Starting phenix.real_space_refine (version: dev) on Sat Feb 18 07:14:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1c_9567/02_2023/5h1c_9567_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1c_9567/02_2023/5h1c_9567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1c_9567/02_2023/5h1c_9567.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1c_9567/02_2023/5h1c_9567.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1c_9567/02_2023/5h1c_9567_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1c_9567/02_2023/5h1c_9567_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 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: "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: 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} Time building chain proxies: 4.66, per 1000 atoms: 0.61 Number of scatterers: 7602 At special positions: 0 Unit cell: (104.48, 82.278, 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: 3.86 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 43.0% alpha, 10.9% beta 9 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 2.84 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 199 through 211 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: 3.961A 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: 3.638A 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: 4.121A 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 198 through 211 removed outlier: 3.587A pdb=" N GLN B 206 " --> pdb=" O LEU B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.710A pdb=" N THR B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 259 removed outlier: 3.960A 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: 3.638A 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: 4.121A 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: 4.940A 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 198 through 211 removed outlier: 3.587A pdb=" N GLN C 206 " --> pdb=" O LEU C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 removed outlier: 3.710A 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: 3.907A pdb=" N GLU C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.740A pdb=" N ALA C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 3.638A 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: 7.257A 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: 7.083A pdb=" N LEU A 219 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N THR A 266 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 7.378A 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: 6.398A pdb=" N LEU A 219 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET A 158 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.064A 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: 6.266A pdb=" N ALA A 190 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 6.940A 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: 8.450A pdb=" N MET B 125 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE B 265 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 8.366A 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: 8.492A pdb=" N THR B 266 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 7.378A 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: 6.064A 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: 6.941A 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: 7.257A pdb=" N VAL C 263 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N MET C 125 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 7.553A 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: 8.492A pdb=" N THR C 266 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL C 221 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LYS C 156 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU C 219 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET C 158 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL C 221 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 7.302A 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: 6.942A 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 304 233 hydrogen bonds defined for protein. 612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 4.02 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: 2419 1.33 - 1.45: 1181 1.45 - 1.57: 4035 1.57 - 1.69: 52 1.69 - 1.81: 63 Bond restraints: 7750 Sorted by residual: bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" O3A ANP B 602 " pdb=" PB ANP B 602 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" O3A ANP A 602 " pdb=" PB ANP A 602 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" C MET A 158 " pdb=" N TYR A 159 " ideal model delta sigma weight residual 1.332 1.255 0.077 1.31e-02 5.83e+03 3.42e+01 bond pdb=" C MET C 158 " pdb=" N TYR C 159 " ideal model delta sigma weight residual 1.332 1.255 0.076 1.31e-02 5.83e+03 3.40e+01 ... (remaining 7745 not shown) Histogram of bond angle deviations from ideal: 100.26 - 106.72: 314 106.72 - 113.17: 4187 113.17 - 119.63: 2182 119.63 - 126.08: 3758 126.08 - 132.53: 111 Bond angle restraints: 10552 Sorted by residual: 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 4.42e+01 angle pdb=" C LYS C 285 " pdb=" N PRO C 286 " pdb=" CA PRO C 286 " ideal model delta sigma weight residual 119.78 126.60 -6.82 1.03e+00 9.43e-01 4.38e+01 angle pdb=" C LYS B 285 " pdb=" N PRO B 286 " pdb=" CA PRO B 286 " ideal model delta sigma weight residual 119.78 126.60 -6.82 1.03e+00 9.43e-01 4.38e+01 angle pdb=" N GLU C 124 " pdb=" CA GLU C 124 " pdb=" C GLU C 124 " ideal model delta sigma weight residual 108.48 118.38 -9.90 1.80e+00 3.09e-01 3.03e+01 angle pdb=" N GLU A 124 " pdb=" CA GLU A 124 " pdb=" C GLU A 124 " ideal model delta sigma weight residual 108.48 118.37 -9.89 1.80e+00 3.09e-01 3.02e+01 ... (remaining 10547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.87: 4432 32.87 - 65.75: 150 65.75 - 98.62: 11 98.62 - 131.50: 0 131.50 - 164.37: 3 Dihedral angle restraints: 4596 sinusoidal: 1935 harmonic: 2661 Sorted by residual: 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 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 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 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+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 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 4593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 992 0.065 - 0.131: 201 0.131 - 0.196: 4 0.196 - 0.261: 3 0.261 - 0.327: 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 -2.68 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C3' ANP B 602 " pdb=" C2' ANP B 602 " pdb=" C4' ANP B 602 " pdb=" O3' ANP B 602 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" C3' ANP A 602 " pdb=" C2' ANP A 602 " pdb=" C4' ANP A 602 " pdb=" O3' ANP A 602 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.33 2.00e-01 2.50e+01 2.66e+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 3.01e-02 9.08e+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 3.01e-02 9.06e+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 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C MET C 158 " 0.052 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: 66 2.14 - 2.83: 2653 2.83 - 3.52: 10923 3.52 - 4.21: 17993 4.21 - 4.90: 30324 Nonbonded interactions: 61959 Sorted by model distance: nonbonded pdb=" O ALA C 217 " pdb=" CG1 VAL C 261 " model vdw 1.454 3.460 nonbonded pdb=" O ALA B 217 " pdb=" CG1 VAL B 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 B 270 " pdb=" CG2 ILE B 287 " model vdw 1.579 3.880 nonbonded pdb=" CG2 VAL C 270 " pdb=" CG2 ILE C 287 " model vdw 1.580 3.880 ... (remaining 61954 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.400 Check model and map are aligned: 0.110 Process input model: 26.550 Find NCS groups from input model: 0.500 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 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 0.149 7750 Z= 0.551 Angle : 1.297 15.919 10552 Z= 0.837 Chirality : 0.052 0.327 1203 Planarity : 0.005 0.047 1296 Dihedral : 14.980 164.369 2892 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 41.46 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 (0.46), 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 97 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 64 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 6 residues processed: 91 average time/residue: 0.2849 time to fit residues: 32.8273 Evaluate side-chains 41 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1611 time to fit residues: 2.5170 ------------------------------------------------------------------------------- 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: 5.9990 chunk 70 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 37 optimal weight: 30.0000 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 138 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN A 313 GLN B 138 HIS ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN B 313 GLN C 138 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 7750 Z= 0.321 Angle : 0.738 9.476 10552 Z= 0.392 Chirality : 0.041 0.139 1203 Planarity : 0.005 0.038 1296 Dihedral : 17.260 176.283 1203 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 1.19 % Allowed : 4.02 % Favored : 94.79 % Rotamer Outliers : 0.13 % 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: -0.78 (0.27), residues: 921 helix: -0.19 (0.23), residues: 417 sheet: -1.45 (0.43), residues: 123 loop : -0.32 (0.34), residues: 381 *********************** 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 42 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.988 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 0.2029 time to fit residues: 12.3006 Evaluate side-chains 30 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2015 ------------------------------------------------------------------------------- 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: 6.9990 chunk 26 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** 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: 0.6881 moved from start: 0.4291 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= 0.306 Angle : 0.656 9.564 10552 Z= 0.345 Chirality : 0.038 0.129 1203 Planarity : 0.004 0.043 1296 Dihedral : 16.708 178.122 1203 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.89 % Favored : 94.14 % Rotamer Outliers : 0.00 % 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 (0.27), residues: 921 helix: 0.47 (0.24), residues: 420 sheet: -1.18 (0.46), residues: 123 loop : -0.45 (0.33), residues: 378 *********************** 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 35 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.926 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1625 time to fit residues: 9.2756 Evaluate side-chains 29 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2620 ------------------------------------------------------------------------------- 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: 9.9990 chunk 63 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 202 GLN ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN C 202 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 7750 Z= 0.303 Angle : 0.648 9.706 10552 Z= 0.338 Chirality : 0.038 0.128 1203 Planarity : 0.004 0.044 1296 Dihedral : 16.714 176.464 1203 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.89 % Favored : 94.14 % Rotamer Outliers : 0.00 % 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: 0.94 (0.25), residues: 396 sheet: -1.18 (0.48), residues: 123 loop : -0.42 (0.31), residues: 402 *********************** 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 36 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.938 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1814 time to fit residues: 10.2655 Evaluate side-chains 28 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2834 ------------------------------------------------------------------------------- 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: 8.9990 chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 0.2980 chunk 76 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 7750 Z= 0.190 Angle : 0.561 9.942 10552 Z= 0.292 Chirality : 0.037 0.120 1203 Planarity : 0.004 0.047 1296 Dihedral : 16.372 175.461 1203 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.99 % Favored : 94.03 % Rotamer Outliers : 0.00 % 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: 0.40 (0.28), residues: 921 helix: 1.30 (0.26), residues: 396 sheet: -0.72 (0.50), residues: 123 loop : -0.35 (0.31), residues: 402 *********************** 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 42 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.808 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1724 time to fit residues: 10.9380 Evaluate side-chains 32 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1226 ------------------------------------------------------------------------------- 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: 