Starting phenix.real_space_refine on Mon Mar 11 10:53:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc8_37434/03_2024/8wc8_37434_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc8_37434/03_2024/8wc8_37434.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc8_37434/03_2024/8wc8_37434_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc8_37434/03_2024/8wc8_37434_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc8_37434/03_2024/8wc8_37434_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc8_37434/03_2024/8wc8_37434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc8_37434/03_2024/8wc8_37434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc8_37434/03_2024/8wc8_37434_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc8_37434/03_2024/8wc8_37434_neut_updated.pdb" } resolution = 2.9 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= 0.003 sd= 0.098 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: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 55 5.16 5 C 5174 2.51 5 N 1372 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8062 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1695 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 218} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 7, 'PHE:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2333 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 119 Chain: "R" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2030 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 2, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 104 Chain: "S" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1666 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 70 Chain: "Y" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 328 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'VMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.37, per 1000 atoms: 0.54 Number of scatterers: 8062 At special positions: 0 Unit cell: (86.92, 117.26, 121.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 55 16.00 O 1460 8.00 N 1372 7.00 C 5174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.00 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.3 seconds 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 12 sheets defined 34.3% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 275 through 278 No H-bonds generated for 'chain 'A' and resid 275 through 278' Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 299 through 318 removed outlier: 4.280A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 357 Processing helix chain 'B' and resid 16 through 25 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'R' and resid 22 through 50 Processing helix chain 'R' and resid 57 through 85 removed outlier: 3.933A pdb=" N LEU R 61 " --> pdb=" O PRO R 57 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE R 62 " --> pdb=" O THR R 58 " (cutoff:3.500A) Proline residue: R 78 - end of helix Processing helix chain 'R' and resid 93 through 126 Processing helix chain 'R' and resid 131 through 134 No H-bonds generated for 'chain 'R' and resid 131 through 134' Processing helix chain 'R' and resid 137 through 160 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 169 through 178 Processing helix chain 'R' and resid 188 through 199 removed outlier: 3.722A pdb=" N VAL R 192 " --> pdb=" O LYS R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 226 Processing helix chain 'R' and resid 248 through 277 removed outlier: 4.051A pdb=" N CYS R 263 " --> pdb=" O VAL R 259 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP R 264 " --> pdb=" O PHE R 260 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 283 through 304 removed outlier: 3.679A pdb=" N GLY R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 309 through 314 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'Y' and resid 16 through 23 Processing helix chain 'Y' and resid 30 through 47 removed outlier: 4.700A pdb=" N LYS Y 46 " --> pdb=" O GLU Y 42 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLU Y 47 " --> pdb=" O ALA Y 43 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 326 through 330 removed outlier: 7.293A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.776A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.792A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.827A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.045A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.650A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.780A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.708A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 93 through 99 removed outlier: 