Starting phenix.real_space_refine on Tue Mar 3 20:08:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ejx_31164/03_2026/7ejx_31164_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ejx_31164/03_2026/7ejx_31164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ejx_31164/03_2026/7ejx_31164_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ejx_31164/03_2026/7ejx_31164_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ejx_31164/03_2026/7ejx_31164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ejx_31164/03_2026/7ejx_31164.map" } resolution = 2.4 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 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= 0.020 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5321 2.51 5 N 1429 2.21 5 O 1527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8334 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1728 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1710 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2577 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1768 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Unusual residues: {'CLR': 3, 'J5F': 1} Classifications: {'undetermined': 4, 'water': 2} Link IDs: {None: 5} Time building chain proxies: 1.91, per 1000 atoms: 0.23 Number of scatterers: 8334 At special positions: 0 Unit cell: (89.64, 118.69, 125.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1527 8.00 N 1429 7.00 C 5321 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 213.7 milliseconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1982 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.5% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'R' and resid 37 through 59 removed outlier: 4.017A pdb=" N LEU R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA R 42 " --> pdb=" O TYR R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 64 removed outlier: 5.690A pdb=" N THR R 64 " --> pdb=" O LYS R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 85 removed outlier: 3.930A pdb=" N PHE R 69 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE R 70 " --> pdb=" O SER R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 144 Processing helix chain 'R' and resid 145 through 153 Processing helix chain 'R' and resid 154 through 175 Processing helix chain 'R' and resid 192 through 228 removed outlier: 3.802A pdb=" N VAL R 223 " --> pdb=" O VAL R 219 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL R 228 " --> pdb=" O LYS R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 309 removed outlier: 3.650A pdb=" N CYS R 290 " --> pdb=" O VAL R 286 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 314 through 338 removed outlier: 3.838A pdb=" N SER R 329 " --> pdb=" O CYS R 325 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA R 330 " --> pdb=" O CYS R 326 " (cutoff:3.500A) Proline residue: R 333 - end of helix Processing helix chain 'R' and resid 340 through 351 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.609A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.545A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.160A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.922A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 329 through 352 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.841A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.528A pdb=" N GLU G 58 " --> pdb=" O PRO G 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.086A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.587A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.397A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.641A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.983A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.359A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.791A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.180A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.759A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.728A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.179A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 4.056A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 4.056A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1323 1.31 - 1.43: 2309 1.43 - 1.56: 4792 1.56 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 8504 Sorted by residual: bond pdb=" C2 J5F R 401 " pdb=" N12 J5F R 401 " ideal model delta sigma weight residual 1.362 1.483 -0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" N LEU R 176 " pdb=" CA LEU R 176 " ideal model delta sigma weight residual 1.455 1.499 -0.044 9.60e-03 1.09e+04 2.10e+01 bond pdb=" N PRO