Starting phenix.real_space_refine on Wed Mar 12 09:51:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5h1c_9567/03_2025/5h1c_9567.cif Found real_map, /net/cci-nas-00/data/ceres_data/5h1c_9567/03_2025/5h1c_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/cci-nas-00/data/ceres_data/5h1c_9567/03_2025/5h1c_9567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5h1c_9567/03_2025/5h1c_9567.map" model { file = "/net/cci-nas-00/data/ceres_data/5h1c_9567/03_2025/5h1c_9567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5h1c_9567/03_2025/5h1c_9567.cif" } resolution = 4.5 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= 0.000 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 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. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7602 Number of models: 1 Model: "" Number of chains: 6 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: "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} Restraints were copied for chains: B, C Time building chain proxies: 4.88, per 1000 atoms: 0.64 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 - 3.00 Amino acid : True - 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: 2.08 Conformation dependent library (CDL) restraints added in 1.0 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... Secondary structure from input PDB file: 51 helices and 9 sheets defined 52.2% alpha, 11.8% beta 9 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 34 through 42 Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.777A pdb=" N ILE A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 88 through 97 Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 145 through 146 No H-bonds generated for 'chain 'A' and resid 145 through 146' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.563A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 188 removed outlier: 3.855A pdb=" N ASN A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 3.570A pdb=" N GLN A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.535A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 260 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) removed outlier: 3.552A pdb=" N GLY A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.923A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) 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 24 through 29 Processing helix chain 'B' and resid 34 through 42 Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 56 through 63 removed outlier: 3.777A pdb=" N ILE B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 82 Processing helix chain 'B' and resid 89 through 97 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 145 through 146 No H-bonds generated for 'chain 'B' and resid 145 through 146' Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.563A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 removed outlier: 3.856A pdb=" N ASN B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 removed outlier: 3.571A pdb=" N GLN B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 3.536A pdb=" N ARG B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 260 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) removed outlier: 3.552A pdb=" N GLY B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.923A pdb=" N ILE B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) 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 24 through 29 Processing helix chain 'C' and resid 34 through 42 Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.777A pdb=" N ILE C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 82 Processing helix chain 'C' and resid 89 through 97 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 132 through 144 Processing helix chain 'C' and resid 145 through 146 No H-bonds generated for 'chain 'C' and resid 145 through 146' Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.563A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 188 removed outlier: 3.856A pdb=" N ASN C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 212 removed outlier: 3.571A pdb=" N GLN C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 3.536A pdb=" N ARG C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 260 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) removed outlier: 3.551A pdb=" N GLY C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.924A pdb=" N ILE C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) 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=AA1, first strand: chain 'A' and resid 122 through 126 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: 7.479A pdb=" N ALA A 157 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ALA A 192 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR A 159 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 304 Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 126 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: 7.479A pdb=" N ALA B 157 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ALA B 192 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR B 159 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 299 through 304 Processing sheet with id=AA6, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA7, first strand: chain 'C' and resid 122 through 126 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: 7.479A pdb=" N ALA C 157 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ALA C 192 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR C 159 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 299 through 304 Processing sheet with id=AA9, first strand: chain 'C' and resid 329 through 330 311 hydrogen bonds defined for protein. 