5.558A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= L, first strand: chain 'S' and resid 243 through 245 removed outlier: 4.057A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1128 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: 2.42 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.41: 3495 1.41 - 1.65: 4668 1.65 - 1.89: 81 1.89 - 2.13: 1 2.13 - 2.37: 1 Bond restraints: 8246 Sorted by residual: bond pdb=" C GLY A 320 " pdb=" N GLY A 322 " ideal model delta sigma weight residual 1.331 2.375 -1.044 1.46e-02 4.69e+03 5.12e+03 bond pdb=" C LEU R 289 " pdb=" O LEU R 289 " ideal model delta sigma weight residual 1.237 1.169 0.067 1.17e-02 7.31e+03 3.33e+01 bond pdb=" C TYR R 294 " pdb=" O TYR R 294 " ideal model delta sigma weight residual 1.237 1.170 0.067 1.17e-02 7.31e+03 3.26e+01 bond pdb=" C PHE R 292 " pdb=" O PHE R 292 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.16e-02 7.43e+03 2.94e+01 bond pdb=" C PHE R 185 " pdb=" O PHE R 185 " ideal model delta sigma weight residual 1.234 1.170 0.064 1.22e-02 6.72e+03 2.75e+01 ... (remaining 8241 not shown) Histogram of bond angle deviations from ideal: 87.02 - 101.69: 28 101.69 - 116.36: 5457 116.36 - 131.04: 5716 131.04 - 145.71: 43 145.71 - 160.38: 1 Bond angle restraints: 11245 Sorted by residual: angle pdb=" O GLY A 320 " pdb=" C GLY A 320 " pdb=" N GLY A 322 " ideal model delta sigma weight residual 123.05 87.02 36.03 1.03e+00 9.43e-01 1.22e+03 angle pdb=" C GLY A 320 " pdb=" N GLY A 322 " pdb=" CA GLY A 322 " ideal model delta sigma weight residual 121.41 160.38 -38.97 1.96e+00 2.60e-01 3.95e+02 angle pdb=" N PRO S 236 " pdb=" CA PRO S 236 " pdb=" C PRO S 236 " ideal model delta sigma weight residual 112.47 97.97 14.50 2.06e+00 2.36e-01 4.96e+01 angle pdb=" C THR R 37 " pdb=" CA THR R 37 " pdb=" CB THR R 37 " ideal model delta sigma weight residual 110.96 100.82 10.14 1.54e+00 4.22e-01 4.33e+01 angle pdb=" CA GLY A 320 " pdb=" C GLY A 320 " pdb=" N GLY A 322 " ideal model delta sigma weight residual 114.28 123.01 -8.73 1.56e+00 4.11e-01 3.13e+01 ... (remaining 11240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4384 17.31 - 34.62: 315 34.62 - 51.93: 52 51.93 - 69.23: 5 69.23 - 86.54: 5 Dihedral angle restraints: 4761 sinusoidal: 1562 harmonic: 3199 Sorted by residual: dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 182 " pdb=" CB CYS R 182 " ideal model delta sinusoidal sigma weight residual -86.00 -162.39 76.39 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CA GLY A 320 " pdb=" C GLY A 320 " pdb=" N GLY A 322 " pdb=" CA GLY A 322 " ideal model delta harmonic sigma weight residual -180.00 -148.86 -31.14 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" C PHE R 292 " pdb=" N PHE R 292 " pdb=" CA PHE R 292 " pdb=" CB PHE R 292 " ideal model delta harmonic sigma weight residual -122.60 -136.35 13.75 0 2.50e+00 1.60e-01 3.03e+01 ... (remaining 4758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 1293 0.136 - 0.273: 10 0.273 - 0.409: 1 0.409 - 0.546: 2 0.546 - 0.682: 4 Chirality restraints: 1310 Sorted by residual: chirality pdb=" CA LEU R 289 " pdb=" N LEU R 289 " pdb=" C LEU R 289 " pdb=" CB LEU R 289 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA PHE R 292 " pdb=" N PHE R 292 " pdb=" C PHE R 292 " pdb=" CB PHE R 292 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA TRP R 291 " pdb=" N TRP R 291 " pdb=" C TRP R 291 " pdb=" CB TRP R 291 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.74e+00 ... (remaining 1307 not shown) Planarity restraints: 1417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 320 " -0.146 2.00e-02 2.50e+03 2.03e-01 4.13e+02 pdb=" C GLY A 320 " 0.347 2.00e-02 2.50e+03 pdb=" O GLY A 320 " -0.142 2.00e-02 2.50e+03 pdb=" N GLY A 322 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL S 199 " 0.055 5.00e-02 4.00e+02 8.42e-02 1.13e+01 pdb=" N PRO S 200 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO S 200 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO S 200 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 56 " -0.053 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO R 57 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO R 57 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 57 " -0.044 5.00e-02 4.00e+02 ... (remaining 1414 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1849 2.78 - 3.31: 7576 3.31 - 3.84: 13797 3.84 - 4.37: 15852 4.37 - 4.90: 28433 Nonbonded interactions: 67507 Sorted by model distance: nonbonded pdb=" O ARG S 67 " pdb=" OG1 THR S 84 " model vdw 2.252 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.258 2.440 nonbonded pdb=" O ARG A 250 " pdb=" OG1 THR A 251 " model vdw 2.288 2.440 nonbonded pdb=" O SER