10.0000 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 7 optimal weight: 0.0980 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 7750 Z= 0.158 Angle : 0.534 10.226 10552 Z= 0.276 Chirality : 0.036 0.119 1203 Planarity : 0.003 0.049 1296 Dihedral : 16.163 174.764 1203 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.02 % Favored : 95.01 % Rotamer Outliers : 0.00 % 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: 0.57 (0.28), residues: 921 helix: 1.43 (0.26), residues: 399 sheet: -0.56 (0.50), residues: 126 loop : -0.30 (0.32), residues: 396 *********************** 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 41 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1627 time to fit residues: 10.8149 Evaluate side-chains 29 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3309 ------------------------------------------------------------------------------- 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: 30.0000 chunk 10 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN B 196 ASN C 30 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 7750 Z= 0.218 Angle : 0.575 9.970 10552 Z= 0.296 Chirality : 0.037 0.142 1203 Planarity : 0.003 0.048 1296 Dihedral : 16.020 170.784 1203 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.56 % Favored : 94.46 % Rotamer Outliers : 0.00 % 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: 0.64 (0.28), residues: 921 helix: 1.55 (0.26), residues: 396 sheet: -0.74 (0.54), residues: 108 loop : -0.27 (0.31), residues: 417 *********************** 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 35 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.897 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1579 time to fit residues: 9.1018 Evaluate side-chains 28 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.901 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1736 ------------------------------------------------------------------------------- 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: 8.9990 chunk 53 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 61 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 7750 Z= 0.260 Angle : 0.614 10.199 10552 Z= 0.314 Chirality : 0.038 0.139 1203 Planarity : 0.004 0.047 1296 Dihedral : 16.144 173.068 1203 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.98 % Allowed : 5.10 % Favored : 93.92 % Rotamer Outliers : 0.00 % 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: 0.42 (0.28), residues: 921 helix: 1.33 (0.26), residues: 399 sheet: -1.13 (0.44), residues: 156 loop : -0.09 (0.33), residues: 366 *********************** 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 34 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.939 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1656 time to fit residues: 9.2300 Evaluate side-chains 27 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3562 ------------------------------------------------------------------------------- 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: 0.9980 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 7750 Z= 0.207 Angle : 0.582 10.366 10552 Z= 0.297 Chirality : 0.038 0.156 1203 Planarity : 0.003 0.049 1296 Dihedral : 16.168 174.416 1203 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.67 % Favored : 94.35 % Rotamer Outliers : 0.00 % 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: 0.49 (0.28), residues: 921 helix: 1.47 (0.26), residues: 393 sheet: -0.97 (0.44), residues: 153 loop : -0.21 (0.32), residues: 375 *********************** 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 35 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.852 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1557 time to fit residues: 8.8398 Evaluate side-chains 28 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0781 ------------------------------------------------------------------------------- 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: 6.9990 chunk 41 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 92 optimal weight: 30.0000 chunk 85 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 7 optimal weight: 0.0020 chunk 56 optimal weight: 0.0980 chunk 45 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 overall best weight: 2.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7750 Z= 0.175 Angle : 0.558 10.282 10552 Z= 0.285 Chirality : 0.037 0.130 1203 Planarity : 0.003 0.048 1296 Dihedral : 16.100 174.491 1203 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.56 % Favored : 94.46 % Rotamer Outliers : 0.00 % 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: 0.62 (0.28), residues: 921 helix: 1.57 (0.26), residues: 393 sheet: -0.79 (0.44), residues: 153 loop : -0.20 (0.32), residues: 375 ********************** 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 38 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.922 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1608 time to fit residues: 9.7538 Evaluate side-chains 28 residues out of total 744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.896 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1778 ------------------------------------------------------------------------------- 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: 40.0000 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.0770 chunk 73 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 75 optimal weight: 30.0000 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 overall best weight: 1.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.032595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.026265 restraints weight = 79929.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.027056 restraints weight = 46734.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.027586 restraints weight = 32252.209| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 7750 Z= 0.139 Angle : 0.550 10.316 10552 Z= 0.276 Chirality : 0.037 0.131 1203 Planarity : 0.003 0.049 1296 Dihedral : 15.993 177.313 1203 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.23 % Favored : 94.79 % Rotamer Outliers : 0.00 % 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: 0.67 (0.29), residues: 921 helix: 1.48 (0.26), residues: 408 sheet: -0.51 (0.44), residues: 153 loop : -0.21 (0.33), residues: 360 =============================================================================== Job complete usr+sys time: 1279.81 seconds wall clock time: 24 minutes 36.85 seconds (1476.85 seconds total)