Starting phenix.real_space_refine on Wed Jan 15 18:05:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjd_60141/01_2025/8zjd_60141.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjd_60141/01_2025/8zjd_60141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zjd_60141/01_2025/8zjd_60141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjd_60141/01_2025/8zjd_60141.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjd_60141/01_2025/8zjd_60141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjd_60141/01_2025/8zjd_60141.cif" } resolution = 3.06 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= 0.007 sd= 0.058 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 55 5.16 5 C 5617 2.51 5 N 1521 2.21 5 O 1627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8820 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2204 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 268} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 94 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2555 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "S" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1741 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 386 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 50} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1840 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 5.42, per 1000 atoms: 0.61 Number of scatterers: 8820 At special positions: 0 Unit cell: (97.09, 115.34, 129.21, 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 55 16.00 O 1627 8.00 N 1521 7.00 C 5617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 191 " distance=2.33 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: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 13 sheets defined 40.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'R' and resid 43 through 69 removed outlier: 3.823A pdb=" N LEU R 47 " --> pdb=" O TRP R 43 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG R 69 " --> pdb=" O TYR R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 94 Processing helix chain 'R' and resid 95 through 103 removed outlier: 3.624A pdb=" N ALA R 100 " --> pdb=" O VAL R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 146 Processing helix chain 'R' and resid 148 through 152 removed outlier: 3.571A pdb=" N HIS R 152 " --> pdb=" O ARG R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 174 Processing helix chain 'R' and resid 175 through 180 removed outlier: 4.307A pdb=" N ALA R 179 " --> pdb=" O ALA R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 213 Processing helix chain 'R' and resid 213 through 234 Processing helix chain 'R' and resid 244 through 289 removed outlier: 5.285A pdb=" N ALA R 256 " --> pdb=" O GLU R 252 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL R 257 " --> pdb=" O ARG R 253 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 298 through 324 removed outlier: 3.729A pdb=" N SER R 316 " --> pdb=" O SER R 312 " (cutoff:3.500A) Proline residue: R 320 - end of helix Processing helix chain 'R' and resid 327 through 337 Processing helix chain 'L' and resid 212 through 216 Processing helix chain 'B' and resid 10 through 31 removed outlier: 4.435A pdb=" N GLN B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.781A pdb=" N ILE B 275 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 31 Processing helix chain 'S' and resid 52 through 55 Processing helix chain 'S' and resid 61 through 64 removed outlier: 3.588A pdb=" N LYS S 64 " --> pdb=" O ASP S 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 61 through 64' Processing helix chain 'S' and resid 73 through 75 No H-bonds generated for 'chain 'S' and resid 73 through 75' Processing helix chain 'S' and resid 86 through 90 Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.580A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 43 Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.603A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 214 through 223 removed outlier: 4.427A pdb=" N ILE A 219 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N HIS A 220 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 277 through 285 Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 337 through 358 Processing sheet with id=AA1, first strand: chain 'R' and resid 181 through 184 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 57 removed outlier: 4.171A pdb=" N PHE B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 336 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS B 322 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.763A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.787A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 4.388A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.798A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA B 213 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR B 226 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 215 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET B 222 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.620A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 282 through 283 removed outlier: 3.781A pdb=" N CYS B 299 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 2 through 5 removed outlier: 5.411A pdb=" N GLY S 15 " --> pdb=" O SER S 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 9 through 11 removed outlier: 6.951A pdb=" N MET S 33 " --> pdb=" O TYR S 49 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR S 49 " --> pdb=" O MET S 33 