855 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: 2.13 Time building geometry restraints manager: 2.42 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: 0.00 - 3.18: 10259 3.18 - 6.37: 255 6.37 - 9.55: 29 9.55 - 12.74: 6 12.74 - 15.92: 3 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: 4529 32.87 - 65.75: 173 65.75 - 98.62: 11 98.62 - 131.50: 0 131.50 - 164.37: 3 Dihedral angle restraints: 4716 sinusoidal: 2055 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 4713 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: 2630 2.83 - 3.52: 10835 3.52 - 4.21: 17830 4.21 - 4.90: 30286 Nonbonded interactions: 61647 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 61642 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.000 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.020 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 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= 0.553 Angle : 1.297 15.919 10552 Z= 0.838 Chirality : 0.052 0.327 1203 Planarity : 0.005 0.047 1296 Dihedral : 15.373 164.369 3012 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 % 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 (0.46), residues: 114 loop : -0.07 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 138 PHE 0.019 0.002 PHE C 259 TYR 0.030 0.004 TYR A 315 ARG 0.007 0.001 ARG B 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 97 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 64 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7213 (mp) REVERT: A 205 TYR cc_start: 0.6809 (m-80) cc_final: 0.6554 (m-80) REVERT: A 235 ARG cc_start: 0.5757 (OUTLIER) cc_final: 0.5355 (tmt170) outliers start: 33 outliers final: 6 residues processed: 91 average time/residue: 0.2713 time to fit residues: 31.3890 Evaluate side-chains 43 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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: 8.9990 chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 200 GLN A 313 GLN B 47 HIS B 138 HIS B 200 GLN B 313 GLN C 47 HIS C 138 HIS C 200 GLN C 313 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.032884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.026455 restraints weight = 77337.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.027260 restraints weight = 44934.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.027829 restraints weight = 30959.492| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 7750 Z= 0.275 Angle : 0.706 6.053 10552 Z= 0.384 Chirality : 0.041 0.150 1203 Planarity : 0.006 0.054 1296 Dihedral : 17.637 176.481 1323 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.47 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: -0.84 (0.27), residues: 921 helix: -0.39 (0.22), residues: 423 sheet: -1.02 (0.45), residues: 126 loop : -0.32 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS B 294 PHE 0.023 0.003 PHE B 259 TYR 0.024 0.002 TYR C 315 ARG 0.005 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 46 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.908 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1849 time to fit residues: 12.5612 Evaluate side-chains 31 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 31 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 28 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- 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** ** B 188 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 = 0.2870 r_free = 0.2870 target = 0.031871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.025322 restraints weight = 81885.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.026100 restraints weight = 47076.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.026645 restraints weight = 32415.456| |-----------------------------------------------------------------------------| r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7750 Z= 0.300 Angle : 0.675 6.577 10552 Z= 0.359 Chirality : 0.040 0.139 1203 Planarity : 0.005 0.044 1296 Dihedral : 17.096 166.443 1323 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.23 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: -0.13 (0.27), residues: 921 helix: 0.71 (0.25), residues: 408 sheet: -0.84 (0.46), residues: 126 loop : -0.56 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 294 PHE 0.012 0.002 PHE C 126 TYR 0.017 0.002 TYR B 216 ARG 0.007 0.001 ARG B 235 *********************** 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 37 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: B 46 PHE cc_start: 0.8528 (m-10) cc_final: 0.8305 (m-80) REVERT: B 211 MET cc_start: 0.8656 (mmm) cc_final: 0.8431 (mmm) REVERT: C 158 MET cc_start: 0.8546 (mtm) cc_final: 0.8005 (mpp) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1760 time to fit residues: 9.9393 Evaluate side-chains 31 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 62 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 92 optimal weight: 30.0000 chunk 56 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- 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 = 0.2873 r_free = 0.2873 target = 0.031876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.025315 restraints weight = 79127.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.026093 restraints weight = 45823.