B 236 " pdb=" CD PRO B 236 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.83e+01 bond pdb=" C PHE B 235 " pdb=" N PRO B 236 " ideal model delta sigma weight residual 1.334 1.390 -0.056 1.51e-02 4.39e+03 1.36e+01 bond pdb=" C SER R 304 " pdb=" O SER R 304 " ideal model delta sigma weight residual 1.237 1.195 0.041 1.17e-02 7.31e+03 1.25e+01 ... (remaining 8499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 11381 2.63 - 5.25: 138 5.25 - 7.88: 18 7.88 - 10.50: 4 10.50 - 13.13: 2 Bond angle restraints: 11543 Sorted by residual: angle pdb=" N SER R 307 " pdb=" CA SER R 307 " pdb=" C SER R 307 " ideal model delta sigma weight residual 112.54 103.34 9.20 1.22e+00 6.72e-01 5.68e+01 angle pdb=" N THR A 324 " pdb=" CA THR A 324 " pdb=" C THR A 324 " ideal model delta sigma weight residual 108.56 121.45 -12.89 1.74e+00 3.30e-01 5.49e+01 angle pdb=" CA LEU R 176 " pdb=" C LEU R 176 " pdb=" N PRO R 177 " ideal model delta sigma weight residual 117.95 122.35 -4.40 7.70e-01 1.69e+00 3.26e+01 angle pdb=" N ARG A 205 " pdb=" CA ARG A 205 " pdb=" C ARG A 205 " ideal model delta sigma weight residual 108.63 117.24 -8.61 1.60e+00 3.91e-01 2.89e+01 angle pdb=" N PRO R 178 " pdb=" CA PRO R 178 " pdb=" C PRO R 178 " ideal model delta sigma weight residual 113.40 120.37 -6.97 1.34e+00 5.57e-01 2.71e+01 ... (remaining 11538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4598 17.66 - 35.31: 442 35.31 - 52.97: 116 52.97 - 70.62: 24 70.62 - 88.28: 11 Dihedral angle restraints: 5191 sinusoidal: 2113 harmonic: 3078 Sorted by residual: dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C LEU B 198 " pdb=" N LEU B 198 " pdb=" CA LEU B 198 " pdb=" CB LEU B 198 " ideal model delta harmonic sigma weight residual -122.60 -113.91 -8.69 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 162.81 17.19 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1204 0.071 - 0.142: 105 0.142 - 0.213: 16 0.213 - 0.285: 5 0.285 - 0.356: 2 Chirality restraints: 1332 Sorted by residual: chirality pdb=" CA THR A 324 " pdb=" N THR A 324 " pdb=" C THR A 324 " pdb=" CB THR A 324 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA LEU R 281 " pdb=" N LEU R 281 " pdb=" C LEU R 281 " pdb=" CB LEU R 281 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA LEU B 198 " pdb=" N LEU B 198 " pdb=" C LEU B 198 " pdb=" CB LEU B 198 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1329 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 281 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.80e+00 pdb=" C LEU R 281 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU R 281 " 0.016 2.00e-02 2.50e+03 pdb=" N SER R 282 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 J5F R 401 " 0.020 2.00e-02 2.50e+03 1.53e-02 3.51e+00 pdb=" C2 J5F R 401 " -0.007 2.00e-02 2.50e+03 pdb=" C20 J5F R 401 " 0.002 2.00e-02 2.50e+03 pdb=" C3 J5F R 401 " 0.015 2.00e-02 2.50e+03 pdb=" N12 J5F R 401 " -0.027 2.00e-02 2.50e+03 pdb=" O1 J5F R 401 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 280 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C ARG R 280 " -0.028 2.00e-02 2.50e+03 pdb=" O ARG R 280 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU R 281 " 0.010 2.00e-02 2.50e+03 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 81 2.59 - 3.17: 7031 3.17 - 3.75: 12803 3.75 - 4.32: 18907 4.32 - 4.90: 31478 Nonbonded interactions: 70300 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.016 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.044 3.040 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.073 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.121 3.040 nonbonded pdb=" OG SER S 149 " pdb=" O LYS S 151 " model vdw 2.141 3.040 ... (remaining 70295 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 3.050 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.090 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:9.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.004 0.121 8506 Z= 0.263 Angle : 0.713 13.127 11547 Z= 0.420 Chirality : 0.047 0.356 1332 Planarity : 0.002 0.024 1438 Dihedral : 15.550 88.279 3203 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.25 % Allowed : 17.52 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.27), residues: 1045 helix: 3.06 (0.27), residues: 354 sheet: 0.94 (0.32), residues: 265 loop : -0.43 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.009 0.001 TYR S 103 PHE 0.009 0.001 PHE B 234 TRP 0.006 0.001 TRP R 322 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 8504) covalent geometry : angle 0.71294 (11543) SS BOND : bond 0.00220 ( 2) SS BOND : angle 0.74149 ( 4) hydrogen bonds : bond 0.18814 ( 448) hydrogen bonds : angle 6.64796 ( 1263) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.293 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: A 6 SER cc_start: 0.8274 (t) cc_final: 0.7999 (p) REVERT: A 17 LYS cc_start: 0.7391 (mmtt) cc_final: 0.7011 (mtpt) REVERT: A 24 ARG cc_start: 0.7748 (ttp-110) cc_final: 0.7538 (ttp80) REVERT: A 208 ARG cc_start: 0.7965 (ttm170) cc_final: 0.7333 (ttp-110) REVERT: A 269 ASN cc_start: 0.8514 (m110) cc_final: 0.8307 (m110) REVERT: B 44 GLN cc_start: 0.8459 (mm-40) cc_final: 0.7951 (mt0) REVERT: G 47 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7908 (mt-10) REVERT: S 120 SER cc_start: 0.8590 (t) cc_final: 0.8118 (p) REVERT: S 174 GLN cc_start: 0.8282 (tt0) cc_final: 0.8040 (tt0) outliers start: 11 outliers final: 5 residues processed: 146 average time/residue: 0.5943 time to fit residues: 91.8066 Evaluate side-chains 120 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0070 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 237 ASN B 340 ASN S 130 GLN S 167 GLN S 182 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.128852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.085901 restraints weight = 10480.395| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.22 r_work: 0.2913 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8506 Z= 0.129 Angle : 0.569 14.925 11547 Z= 0.290 Chirality : 0.042 0.269 1332 Planarity : 0.004 0.034 1438 Dihedral : 6.603 56.196 1390 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.53 % Allowed : 19.23 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.27), residues: 1045 helix: 3.20 (0.26), residues: 363 sheet: 0.60 (0.31), residues: 264 loop : -0.32 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 46 TYR 0.014 0.001 TYR S 178 PHE 0.010 0.001 PHE B 151 TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8504) covalent geometry : angle 0.56932 (11543) SS BOND : bond 0.00304 ( 2) SS BOND : angle 0.90622 ( 4) hydrogen bonds : bond 0.04271 ( 448) hydrogen bonds : angle 4.69979 ( 1263) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.311 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 196 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7605 (pp) REVERT: R 204 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7324 (tm-30) REVERT: A 6 SER cc_start: 0.8363 (t) cc_final: 0.7995 (p) REVERT: A 17 LYS cc_start: 0.7703 (mmtt) cc_final: 0.7132 (mtpt) REVERT: A 24 ARG cc_start: 0.7731 (ttp-110) cc_final: 0.7484 (ttp80) REVERT: A 208 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7290 (ttp-110) REVERT: B 44 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8034 (mt0) REVERT: G 17 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7237 (mm-30) REVERT: G 47 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8143 (mt-10) REVERT: S 93 MET cc_start: 0.8836 (tpp) cc_final: 0.8278 (tpp) outliers start: 31 outliers final: 15 residues processed: 142 average time/residue: 0.6321 time to fit residues: 94.9043 Evaluate side-chains 125 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 204 GLN Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 85 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 49 ASN R 332 ASN A 244 HIS B 75 GLN S 13 GLN S 39 GLN S 167 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.084580 restraints weight = 10261.289| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.24 r_work: 0.2859 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8506 Z= 0.138 Angle : 0.546 11.056 11547 Z= 0.281 Chirality : 0.042 0.233 1332 Planarity : 0.004 0.033 1438 Dihedral : 6.236 52.021 1386 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.44 % Allowed : 18.54 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.26), residues: 1045 helix: 3.29 (0.26), residues: 363 sheet: 0.30 (0.29), residues: 280 loop : -0.29 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 46 TYR 0.012 0.001 TYR S 178 PHE 0.013 0.001 PHE B 151 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8504) covalent geometry : angle 0.54542 (11543) SS BOND : bond 0.00423 ( 2) SS BOND : angle 1.18184 ( 4) hydrogen bonds : bond 0.03953 ( 448) hydrogen bonds : angle 4.46402 ( 1263) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.242 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 51 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7333 (ttm) REVERT: R 196 LEU cc_start: 0.8051 (tt) cc_final: 0.7575 (pp) REVERT: R 342 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: A 6 SER cc_start: 0.8395 (t) cc_final: 0.7976 (p) REVERT: A 17 LYS cc_start: 0.7578 (mmtt) cc_final: 0.7039 (mttp) REVERT: A 24 ARG