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP S 35 " --> pdb=" O VAL S 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.714A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 192 through 197 removed outlier: 9.849A pdb=" N SER A 227 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS A 35 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N MET A 229 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A 37 " --> pdb=" O MET A 229 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU A 231 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 39 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N ALA A 233 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE A 228 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N PHE A 274 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE A 230 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASN A 276 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL A 232 " --> pdb=" O ASN A 276 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1308 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: 2.58 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1432 1.31 - 1.44: 2527 1.44 - 1.56: 4973 1.56 - 1.69: 1 1.69 - 1.82: 79 Bond restraints: 9012 Sorted by residual: bond pdb=" CA VAL R 138 " pdb=" C VAL R 138 " ideal model delta sigma weight residual 1.525 1.465 0.060 1.27e-02 6.20e+03 2.25e+01 bond pdb=" C ASP R 139 " pdb=" O ASP R 139 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.19e-02 7.06e+03 1.61e+01 bond pdb=" CA LYS A 356 " pdb=" C LYS A 356 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.40e-02 5.10e+03 1.59e+01 bond pdb=" C ARG R 140 " pdb=" O ARG R 140 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.25e-02 6.40e+03 1.48e+01 bond pdb=" CA ASP R 139 " pdb=" C ASP R 139 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.29e-02 6.01e+03 1.46e+01 ... (remaining 9007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11956 1.92 - 3.83: 246 3.83 - 5.75: 32 5.75 - 7.67: 5 7.67 - 9.59: 5 Bond angle restraints: 12244 Sorted by residual: angle pdb=" N ASP B 81 " pdb=" CA ASP B 81 " pdb=" C ASP B 81 " ideal model delta sigma weight residual 113.16 103.83 9.33 1.24e+00 6.50e-01 5.67e+01 angle pdb=" N TYR A 358 " pdb=" CA TYR A 358 " pdb=" C TYR A 358 " ideal model delta sigma weight residual 112.97 106.95 6.02 1.06e+00 8.90e-01 3.22e+01 angle pdb=" N VAL R 249 " pdb=" CA VAL R 249 " pdb=" C VAL R 249 " ideal model delta sigma weight residual 110.74 105.63 5.11 9.10e-01 1.21e+00 3.15e+01 angle pdb=" N VAL R 138 " pdb=" CA VAL R 138 " pdb=" C VAL R 138 " ideal model delta sigma weight residual 113.16 106.38 6.78 1.49e+00 4.50e-01 2.07e+01 angle pdb=" N ASP R 139 " pdb=" CA ASP R 139 " pdb=" C ASP R 139 " ideal model delta sigma weight residual 111.40 105.88 5.52 1.22e+00 6.72e-01 2.05e+01 ... (remaining 12239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4796 17.79 - 35.57: 397 35.57 - 53.36: 100 53.36 - 71.15: 14 71.15 - 88.94: 10 Dihedral angle restraints: 5317 sinusoidal: 1999 harmonic: 3318 Sorted by residual: dihedral pdb=" CB CYS R 115 " pdb=" SG CYS R 115 " pdb=" SG CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sinusoidal sigma weight residual 93.00 4.06 88.94 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CA GLN S 12 " pdb=" C GLN S 12 " pdb=" N PRO S 13 " pdb=" CA PRO S 13 " ideal model delta harmonic sigma weight residual -180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LYS B 83 " pdb=" C LYS B 83 " pdb=" N LEU B 84 " pdb=" CA LEU B 84 " ideal model delta harmonic sigma weight residual 180.00 160.47 19.53 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 5314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1300 0.091 - 0.182: 84 0.182 - 0.272: 6 0.272 - 0.363: 2 0.363 - 0.454: 1 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA ASN A 359 " pdb=" N ASN A 359 " pdb=" C ASN A 359 " pdb=" CB ASN A 359 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CA VAL R 249 " pdb=" N VAL R 249 " pdb=" C VAL R 249 " pdb=" CB VAL R 249 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA LEU R 245 " pdb=" N LEU R 245 " pdb=" C LEU R 245 " pdb=" CB LEU R 245 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1390 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET R 136 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.67e+00 pdb=" C MET R 136 " 0.037 2.00e-02 2.50e+03 pdb=" O MET R 136 " -0.013 2.00e-02 2.50e+03 pdb=" N SER R 137 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 256 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C ALA R 256 " -0.036 2.00e-02 2.50e+03 pdb=" O ALA R 256 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL R 257 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 338 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C ASP B 338 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP B 338 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B 339 " -0.011 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 839 2.74 - 3.28: 9025 3.28 - 3.82: 14756 3.82 - 4.36: 17644 4.36 - 4.90: 31154 Nonbonded interactions: 73418 Sorted by model distance: nonbonded pdb=" OH TYR A 237 " pdb=" OG SER A 288 " model vdw 2.200 3.040 nonbonded pdb=" O ARG R 297 " pdb=" OH TYR L 211 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR B 150 " pdb=" OD2 ASP B 191 " model vdw 2.302 3.040 nonbonded pdb=" O VAL R 96 " pdb=" OG1 THR R 99 " model vdw 2.308 3.040 nonbonded pdb=" O ASP B 210 " pdb=" OD1 ASP B 210 " model vdw 2.322 3.040 ... (remaining 73413 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.820 