Starting phenix.real_space_refine on Mon Mar 11 07:43:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eje_31160/03_2024/7eje_31160_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eje_31160/03_2024/7eje_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_31160/03_2024/7eje_31160.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eje_31160/03_2024/7eje_31160.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eje_31160/03_2024/7eje_31160_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eje_31160/03_2024/7eje_31160_updated.pdb" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.52, per 1000 atoms: 0.59 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 1.3 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: 3.25 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: 1.94 Time building geometry restraints manager: 3.52 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: 4528 32.88 - 65.76: 174 65.76 - 98.64: 11 98.64 - 131.51: 0 131.51 - 164.39: 3 Dihedral angle restraints: 4716 sinusoidal: 2055 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 4713 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 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: 0.810 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: 3.760 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.000 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 : 1.298 15.821 10552 Z= 0.838 Chirality : 0.052 0.331 1203 Planarity : 0.005 0.047 1296 Dihedral : 15.521 164.392 3012 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 % Allowed : 2.82 % Favored : 92.74 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 138 PHE 0.020 0.002 PHE A 259 TYR 0.031 0.004 TYR A 315 ARG 0.007 0.001 ARG A 170 *********************** 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 : 0.872 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 REVERT: A 220 ILE cc_start: 0.9123 (mt) cc_final: 0.8756 (mp) REVERT: A 266 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8126 (m) REVERT: A 290 ASN cc_start: 0.7529 (m110) cc_final: 0.7262 (m110) REVERT: B 171 LEU cc_start: 0.8804 (mt) cc_final: 0.8331 (mt) REVERT: B 220 ILE cc_start: 0.8980 (mt) cc_final: 0.8519 (mt) REVERT: B 266 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.7995 (m) REVERT: C 291 ILE cc_start: 0.9330 (mt) cc_final: 0.8868 (tt) REVERT: C 301 TYR cc_start: 0.8033 (t80) cc_final: 0.7759 (t80) outliers start: 33 outliers final: 8 residues processed: 310 average time/residue: 0.2825 time to fit residues: 107.4560 Evaluate side-chains 164 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 154 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 263 VAL 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: 0.8980 chunk 47 optimal weight: 0.3980 chunk 37 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 93 HIS C 200 GLN C 244 HIS C 267 ASN C 313 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7750 Z= 0.226 Angle : 0.730 7.913 10552 Z= 0.385 Chirality : 0.041 0.158 1203 Planarity : 0.005 0.056 1296 Dihedral : 17.542 179.021 1345 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 1.30 % Allowed : 3.26 % Favored : 95.44 % Rotamer: Outliers : 4.30 % Allowed : 12.63 % Favored : 83.06 % 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: -0.92 (0.26), residues: 921 helix: -0.40 (0.23), residues: 402 sheet: -1.00 (0.43), residues: 126 loop : -0.48 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 47 PHE 0.025 0.003 PHE A 126 TYR 0.018 0.002 TYR C 315 ARG 0.007 0.001 ARG A 130 *********************** 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 213 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 181 time to evaluate : 0.780 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 revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8616 (tp) cc_final: 0.8345 (tp) REVERT: A 228 TYR cc_start: 0.8523 (m-80) cc_final: 0.8261 (m-80) REVERT: B 124 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7467 (mm-30) REVERT: B 129 PHE cc_start: 0.7896 (p90) cc_final: 0.7694 (p90) REVERT: B 158 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6715 (mpp) REVERT: B 171 LEU cc_start: 0.8897 (mt) cc_final: 0.8374 (mt) REVERT: B 205 TYR cc_start: 0.7287 (m-10) cc_final: 0.7019 (m-10) REVERT: B 228 TYR cc_start: 0.8339 (m-80) cc_final: 0.8095 (m-80) REVERT: C 235 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.6613 (pmt170) outliers start: 32 outliers final: 13 residues processed: 202 average time/residue: 0.1992 time to fit residues: 53.7099 Evaluate side-chains 164 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 253 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7750 Z= 0.330 Angle : 0.719 6.578 10552 Z= 0.374 Chirality : 0.040 0.150 1203 Planarity : 0.005 0.052 1296 Dihedral : 17.224 173.020 1334 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 1.19 % Allowed : 4.45 % Favored : 94.35 % Rotamer: Outliers : 4.97 % Allowed : 15.46 % Favored : 79.57 % 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: -0.39 (0.26), residues: 921 helix: 0.49 (0.25), residues: 396 sheet: -0.93 (0.46), residues: 114 loop : -0.69 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 47 PHE 0.020 0.002 PHE A 129 TYR 0.018 0.002 TYR C 315 ARG 0.004 0.001 ARG A 193 *********************** 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 182 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 0.838 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 REVERT: A 124 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7382 (mm-30) REVERT: A 195 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: B 171 LEU cc_start: 