cc_start: 0.7597 (ttp-110) cc_final: 0.7345 (ttp80) REVERT: A 51 LYS cc_start: 0.8880 (ttmm) cc_final: 0.8564 (pptt) REVERT: A 208 ARG cc_start: 0.8006 (ttm170) cc_final: 0.7137 (ttp-110) REVERT: B 44 GLN cc_start: 0.8509 (mm-40) cc_final: 0.7988 (mt0) REVERT: B 276 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8476 (p) REVERT: G 17 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7247 (mm-30) REVERT: G 47 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8071 (mt-10) REVERT: S 93 MET cc_start: 0.8745 (tpp) cc_final: 0.8259 (tpp) outliers start: 39 outliers final: 21 residues processed: 142 average time/residue: 0.5868 time to fit residues: 88.1797 Evaluate side-chains 135 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 51 MET Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 342 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 49 ASN A 244 HIS S 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.126825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.082949 restraints weight = 10470.176| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.21 r_work: 0.2860 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8506 Z= 0.170 Angle : 0.554 9.069 11547 Z= 0.288 Chirality : 0.042 0.203 1332 Planarity : 0.004 0.036 1438 Dihedral : 6.398 52.307 1386 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 5.01 % Allowed : 18.20 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.26), residues: 1045 helix: 3.27 (0.26), residues: 363 sheet: 0.23 (0.29), residues: 280 loop : -0.31 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 46 TYR 0.011 0.001 TYR S 178 PHE 0.014 0.001 PHE B 151 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 8504) covalent geometry : angle 0.55403 (11543) SS BOND : bond 0.00509 ( 2) SS BOND : angle 1.24482 ( 4) hydrogen bonds : bond 0.04014 ( 448) hydrogen bonds : angle 4.49349 ( 1263) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 0.328 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 196 LEU cc_start: 0.8061 (tt) cc_final: 0.7560 (pp) REVERT: A 6 SER cc_start: 0.8518 (t) cc_final: 0.8116 (p) REVERT: A 17 LYS cc_start: 0.7782 (mmtt) cc_final: 0.7287 (mttp) REVERT: A 24 ARG cc_start: 0.7780 (ttp-110) cc_final: 0.7528 (ttp80) REVERT: A 208 ARG cc_start: 0.8076 (ttm170) cc_final: 0.7277 (ttp-110) REVERT: B 44 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8095 (mt0) REVERT: B 276 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8565 (p) REVERT: G 17 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7298 (mm-30) REVERT: G 42 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: G 47 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8155 (mt-10) REVERT: S 19 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8232 (tttm) REVERT: S 93 MET cc_start: 0.8808 (tpp) cc_final: 0.8350 (tpp) outliers start: 44 outliers final: 22 residues processed: 145 average time/residue: 0.5580 time to fit residues: 86.0259 Evaluate side-chains 134 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 191 HIS A 204 GLN A 244 HIS B 75 GLN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.125729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.081781 restraints weight = 10372.441| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.19 r_work: 0.2841 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8506 Z= 0.197 Angle : 0.580 7.654 11547 Z= 0.303 Chirality : 0.043 0.241 1332 Planarity : 0.004 0.041 1438 Dihedral : 6.699 59.284 1386 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 5.23 % Allowed : 18.77 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.26), residues: 1045 helix: 3.11 (0.26), residues: 364 sheet: 0.19 (0.29), residues: 281 loop : -0.30 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 46 TYR 0.011 0.001 TYR S 103 PHE 0.015 0.002 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 8504) covalent geometry : angle 0.57930 (11543) SS BOND : bond 0.00575 ( 2) SS BOND : angle 1.18284 ( 4) hydrogen bonds : bond 0.04142 ( 448) hydrogen bonds : angle 4.56247 ( 1263) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 0.384 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 196 LEU cc_start: 0.8070 (tt) cc_final: 0.7568 (pp) REVERT: R 342 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: A 6 SER cc_start: 0.8546 (t) cc_final: 0.8114 (p) REVERT: A 17 LYS cc_start: 0.7796 (mmtt) cc_final: 0.7283 (mtpt) REVERT: A 24 ARG cc_start: 0.7783 (ttp-110) cc_final: 0.7541 (ttp80) REVERT: A 208 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7362 (ttp-110) REVERT: A 275 GLU cc_start: 0.8266 (tt0) cc_final: 0.8028 (tp30) REVERT: B 44 