored : 92.83 % Rotamer Outliers : 4.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % 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: -2.37 (0.25), residues: 921 helix: -2.32 (0.16), residues: 408 sheet: -2.56 (0.47), residues: 114 loop : -0.07 (0.32), residues: 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 294 time to evaluate : 0.854 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: symmetry clash outliers start: 33 outliers final: 8 residues processed: 310 average time/residue: 0.2843 time to fit residues: 108.0759 Evaluate side-chains 161 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 0.944 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2060 time to fit residues: 3.3031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 HIS A 200 GLN A 313 GLN B 36 ASN B 93 HIS B 200 GLN B 267 ASN B 313 GLN C 47 HIS C 200 GLN C 244 HIS C 267 ASN C 313 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 7750 Z= 0.231 Angle : 0.747 9.948 10552 Z= 0.388 Chirality : 0.041 0.160 1203 Planarity : 0.005 0.056 1296 Dihedral : 16.842 176.579 1203 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 1.19 % Allowed : 3.37 % Favored : 95.44 % Rotamer Outliers : 4.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.26), residues: 921 helix: -0.44 (0.23), residues: 402 sheet: -1.00 (0.43), residues: 126 loop : -0.51 (0.31), residues: 393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 175 time to evaluate : 0.967 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: symmetry clash outliers start: 30 outliers final: 12 residues processed: 195 average time/residue: 0.2001 time to fit residues: 52.3353 Evaluate side-chains 157 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 0.854 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0743 time to fit residues: 2.8386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 7750 Z= 0.289 Angle : 0.697 9.748 10552 Z= 0.359 Chirality : 0.039 0.152 1203 Planarity : 0.005 0.052 1296 Dihedral : 16.551 174.230 1203 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.56 % Favored : 94.46 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.26), residues: 921 helix: 0.25 (0.24), residues: 411 sheet: -0.82 (0.43), residues: 126 loop : -0.57 (0.30), residues: 384 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 155 average time/residue: 0.2076 time to fit residues: 43.3830 Evaluate side-chains 151 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 1.640 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0772 time to fit residues: 3.8210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 7750 Z= 0.208 Angle : 0.637 9.647 10552 Z= 0.325 Chirality : 0.038 0.142 1203 Planarity : 0.004 0.053 1296 Dihedral : 16.306 167.403 1203 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.69 % Favored : 95.33 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.27), residues: 921 helix: 0.69 (0.26), residues: 405 sheet: -0.69 (0.48), residues: 117 loop : -0.66 (0.29), residues: 399 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 156 time to evaluate : 0.889 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: 18 outliers final: 10 residues processed: 161 average time/residue: 0.2280 time to fit residues: 48.7066 Evaluate side-chains 153 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0792 time to fit residues: 2.6289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 66 optimal weight: 0.4980 chunk 37 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.6749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 7750 Z= 0.332 Angle : 0.710 9.628 10552 Z= 0.358 Chirality : 0.040 0.155 1203 Planarity : 0.005 0.051 1296 Dihedral : 16.201 165.794 1203 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.89 % Favored : 94.14 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 921 helix: 0.69 (0.25), residues: 417 sheet: -0.78 (0.48), residues: 114 loop : -0.85 (0.28), residues: 390 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.906 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: 20 outliers final: 9 residues processed: 133 average time/residue: 0.2199 time to fit residues: 38.4799 Evaluate side-chains 121 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 0.760 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0759 time to fit residues: 2.1896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 0.0040 chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.6980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 7750 Z= 0.187 Angle : 0.644 9.760 10552 Z= 0.324 Chirality : 0.039 0.136 1203 Planarity : 0.004 0.053 1296 Dihedral : 16.032 164.609 1203 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.69 % Favored : 95.33 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.27), residues: 921 helix: 0.86 (0.26), residues: 405 sheet: -0.57 (0.49), residues: 117 loop : -0.73 (0.28), residues: 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 136 average time/residue: 0.2074 time to fit residues: 37.9255 Evaluate side-chains 131 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 0.851 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0957 time to fit residues: 1.6349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 54 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.7220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 7750 Z= 0.268 Angle : 0.676 9.647 10552 Z= 0.339 Chirality : 0.039 0.144 1203 Planarity : 0.004 0.054 1296 Dihedral : 16.062 164.816 1203 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.45 % Favored : 94.57 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 921 helix: 1.18 (0.26), residues: 378 sheet: -0.67 (0.48), residues: 117 loop : -0.81 (0.27), residues: 426 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 132 average time/residue: 0.2104 time to fit residues: 37.2721 Evaluate side-chains 126 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0860 time to fit residues: 2.0636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.7383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 7750 Z= 0.254 Angle : 0.681 10.069 10552 Z= 0.339 Chirality : 0.039 0.146 1203 Planarity : 0.004 0.054 1296 Dihedral : 16.018 170.164 1203 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.13 % Favored : 94.90 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.27), residues: 921 helix: 1.30 (0.27), residues: 366 sheet: -0.89 (0.42), residues: 150 loop : -0.45 (0.28), residues: 405 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 125 average time/residue: 0.1969 time to fit residues: 33.7185 Evaluate side-chains 125 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 0.781 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1239 time to fit residues: 1.9366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.0570 chunk 83 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN C 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.7557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 7750 Z= 0.195 Angle : 0.645 10.810 10552 Z= 0.324 Chirality : 0.039 0.156 1203 Planarity : 0.004 0.056 1296 Dihedral : 15.947 170.349 1203 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.23 % Favored : 94.79 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.27), residues: 921 helix: 1.23 (0.27), residues: 366 sheet: -0.54 (0.40), residues: 162 loop : -0.44 (0.29), residues: 393 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 141 average time/residue: 0.2003 time to fit residues: 38.6084 Evaluate side-chains 132 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1016 time to fit residues: 1.8588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.7622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 7750 Z= 0.290 Angle : 0.703 11.671 10552 Z= 0.351 Chirality : 0.040 0.164 1203 Planarity : 0.004 0.053 1296 Dihedral : 16.061 171.962 1203 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.56 % Favored : 94.46 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.27), residues: 921 helix: 1.21 (0.28), residues: 366 sheet: -0.54 (0.41), residues: 162 loop : -0.38 (0.30), residues: 393 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 126 average time/residue: 0.1847 time to fit residues: 32.2984 Evaluate side-chains 124 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0894 time to fit residues: 1.4452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 9 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 0.0000 chunk 4 optimal weight: 4.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN C 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.082158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.065850 restraints weight = 21572.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.068187 restraints weight = 11850.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.069755 restraints weight = 7876.580| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.7807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 7750 Z= 0.200 Angle : 0.678 11.431 10552 Z= 0.336 Chirality : 0.039 0.158 1203 Planarity : 0.004 0.054 1296 Dihedral : 16.019 177.002 1203 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.02 % Favored : 95.01 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.28), residues: 921 helix: 1.18 (0.28), residues: 366 sheet: -0.25 (0.41), residues: 162 loop : -0.39 (0.30), residues: 393 =============================================================================== Job complete usr+sys time: 1662.71 seconds wall clock time: 31 minutes 13.39 seconds (1873.39 seconds total)