0.8881 (mt) cc_final: 0.8379 (mt) REVERT: B 220 ILE cc_start: 0.9335 (mm) cc_final: 0.8482 (mm) REVERT: C 159 TYR cc_start: 0.8060 (t80) cc_final: 0.7699 (t80) REVERT: C 301 TYR cc_start: 0.8229 (t80) cc_final: 0.8027 (t80) outliers start: 37 outliers final: 26 residues processed: 168 average time/residue: 0.2081 time to fit residues: 46.3604 Evaluate side-chains 156 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 291 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 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: 0.7758 moved from start: 0.6421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7750 Z= 0.306 Angle : 0.690 7.151 10552 Z= 0.357 Chirality : 0.039 0.144 1203 Planarity : 0.004 0.051 1296 Dihedral : 16.956 179.201 1323 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.91 % Favored : 95.11 % Rotamer: Outliers : 5.11 % Allowed : 16.13 % Favored : 78.76 % 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: -0.30 (0.26), residues: 921 helix: 0.70 (0.25), residues: 417 sheet: -1.04 (0.45), residues: 114 loop : -0.82 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 47 PHE 0.015 0.002 PHE B 195 TYR 0.021 0.002 TYR B 54 ARG 0.006 0.001 ARG A 229 *********************** 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 176 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 138 time to evaluate : 0.836 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: B 54 TYR cc_start: 0.8380 (m-80) cc_final: 0.8154 (m-80) REVERT: B 171 LEU cc_start: 0.8896 (mt) cc_final: 0.8506 (mt) REVERT: B 204 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8692 (mm) REVERT: C 54 TYR cc_start: 0.8602 (m-80) cc_final: 0.8263 (m-80) outliers start: 38 outliers final: 26 residues processed: 160 average time/residue: 0.1882 time to fit residues: 40.8568 Evaluate side-chains 151 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 270 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 66 optimal weight: 0.0870 chunk 37 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 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: 0.8980 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 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: 0.7740 moved from start: 0.6816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7750 Z= 0.253 Angle : 0.653 7.678 10552 Z= 0.336 Chirality : 0.038 0.141 1203 Planarity : 0.004 0.050 1296 Dihedral : 16.779 177.806 1323 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.34 % Favored : 94.68 % Rotamer: Outliers : 4.97 % Allowed : 18.15 % Favored : 76.88 % 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: -0.15 (0.27), residues: 921 helix: 0.89 (0.26), residues: 405 sheet: -1.10 (0.46), residues: 117 loop : -0.72 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 47 PHE 0.012 0.002 PHE B 195 TYR 0.014 0.002 TYR B 54 ARG 0.004 0.000 ARG A 229 *********************** 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 169 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7838 (mm) REVERT: C 54 TYR cc_start: 0.8625 (m-80) cc_final: 0.8221 (m-80) outliers start: 37 outliers final: 28 residues processed: 156 average time/residue: 0.2003 time to fit residues: 43.9767 Evaluate side-chains 151 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 270 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 29 optimal weight: 0.0870 chunk 47 optimal weight: 9.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 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: 0.7685 moved from start: 0.7044 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= 0.195 Angle : 0.634 7.872 10552 Z= 0.328 Chirality : 0.038 0.134 1203 Planarity : 0.004 0.052 1296 Dihedral : 16.642 176.319 1323 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.80 % Favored : 95.22 % Rotamer: Outliers : 4.97 % Allowed : 19.35 % Favored : 75.67 % 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 (0.27), residues: 921 helix: 0.95 (0.26), residues: 399 sheet: -0.69 (0.47), residues: 117 loop : -0.71 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 47 PHE 0.012 0.001 PHE A 195 TYR 0.019 0.002 TYR B 54 ARG 0.004 0.000 ARG A 130 *********************** 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 172 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 135 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 TYR cc_start: 0.8196 (t80) cc_final: 0.7953 (t80) REVERT: A 171 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7705 (mm) REVERT: C 54 TYR cc_start: 0.8534 (m-80) cc_final: 0.8024 (m-80) REVERT: C 159 TYR cc_start: 0.8047 (t80) cc_final: 0.7841 (t80) outliers start: 37 outliers final: 26 residues processed: 153 average time/residue: 0.1832 time to fit residues: 39.1172 Evaluate side-chains 151 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 220 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.7260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7750 Z= 0.212 Angle : 0.645 7.776 10552 Z= 0.331 Chirality : 0.038 0.159 1203 Planarity : 0.004 0.050 1296 Dihedral : 16.553 173.701 1323 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.91 % Favored : 95.11 % Rotamer: Outliers : 3.90 % Allowed : 22.04 % Favored : 74.06 % 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: 0.01 (0.27), residues: 921 helix: 0.99 (0.26), residues: 402 sheet: -0.60 (0.47), residues: 117 loop : -0.75 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 47 PHE 0.032 0.001 PHE A 129 TYR 0.013 0.001 TYR B 178 ARG 0.003 0.000 ARG A 310 *********************** 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 159 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7703 (mm) REVERT: C 54 TYR cc_start: 0.8652 (m-80) cc_final: 0.8194 (m-80) outliers start: 29 outliers final: 25 residues processed: 147 average time/residue: 0.1800 time to fit residues: 36.5406 Evaluate side-chains 150 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 220 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 70 optimal weight: 9.9990 chunk 81 optimal weight: 0.0000 chunk 85 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.7391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7750 Z= 0.184 Angle : 0.627 9.967 10552 Z= 0.321 Chirality : 0.038 0.135 1203 Planarity : 0.003 0.049 1296 Dihedral : 16.440 172.879 1323 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.69 % Favored : 95.33 % Rotamer: Outliers : 3.49 % Allowed : 22.31 % Favored : 74.19 % 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: 0.22 (0.27), residues: 921 helix: 1.11 (0.26), residues: 396 sheet: -0.80 (0.41), residues: 153 loop : -0.36 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 47 PHE 0.012 0.001 PHE A 195 TYR 0.015 0.001 TYR C 191 ARG 0.003 0.000 ARG A 229 *********************** 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 165 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.7916 (p90) cc_final: 0.7710 (p90) REVERT: A 171 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7778 (mt) REVERT: A 228 TYR cc_start: 0.8620 (m-80) cc_final: 0.8273 (m-80) REVERT: C 54 TYR cc_start: 0.8626 (m-80) cc_final: 0.7982 (m-80) outliers start: 26 outliers final: 18 residues processed: 153 average time/residue: 0.1876 time to fit residues: 39.1637 Evaluate side-chains 146 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 220 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 25 optimal weight: 0.0670 chunk 75 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.7577 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= 0.188 Angle : 0.671 16.121 10552 Z= 0.337 Chirality : 0.038 0.136 1203 Planarity : 0.003 0.049 1296 Dihedral : 16.369 173.103 1323 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.80 % Favored : 95.22 % Rotamer: Outliers : 2.96 % Allowed : 23.52 % Favored : 73.52 % 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: 0.24 (0.27), residues: 921 helix: 1.03 (0.27), residues: 396 sheet: -0.58 (0.40), residues: 162 loop : -0.31 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 47 PHE 0.012 0.001 PHE A 195 TYR 0.023 0.001 TYR B 191 ARG 0.003 0.000 ARG A 229 *********************** 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 157 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 TYR cc_start: 0.8633 (m-80) cc_final: 0.8255 (m-80) REVERT: B 54 TYR cc_start: 0.6856 (m-80) cc_final: 0.6656 (m-80) REVERT: B 225 THR cc_start: 0.8256 (p) cc_final: 0.7837 (p) REVERT: B 243 MET cc_start: 0.6904 (tpp) cc_final: 0.6632 (mpp) outliers start: 22 outliers final: 18 residues processed: 147 average time/residue: 0.1727 time to fit residues: 35.3104 Evaluate side-chains 148 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 220 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 0.2980 chunk 92 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.7673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7750 Z= 0.204 Angle : 0.708 18.581 10552 Z= 0.351 Chirality : 0.039 0.144 1203 Planarity : 0.004 0.050 1296 Dihedral : 16.333 173.497 1323 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.13 % Favored : 94.90 % Rotamer: Outliers : 2.82 % Allowed : 23.92 % Favored : 73.25 % 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: 0.29 (0.27), residues: 921 helix: 0.98 (0.27), residues: 396 sheet: -0.41 (0.40), residues: 162 loop : -0.25 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 294 PHE 0.013 0.001 PHE A 195 TYR 0.013 0.001 TYR B 159 ARG 0.002 0.000 ARG A 229 ********************** 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 150 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 0.912 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: A 171 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7801 (mt) REVERT: A 228 TYR cc_start: 0.8653 (m-80) cc_final: 0.8254 (m-80) REVERT: B 54 TYR cc_start: 0.6946 (m-80) cc_final: 0.6723 (m-80) REVERT: B 243 MET cc_start: 0.6875 (tpp) cc_final: 0.6555 (mpp) outliers start: 21 outliers final: 19 residues processed: 141 average time/residue: 0.1844 time to fit residues: 36.5557 Evaluate side-chains 148 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 220 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 13 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.067174 restraints weight = 21547.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.069408 restraints weight = 11981.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.070935 restraints weight = 8026.071| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.7781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7750 Z= 0.206 Angle : 0.716 18.029 10552 Z= 0.352 Chirality : 0.039 0.137 1203 Planarity : 0.004 0.049 1296 Dihedral : 16.313 172.780 1323 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.23 % Favored : 94.79 % Rotamer: Outliers : 3.23 % Allowed : 23.25 % Favored : 73.52 % 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: 0.28 (0.27), residues: 921 helix: 0.95 (0.27), residues: 396 sheet: -0.36 (0.39), residues: 162 loop : -0.25 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 294 PHE 0.016 0.001 PHE C 259 TYR 0.016 0.002 TYR C 191 ARG 0.002 0.000 ARG A 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1708.88 seconds wall clock time: 31 minutes 48.63 seconds (1908.63 seconds total)