S 52 " pdb=" NH1 ARG S 72 " model vdw 2.295 2.520 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.297 2.440 ... (remaining 67502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.210 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: 3.990 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.440 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 0.013 1.044 8246 Z= 0.414 Angle : 0.854 38.971 11245 Z= 0.555 Chirality : 0.060 0.682 1310 Planarity : 0.008 0.203 1417 Dihedral : 12.498 86.543 2691 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.26 % Allowed : 0.26 % Favored : 99.48 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.02 (0.26), residues: 1077 helix: 2.57 (0.26), residues: 362 sheet: 0.07 (0.31), residues: 266 loop : -0.50 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 291 HIS 0.004 0.001 HIS B 225 PHE 0.036 0.002 PHE R 292 TYR 0.030 0.002 TYR S 235 ARG 0.008 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 0.865 Fit side-chains REVERT: A 17 LYS cc_start: 0.7752 (mtmt) cc_final: 0.7537 (mtmt) REVERT: R 218 LYS cc_start: 0.7698 (ttpp) cc_final: 0.7218 (pttp) outliers start: 2 outliers final: 0 residues processed: 157 average time/residue: 1.0892 time to fit residues: 182.1716 Evaluate side-chains 118 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 0.0000 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 220 GLN B 259 GLN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8246 Z= 0.173 Angle : 0.498 7.091 11245 Z= 0.262 Chirality : 0.041 0.159 1310 Planarity : 0.005 0.065 1417 Dihedral : 4.056 25.094 1177 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.48 % Allowed : 10.97 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.14 (0.26), residues: 1079 helix: 2.65 (0.26), residues: 368 sheet: 0.15 (0.31), residues: 265 loop : -0.47 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 291 HIS 0.004 0.001 HIS A 197 PHE 0.016 0.001 PHE A 189 TYR 0.012 0.001 TYR S 60 ARG 0.008 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 0.921 Fit side-chains REVERT: A 17 LYS cc_start: 0.7765 (mtmt) cc_final: 0.7532 (mtmt) REVERT: A 237 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8244 (mm) REVERT: B 52 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7623 (ptm160) REVERT: R 105 MET cc_start: 0.8278 (ttp) cc_final: 0.8030 (ttt) REVERT: R 218 LYS cc_start: 0.7666 (ttpp) cc_final: 0.7184 (pttp) outliers start: 19 outliers final: 7 residues processed: 141 average time/residue: 1.0700 time to fit residues: 161.1924 Evaluate side-chains 130 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain Y residue 38 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 0.0170 chunk 96 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.6824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 220 GLN B 259 GLN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN S 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8246 Z= 0.305 Angle : 0.552 6.624 11245 Z= 0.293 Chirality : 0.044 0.206 1310 Planarity : 0.005 0.060 1417 Dihedral : 4.246 22.765 1177 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.61 % Allowed : 14.23 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.95 (0.26), residues: 1079 helix: 2.55 (0.26), residues: 363 sheet: -0.09 (0.30), residues: 282 loop : -0.49 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 291 HIS 0.005 0.001 HIS A 324 PHE 0.015 0.002 PHE S 27 TYR 0.014 0.002 TYR A 30 ARG 0.006 0.001 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 0.823 Fit side-chains REVERT: A 17 LYS cc_start: 0.7771 (mtmt) cc_final: 0.7533 (mtmt) REVERT: B 52 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7806 (ptm160) REVERT: R 218 LYS cc_start: 0.7771 (ttpp) cc_final: 0.7224 (pttp) outliers start: 20 outliers final: 11 residues processed: 147 average time/residue: 1.0252 time to fit residues: 161.1687 Evaluate side-chains 138 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 220 GLN B 259 GLN R 41 ASN S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8246 Z= 0.228 Angle : 0.508 6.463 11245 Z= 0.270 Chirality : 0.042 0.178 1310 Planarity : 0.004 0.057 1417 Dihedral : 4.158 24.076 1177 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.79 % Allowed : 15.54 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.97 (0.26), residues: 1079 helix: 2.59 (0.26), residues: 363 sheet: -0.09 (0.30), residues: 282 loop : -0.50 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 211 HIS 0.008 0.001 HIS A 197 PHE 0.016 0.001 PHE A 189 TYR 0.013 0.001 TYR A 30 ARG 0.006 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 0.917 Fit side-chains REVERT: A 17 LYS cc_start: 0.7725 (mtmt) cc_final: 0.7480 (mtmt) REVERT: B 52 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7764 (ptm160) REVERT: R 158 MET cc_start: 0.7244 (ttt) cc_final: 0.6787 (ttm) REVERT: R 196 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.6753 (mpt) REVERT: R 218 LYS cc_start: 0.7770 (ttpp) cc_final: 0.7221 (pttp) outliers start: 29 outliers final: 17 residues processed: 151 average time/residue: 1.0544 time to fit residues: 170.3909 Evaluate side-chains 147 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 220 GLN S 186 GLN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8246 Z= 0.211 Angle : 0.504 7.092 11245 Z= 0.267 Chirality : 0.042 0.179 1310 Planarity : 0.004 0.060 1417 Dihedral : 4.108 25.217 1177 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.18 % Allowed : 16.58 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.97 (0.26), residues: 1079 helix: 2.60 (0.26), residues: 364 sheet: -0.04 (0.30), residues: 271 loop : -0.55 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.008 0.001 HIS A 197 PHE 0.016 0.001 PHE A 189 TYR 0.013 0.001 TYR R 79 ARG 0.006 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 0.869 Fit side-chains REVERT: A 17 LYS cc_start: 0.7736 (mtmt) cc_final: 0.7493 (mtmt) REVERT: B 52 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7789 (ptm160) REVERT: R 158 MET cc_start: 0.7224 (ttt) cc_final: 0.6763 (ttm) REVERT: R 196 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.6747 (mpt) REVERT: R 218 LYS cc_start: 0.7784 (ttpp) cc_final: 0.7229 (pttp) outliers start: 32 outliers final: 17 residues processed: 154 average time/residue: 0.9936 time to fit residues: 163.9423 Evaluate side-chains 144 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 261 GLN B 220 GLN S 186 GLN S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8246 Z= 0.278 Angle : 0.539 8.306 11245 Z= 0.285 Chirality : 0.043 0.204 1310 Planarity : 0.005 0.063 1417 Dihedral : 4.259 29.444 1177 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.44 % Allowed : 17.49 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.83 (0.26), residues: 1079 helix: 2.45 (0.26), residues: 365 sheet: -0.25 (0.29), residues: 283 loop : -0.50 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 211 HIS 0.008 0.001 HIS B 225 PHE 0.015 0.001 PHE A 189 TYR 0.014 0.001 TYR A 30 ARG 0.006 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 0.882 Fit side-chains REVERT: A 17 LYS cc_start: 0.7761 (mtmt) cc_final: 0.7517 (mtmt) REVERT: R 196 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.6815 (mpt) REVERT: R 218 LYS cc_start: 0.7805 (ttpp) cc_final: 0.7228 (pttp) outliers start: 34 outliers final: 20 residues processed: 155 average time/residue: 1.0770 time to fit residues: 178.1968 Evaluate side-chains 149 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.2980 chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 261 GLN B 220 GLN B 259 GLN S 171 ASN S 186 GLN S 194 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8246 Z= 0.183 Angle : 0.500 7.935 11245 Z= 0.267 Chirality : 0.042 0.210 1310 Planarity : 0.004 0.066 1417 Dihedral : 4.109 28.701 1177 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.26 % Allowed : 19.19 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.89 (0.26), residues: 1079 helix: 2.35 (0.26), residues: 373 sheet: -0.02 (0.30), residues: 269 loop : -0.53 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.009 0.001 HIS A 197 PHE 0.015 0.001 PHE A 189 TYR 0.014 0.001 TYR R 79 ARG 0.007 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 0.893 Fit side-chains REVERT: A 17 LYS cc_start: 0.7729 (mtmt) cc_final: 0.7472 (mtmt) REVERT: R 123 TYR cc_start: 0.8105 (m-80) cc_final: 0.7881 (m-80) REVERT: R 196 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.6822 (mpt) REVERT: R 218 LYS cc_start: 0.7798 (ttpp) cc_final: 0.7235 (pttp) outliers start: 25 outliers final: 18 residues processed: 151 average time/residue: 1.0299 time to fit residues: 166.4829 Evaluate side-chains 148 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 93 optimal weight: 0.0050 chunk 98 optimal weight: 2.