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8127 (mt0) REVERT: B 276 VAL cc_start: 0.8810 (OUTLIER) cc_final: 0.8589 (p) REVERT: G 17 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7277 (mm-30) REVERT: G 42 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: G 47 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8171 (mt-10) REVERT: S 19 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8208 (tttm) REVERT: S 93 MET cc_start: 0.8791 (tpp) cc_final: 0.8351 (tpp) outliers start: 46 outliers final: 22 residues processed: 148 average time/residue: 0.5639 time to fit residues: 88.5244 Evaluate side-chains 137 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 342 GLU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 19 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 21 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS G 59 ASN S 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.082096 restraints weight = 10324.030| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.21 r_work: 0.2847 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8506 Z= 0.183 Angle : 0.564 7.497 11547 Z= 0.296 Chirality : 0.042 0.172 1332 Planarity : 0.004 0.041 1438 Dihedral : 6.659 53.135 1386 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.44 % Allowed : 19.34 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.26), residues: 1045 helix: 3.12 (0.26), residues: 365 sheet: 0.18 (0.29), residues: 282 loop : -0.30 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 46 TYR 0.011 0.001 TYR S 103 PHE 0.015 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8504) covalent geometry : angle 0.56331 (11543) SS BOND : bond 0.00451 ( 2) SS BOND : angle 1.53500 ( 4) hydrogen bonds : bond 0.04034 ( 448) hydrogen bonds : angle 4.53631 ( 1263) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 0.321 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 196 LEU cc_start: 0.8050 (tt) cc_final: 0.7551 (pp) REVERT: R 342 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: A 6 SER cc_start: 0.8529 (t) cc_final: 0.8099 (p) REVERT: A 17 LYS cc_start: 0.7775 (mmtt) cc_final: 0.7214 (mttp) REVERT: A 24 ARG cc_start: 0.7786 (ttp-110) cc_final: 0.7542 (ttp80) REVERT: A 208 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7360 (ttp-110) REVERT: B 44 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8129 (mt0) REVERT: B 276 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8577 (p) REVERT: G 17 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7254 (mm-30) REVERT: G 42 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8048 (mt-10) REVERT: G 47 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8138 (mt-10) REVERT: S 19 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8224 (tttm) REVERT: S 93 MET cc_start: 0.8817 (tpp) cc_final: 0.8385 (tpp) outliers start: 39 outliers final: 23 residues processed: 136 average time/residue: 0.5908 time to fit residues: 85.2827 Evaluate side-chains 131 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 342 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 211 ASP Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 94 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.126827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.083158 restraints weight = 10433.950| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.20 r_work: 0.2868 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8506 Z= 0.151 Angle : 0.541 7.485 11547 Z= 0.284 Chirality : 0.041 0.160 1332 Planarity : 0.004 0.037 1438 Dihedral : 6.533 53.085 1386 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.32 % Allowed : 20.25 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.26), residues: 1045 helix: 3.17 (0.26), residues: 364 sheet: 0.19 (0.29), residues: 281 loop : -0.28 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 46 TYR 0.011 0.001 TYR S 178 PHE 0.014 0.001 PHE B 151 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8504) covalent geometry : angle 0.54084 (11543) SS BOND : bond 0.00408 ( 2) SS BOND : angle 1.34748 ( 4) hydrogen bonds : bond 0.03772 ( 448) hydrogen bonds : angle 4.43875 ( 1263) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.308 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 196 LEU cc_start: 0.8000 (tt) cc_final: 0.7498 (pp) REVERT: R 342 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: A 6 SER cc_start: 0.8484 (t) cc_final: 0.8083 (p) REVERT: A 17 LYS cc_start: 0.7775 (mmtt) cc_final: 0.7222 (mttp) REVERT: A 24 ARG cc_start: 0.7770 (ttp-110) cc_final: 0.7509 (ttp80) REVERT: A 208 ARG cc_start: 0.8153 (ttm170) cc_final: 0.7365 (ttp-110) REVERT: A 247 MET