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.026659 restraints weight = 31596.772| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7750 Z= 0.223 Angle : 0.581 6.483 10552 Z= 0.311 Chirality : 0.038 0.134 1203 Planarity : 0.004 0.047 1296 Dihedral : 16.887 169.089 1323 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.47 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: 0.31 (0.27), residues: 921 helix: 1.17 (0.25), residues: 408 sheet: -0.50 (0.48), residues: 126 loop : -0.50 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 294 PHE 0.017 0.002 PHE C 86 TYR 0.012 0.001 TYR B 315 ARG 0.002 0.000 ARG B 130 *********************** 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 40 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8616 (m-10) cc_final: 0.8355 (m-80) REVERT: B 211 MET cc_start: 0.8794 (mmm) cc_final: 0.8521 (mmm) REVERT: C 158 MET cc_start: 0.8640 (mtm) cc_final: 0.7980 (mpp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1735 time to fit residues: 11.0211 Evaluate side-chains 32 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 26 optimal weight: 0.0270 chunk 39 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 overall best weight: 3.4046 ------------------------------------------------------------------------------- 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 = 0.2867 r_free = 0.2867 target = 0.031629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.025067 restraints weight = 79418.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.025842 restraints weight = 46224.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.026386 restraints weight = 31899.518| |-----------------------------------------------------------------------------| r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7750 Z= 0.206 Angle : 0.571 6.574 10552 Z= 0.303 Chirality : 0.038 0.137 1203 Planarity : 0.004 0.048 1296 Dihedral : 16.575 166.946 1323 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.80 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: 0.50 (0.27), residues: 921 helix: 1.41 (0.25), residues: 408 sheet: -0.60 (0.52), residues: 111 loop : -0.45 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 294 PHE 0.011 0.002 PHE B 86 TYR 0.016 0.001 TYR A 216 ARG 0.002 0.000 ARG C 170 *********************** 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 40 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8591 (m-10) cc_final: 0.8368 (m-80) REVERT: C 158 MET cc_start: 0.8706 (mtm) cc_final: 0.8189 (mpp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.2159 time to fit residues: 13.6690 Evaluate side-chains 31 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 90 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 = 0.2854 r_free = 0.2854 target = 0.031350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.024825 restraints weight = 80198.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.025583 restraints weight = 46741.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.026126 restraints weight = 32277.732| |-----------------------------------------------------------------------------| r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7750 Z= 0.243 Angle : 0.602 6.577 10552 Z= 0.318 Chirality : 0.039 0.160 1203 Planarity : 0.004 0.049 1296 Dihedral : 16.588 168.931 1323 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.23 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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 (0.27), residues: 921 helix: 1.36 (0.25), residues: 408 sheet: -0.94 (0.49), residues: 114 loop : -0.45 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 294 PHE 0.013 0.002 PHE B 46 TYR 0.015 0.001 TYR B 216 ARG 0.002 0.000 ARG A 235 *********************** 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 36 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.8589 (mmp) cc_final: 0.6422 (ttt) REVERT: C 158 MET cc_start: 0.8305 (mtm) cc_final: 0.7982 (mpp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1544 time to fit residues: 9.0652 Evaluate side-chains 29 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 37 optimal weight: 20.0000 chunk 43 optimal weight: 0.0670 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 overall best weight: 3.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.031506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.025057 restraints weight = 80366.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.025812 restraints weight = 46751.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.026355 restraints weight = 32248.488| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7750 Z= 0.195 Angle : 0.591 7.130 10552 Z= 0.306 Chirality : 0.038 0.140 1203 Planarity : 0.004 0.051 1296 Dihedral : 16.451 167.976 1323 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.13 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: 0.52 (0.27), residues: 921 helix: 1.51 (0.25), residues: 408 sheet: -0.93 (0.48), residues: 114 loop : -0.40 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 294 PHE 0.007 0.001 PHE B 129 TYR 0.017 0.001 TYR B 216 ARG 0.002 0.000 ARG A 235 *********************** 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 42 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8601 (m-10) cc_final: 0.8326 (m-80) REVERT: C 125 MET cc_start: 0.8766 (mmm) cc_final: 0.8495 (mmm) REVERT: C 158 MET cc_start: 0.8341 (mtm) cc_final: 0.8042 (mpp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1745 time to fit residues: 11.1671 Evaluate side-chains 32 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 90 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 0.0010 chunk 16 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.032143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.025535 restraints weight = 79406.