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 261 GLN B 220 GLN S 186 GLN S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8246 Z= 0.189 Angle : 0.507 7.577 11245 Z= 0.273 Chirality : 0.042 0.216 1310 Planarity : 0.004 0.066 1417 Dihedral : 4.090 28.210 1177 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.13 % Allowed : 20.10 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.87 (0.26), residues: 1079 helix: 2.37 (0.26), residues: 372 sheet: -0.07 (0.30), residues: 268 loop : -0.53 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.009 0.001 HIS A 197 PHE 0.014 0.001 PHE A 189 TYR 0.012 0.001 TYR A 30 ARG 0.007 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 0.844 Fit side-chains REVERT: A 17 LYS cc_start: 0.7743 (mtmt) cc_final: 0.7487 (mtmt) REVERT: A 313 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7861 (mm) REVERT: R 123 TYR cc_start: 0.8099 (m-80) cc_final: 0.7882 (m-80) REVERT: R 196 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.6736 (mpt) REVERT: R 218 LYS cc_start: 0.7788 (ttpp) cc_final: 0.7231 (pttp) REVERT: S 245 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8036 (mp) outliers start: 24 outliers final: 18 residues processed: 148 average time/residue: 1.0260 time to fit residues: 162.4443 Evaluate side-chains 150 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 95 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 101 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 261 GLN B 220 GLN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8246 Z= 0.191 Angle : 0.513 7.663 11245 Z= 0.276 Chirality : 0.042 0.222 1310 Planarity : 0.005 0.072 1417 Dihedral : 4.089 27.109 1177 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.39 % Allowed : 20.10 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.85 (0.26), residues: 1079 helix: 2.35 (0.26), residues: 372 sheet: -0.12 (0.30), residues: 268 loop : -0.52 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 211 HIS 0.012 0.001 HIS A 197 PHE 0.013 0.001 PHE A 189 TYR 0.015 0.001 TYR R 79 ARG 0.008 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 0.881 Fit side-chains REVERT: A 17 LYS cc_start: 0.7747 (mtmt) cc_final: 0.7502 (mtmt) REVERT: A 313 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7824 (mm) REVERT: R 123 TYR cc_start: 0.8081 (m-80) cc_final: 0.7851 (m-80) REVERT: R 196 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.6734 (mpt) REVERT: R 218 LYS cc_start: 0.7783 (ttpp) cc_final: 0.7227 (pttp) REVERT: S 245 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8046 (mp) REVERT: Y 31 SER cc_start: 0.8594 (t) cc_final: 0.8002 (m) outliers start: 26 outliers final: 19 residues processed: 149 average time/residue: 1.0562 time to fit residues: 168.1658 Evaluate side-chains 151 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 70 optimal weight: 5.9990 chunk 106 optimal weight: 0.2980 chunk 98 optimal weight: 0.0000 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 261 GLN B 220 GLN S 186 GLN S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 8246 Z= 0.164 Angle : 0.508 8.033 11245 Z= 0.273 Chirality : 0.041 0.222 1310 Planarity : 0.005 0.074 1417 Dihedral : 4.020 24.665 1177 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.74 % Allowed : 20.63 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.87 (0.25), residues: 1079 helix: 2.38 (0.26), residues: 373 sheet: -0.04 (0.30), residues: 262 loop : -0.58 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 211 HIS 0.010 0.001 HIS A 197 PHE 0.016 0.001 PHE A 189 TYR 0.012 0.001 TYR A 30 ARG 0.007 0.000 ARG R 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 0.957 Fit side-chains REVERT: A 17 LYS cc_start: 0.7748 (mtmt) cc_final: 0.7489 (mtmt) REVERT: A 313 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7826 (mm) REVERT: R 123 TYR cc_start: 0.8020 (m-80) cc_final: 0.7791 (m-80) REVERT: R 196 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.6763 (mpt) REVERT: R 218 LYS cc_start: 0.7770 (ttpp) cc_final: 0.7215 (pttp) REVERT: Y 31 SER cc_start: 0.8579 (t) cc_final: 0.7993 (m) outliers start: 21 outliers final: 12 residues processed: 145 average time/residue: 1.1060 time to fit residues: 170.9539 Evaluate side-chains 141 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 234 GLN A 261 GLN B 183 HIS B 220 GLN S 186 GLN S 194 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.158945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122962 restraints weight = 9458.627| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.98 r_work: 0.3282 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8246 Z= 0.360 Angle : 0.592 7.146 11245 Z= 0.318 Chirality : 0.045 0.218 1310 Planarity : 0.005 0.071 1417 Dihedral : 4.424 31.527 1177 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.00 % Allowed : 21.02 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.71 (0.26), residues: 1079 helix: 2.32 (0.26), residues: 364 sheet: -0.38 (0.29), residues: 283 loop : -0.48 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP S 36 HIS 0.015 0.002 HIS A 197 PHE 0.021 0.002 PHE S 68 TYR 0.014 0.002 TYR A 30 ARG 0.008 0.001 ARG R 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3343.99 seconds wall clock time: 60 minutes 4.58 seconds (3604.58 seconds total)