cc_start: 0.8249 (mtp) cc_final: 0.7959 (mtt) REVERT: B 44 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8127 (mt0) REVERT: B 276 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8564 (p) REVERT: G 17 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7259 (mm-30) REVERT: G 42 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: G 47 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8139 (mt-10) REVERT: S 19 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8213 (tttm) REVERT: S 93 MET cc_start: 0.8836 (tpp) cc_final: 0.8413 (tpp) outliers start: 38 outliers final: 24 residues processed: 134 average time/residue: 0.6341 time to fit residues: 89.7127 Evaluate side-chains 132 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 342 GLU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 211 ASP Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.084274 restraints weight = 10349.071| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.20 r_work: 0.2885 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8506 Z= 0.131 Angle : 0.527 7.983 11547 Z= 0.277 Chirality : 0.041 0.174 1332 Planarity : 0.004 0.038 1438 Dihedral : 6.388 50.964 1386 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.75 % Allowed : 21.27 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.26), residues: 1045 helix: 3.20 (0.26), residues: 366 sheet: 0.32 (0.29), residues: 276 loop : -0.26 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 46 TYR 0.012 0.001 TYR S 178 PHE 0.012 0.001 PHE B 151 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 191 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8504) covalent geometry : angle 0.52642 (11543) SS BOND : bond 0.00372 ( 2) SS BOND : angle 0.98184 ( 4) hydrogen bonds : bond 0.03585 ( 448) hydrogen bonds : angle 4.34326 ( 1263) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.322 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 341 GLU cc_start: 0.7972 (tp30) cc_final: 0.7492 (mm-30) REVERT: R 342 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: A 6 SER cc_start: 0.8450 (t) cc_final: 0.8082 (p) REVERT: A 17 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7208 (mttp) REVERT: A 24 ARG cc_start: 0.7741 (ttp-110) cc_final: 0.7477 (ttp80) REVERT: A 208 ARG cc_start: 0.8097 (ttm170) cc_final: 0.7290 (ttp-110) REVERT: B 44 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8123 (mt0) REVERT: G 17 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7250 (mm-30) REVERT: G 42 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: G 47 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8102 (mt-10) REVERT: S 19 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8199 (tttm) REVERT: S 93 MET cc_start: 0.8841 (tpp) cc_final: 0.8436 (tpp) outliers start: 33 outliers final: 23 residues processed: 134 average time/residue: 0.6476 time to fit residues: 91.7158 Evaluate side-chains 130 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 342 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 211 ASP Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.083708 restraints weight = 10440.730| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.21 r_work: 0.2872 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8506 Z= 0.146 Angle : 0.545 8.477 11547 Z= 0.284 Chirality : 0.041 0.173 1332 Planarity : 0.004 0.035 1438 Dihedral : 6.400 51.350 1386 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.07 % Allowed : 21.50 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.26), residues: 1045 helix: 3.16 (0.26), residues: 366 sheet: 0.28 (0.29), residues: 277 loop : -0.26 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 46 TYR 0.011 0.001 TYR S 178 PHE 0.013 0.001 PHE B 151 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS R 191 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8504) covalent geometry : angle 0.54459 (11543) SS BOND : bond 0.00325 ( 2) SS BOND : angle 1.00249 ( 4) hydrogen bonds : bond 0.03705 ( 448) hydrogen bonds : angle 4.37921 ( 1263) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.284 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 341 GLU cc_start: 0.7916 (tp30) cc_final: 0.7473 (mm-30) REVERT: R 342 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: A 6 SER cc_start: 0.8474 (t) cc_final: 0.8101 (p) REVERT: A 17 LYS cc_start: 0.7745 (mmtt) cc_final: 0.7187 (mttp) REVERT: A 24 ARG cc_start: 0.7749 (ttp-110) cc_final: 0.7488 (ttp80) REVERT: A 208 ARG cc_start: 0.8094 (ttm170) cc_final: 0.7285 (ttp-110) REVERT: A 247 MET cc_start: 0.8225 (mtp) cc_final: 0.7929 (mtt) REVERT: A 275 GLU cc_start: 0.8169 (tp30) cc_final: 0.7958 (mm-30) REVERT: B 44 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8113 (mt0) REVERT: G 17 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: G 42 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7975 (mt-10) REVERT: G 47 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8115 (mt-10) REVERT: S 19 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8194 (tttm) REVERT: S 93 MET cc_start: 0.8846 (tpp) cc_final: 0.8455 (tpp) outliers start: 27 outliers final: 22 residues processed: 126 average time/residue: 0.6759 time to fit residues: 89.6870 Evaluate side-chains 128 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 342 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 211 ASP Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.128082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.084670 restraints weight = 10374.847| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.20 r_work: 0.2890 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8506 Z= 0.132 Angle : 0.536 8.617 11547 Z= 0.279 Chirality : 0.041 0.172 1332 Planarity : 0.004 0.036 1438 Dihedral : 6.290 50.770 1386 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.41 % Allowed : 21.50 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.26), residues: 1045 helix: 3.21 (0.26), residues: 366 sheet: 0.26 (0.29), residues: 280 loop : -0.23 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 46 TYR 0.011 0.001 TYR S 178 PHE 0.012 0.001 PHE B 151 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 191 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8504) covalent geometry : angle 0.53563 (11543) SS BOND : bond 0.00305 ( 2) SS BOND : angle 0.84241 ( 4) hydrogen bonds : bond 0.03566 ( 448) hydrogen bonds : angle 4.31829 ( 1263) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.314 Fit side-chains TARDY: cannot create tardy model for: "PHE A 354 " (corrupted residue). Skipping it. REVERT: R 220 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7528 (mtm-85) REVERT: R 341 GLU cc_start: 0.7942 (tp30) cc_final: 0.7501 (mm-30) REVERT: R 342 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: A 6 SER cc_start: 0.8452 (t) cc_final: 0.8121 (p) REVERT: A 17 LYS cc_start: 0.7745 (mmtt) cc_final: 0.7189 (mttp) REVERT: A 24 ARG cc_start: 0.7739 (ttp-110) cc_final: 0.7477 (ttp80) REVERT: A 208 ARG cc_start: 0.8097 (ttm170) cc_final: 0.7290 (ttp-110) REVERT: A 247 MET cc_start: 0.8228 (mtp) cc_final: 0.7927 (mtt) REVERT: B 44 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8115 (mt0) REVERT: B 217 MET cc_start: 0.8717 (ptt) cc_final: 0.8302 (pmt) REVERT: B 276 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8539 (p) REVERT: G 17 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7234 (mm-30) REVERT: G 42 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: G 47 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8108 (mt-10) REVERT: S 19 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8197 (tttm) REVERT: S 93 MET cc_start: 0.8849 (tpp) cc_final: 0.8473 (tpp) outliers start: 30 outliers final: 21 residues processed: 127 average time/residue: 0.6636 time to fit residues: 88.8858 Evaluate side-chains 127 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 220 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 342 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 211 ASP Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 94 optimal weight: 0.0570 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 76 optimal weight: 0.0270 chunk 99 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.085212 restraints weight = 10323.944| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.23 r_work: 0.2911 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8506 Z= 0.119 Angle : 0.527 8.961 11547 Z= 0.274 Chirality : 0.040 0.173 1332 Planarity : 0.004 0.038 1438 Dihedral : 6.186 49.922 1386 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.53 % Allowed : 21.62 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.26), residues: 1045 helix: 3.25 (0.26), residues: 365 sheet: 0.19 (0.29), residues: 282 loop : -0.21 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 46 TYR 0.011 0.001 TYR S 178 PHE 0.011 0.001 PHE B 151 TRP 0.016 0.001 TRP R 84 HIS 0.005 0.001 HIS R 191 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8504) covalent geometry : angle 0.52691 (11543) SS BOND : bond 0.00265 ( 2) SS BOND : angle 0.73616 ( 4) hydrogen bonds : bond 0.03447 ( 448) hydrogen bonds : angle 4.26510 ( 1263) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3886.94 seconds wall clock time: 66 minutes 48.17 seconds (4008.17 seconds total)