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.026333 restraints weight = 46309.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.026904 restraints weight = 31948.761| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7750 Z= 0.152 Angle : 0.577 7.475 10552 Z= 0.299 Chirality : 0.039 0.139 1203 Planarity : 0.004 0.071 1296 Dihedral : 15.813 165.744 1323 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.91 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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 (0.27), residues: 921 helix: 1.47 (0.25), residues: 408 sheet: -0.51 (0.50), residues: 111 loop : -0.30 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 294 PHE 0.007 0.001 PHE B 129 TYR 0.013 0.001 TYR B 216 ARG 0.004 0.000 ARG B 235 *********************** 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 44 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.745 Fit side-chains REVERT: A 46 PHE cc_start: 0.8603 (m-10) cc_final: 0.8350 (m-80) REVERT: A 84 MET cc_start: 0.8759 (mmm) cc_final: 0.6689 (ttt) REVERT: C 125 MET cc_start: 0.8761 (mmm) cc_final: 0.8392 (mmm) REVERT: C 158 MET cc_start: 0.8321 (mtm) cc_final: 0.8022 (mpp) REVERT: C 211 MET cc_start: 0.8144 (ppp) cc_final: 0.7905 (ppp) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1444 time to fit residues: 10.1350 Evaluate side-chains 32 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 77 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 0.0070 chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 overall best weight: 2.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.032079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.025449 restraints weight = 82099.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.026233 restraints weight = 48074.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.026778 restraints weight = 33319.562| |-----------------------------------------------------------------------------| r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7750 Z= 0.188 Angle : 0.605 11.942 10552 Z= 0.308 Chirality : 0.039 0.146 1203 Planarity : 0.004 0.052 1296 Dihedral : 15.914 170.869 1323 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.47 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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 (0.27), residues: 921 helix: 1.49 (0.25), residues: 408 sheet: -0.65 (0.50), residues: 111 loop : -0.40 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 294 PHE 0.007 0.001 PHE B 129 TYR 0.017 0.001 TYR B 216 ARG 0.002 0.000 ARG C 170 *********************** 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 36 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.289 Fit side-chains REVERT: A 84 MET cc_start: 0.8745 (mmm) cc_final: 0.6752 (ttt) REVERT: A 125 MET cc_start: 0.8778 (mmm) cc_final: 0.8548 (mmm) REVERT: C 125 MET cc_start: 0.8721 (mmm) cc_final: 0.8434 (mmm) REVERT: C 158 MET cc_start: 0.8430 (mtm) cc_final: 0.8181 (mpp) REVERT: C 211 MET cc_start: 0.8107 (ppp) cc_final: 0.7896 (ppp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1695 time to fit residues: 9.9919 Evaluate side-chains 28 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.032033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.025430 restraints weight = 82281.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.026207 restraints weight = 48386.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.026761 restraints weight = 33709.264| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7750 Z= 0.187 Angle : 0.599 11.169 10552 Z= 0.306 Chirality : 0.039 0.151 1203 Planarity : 0.003 0.045 1296 Dihedral : 15.953 173.401 1323 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.58 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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 (0.27), residues: 921 helix: 1.62 (0.25), residues: 402 sheet: -0.88 (0.51), residues: 111 loop : -0.45 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 294 PHE 0.007 0.001 PHE B 129 TYR 0.011 0.001 TYR B 216 ARG 0.003 0.000 ARG A 310 ********************** 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 37 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.890 Fit side-chains REVERT: A 84 MET cc_start: 0.8685 (mmm) cc_final: 0.6689 (ttt) REVERT: C 125 MET cc_start: 0.8716 (mmm) cc_final: 0.8400 (mmm) REVERT: C 158 MET cc_start: 0.8365 (mtm) cc_final: 0.8091 (mpp) REVERT: C 211 MET cc_start: 0.8131 (ppp) cc_final: 0.7921 (ppp) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1701 time to fit residues: 9.9278 Evaluate side-chains 28 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.031779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.025157 restraints weight = 80242.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.025939 restraints weight = 47014.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.026498 restraints weight = 32597.676| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.5988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7750 Z= 0.223 Angle : 0.616 9.445 10552 Z= 0.317 Chirality : 0.039 0.152 1203 Planarity : 0.004 0.037 1296 Dihedral : 16.079 176.864 1323 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.80 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 0.37 (0.27), residues: 921 helix: 1.43 (0.25), residues: 408 sheet: -1.09 (0.51), residues: 111 loop : -0.51 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 294 PHE 0.007 0.001 PHE B 129 TYR 0.010 0.001 TYR C 315 ARG 0.002 0.000 ARG C 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2068.03 seconds wall clock time: 38 minutes 57.93 seconds (2337.93 seconds total)