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 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 0.060 9012 Z= 0.284 Angle : 0.674 9.587 12244 Z= 0.398 Chirality : 0.046 0.454 1393 Planarity : 0.004 0.050 1557 Dihedral : 14.501 85.750 3172 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.54 % Allowed : 14.67 % Favored : 84.79 % 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: 0.74 (0.26), residues: 1121 helix: 1.57 (0.26), residues: 417 sheet: 0.27 (0.32), residues: 278 loop : -0.34 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.002 0.001 HIS B 147 PHE 0.016 0.001 PHE L 220 TYR 0.015 0.001 TYR R 65 ARG 0.010 0.000 ARG L 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 156 time to evaluate : 1.057 Fit side-chains REVERT: R 62 LEU cc_start: 0.8167 (mp) cc_final: 0.7961 (mp) REVERT: R 71 LYS cc_start: 0.6979 (mmmt) cc_final: 0.6734 (tptp) REVERT: R 78 ASN cc_start: 0.8894 (m110) cc_final: 0.8665 (m110) REVERT: R 253 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6590 (ttp-170) REVERT: R 315 ASN cc_start: 0.8264 (t0) cc_final: 0.8042 (t0) REVERT: B 222 MET cc_start: 0.7156 (ptt) cc_final: 0.6885 (ptm) REVERT: B 273 ASN cc_start: 0.8509 (m110) cc_final: 0.8171 (m110) REVERT: S 45 GLU cc_start: 0.7652 (tt0) cc_final: 0.7443 (tt0) REVERT: G 31 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8693 (tptt) REVERT: G 46 GLU cc_start: 0.8252 (mp0) cc_final: 0.7867 (mp0) outliers start: 5 outliers final: 3 residues processed: 160 average time/residue: 0.2673 time to fit residues: 56.8182 Evaluate side-chains 130 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 CYS Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 190 TYR Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 78 ASN R 83 ASN B 273 ASN S 38 GLN S 112 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.153165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.109506 restraints weight = 12253.721| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.90 r_work: 0.3259 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9012 Z= 0.288 Angle : 0.612 6.732 12244 Z= 0.323 Chirality : 0.044 0.156 1393 Planarity : 0.004 0.052 1557 Dihedral : 5.381 57.918 1250 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.27 % Allowed : 15.10 % Favored : 82.63 % 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: 0.81 (0.25), residues: 1121 helix: 1.78 (0.25), residues: 409 sheet: 0.24 (0.31), residues: 285 loop : -0.40 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.004 0.001 HIS B 147 PHE 0.012 0.001 PHE S 28 TYR 0.015 0.002 TYR B 64 ARG 0.005 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.968 Fit side-chains REVERT: R 71 LYS cc_start: 0.6964 (mmmt) cc_final: 0.6659 (tptp) REVERT: R 212 LEU cc_start: 0.8287 (mp) cc_final: 0.8016 (mp) REVERT: R 253 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6444 (ttp-170) REVERT: R 305 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8094 (tmtt) REVERT: B 134 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7779 (ttt90) REVERT: B 135 GLU cc_start: 0.8746 (mp0) cc_final: 0.8417 (mp0) REVERT: B 222 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6971 (ptm) REVERT: B 273 ASN cc_start: 0.8675 (m-40) cc_final: 0.8329 (m110) REVERT: S 81 GLN cc_start: 0.7799 (tp-100) cc_final: 0.7561 (tp-100) REVERT: G 31 LYS cc_start: 0.8990 (ttpt) cc_final: 0.8597 (tptt) REVERT: G 46 GLU cc_start: 0.8316 (mp0) cc_final: 0.8009 (mp0) outliers start: 21 outliers final: 10 residues processed: 150 average time/residue: 0.2318 time to fit residues: 47.8943 Evaluate side-chains 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 190 TYR Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 305 LYS Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain L residue 214 ASN Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 213 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 78 optimal weight: 0.2980 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 83 ASN B 300 ASN S 38 GLN S 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.154682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111998 restraints weight = 12388.661| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.90 r_work: 0.3283 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9012 Z= 0.171 Angle : 0.537 5.830 12244 Z= 0.280 Chirality : 0.041 0.138 1393 Planarity : 0.004 0.048 1557 Dihedral : 5.089 53.104 1249 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.70 % Allowed : 14.24 % Favored : 83.06 % 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: 0.92 (0.26), residues: 1121 helix: 1.98 (0.25), residues: 410 sheet: 0.27 (0.32), residues: 275 loop : -0.42 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 344 HIS 0.002 0.001 HIS R 309 PHE 0.010 0.001 PHE B 246 TYR 0.021 0.001 TYR A 237 ARG 0.004 0.000 ARG S 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: R 71 LYS cc_start: 0.7021 (mmmt) cc_final: 0.6649 (tptp) REVERT: R 212 LEU cc_start: 0.8123 (mp) cc_final: 0.7878 (mp) REVERT: R 253 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6321 (ttp-170) REVERT: B 222 MET cc_start: 0.7317 (ptt) cc_final: 0.7035 (ptm) REVERT: B 273 ASN cc_start: 0.8687 (m-40) cc_final: 0.8446 (m110) REVERT: S 66 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7425 (ttp-110) REVERT: S 81 GLN cc_start: 0.7740 (tp-100) cc_final: 0.7411 (tp-100) REVERT: S 86 ARG cc_start: 0.7334 (mtp85) cc_final: 0.6833 (mtm-85) REVERT: S 194 ASN cc_start: 0.6586 (m110) cc_final: 0.6354 (m110) REVERT: G 31 LYS cc_start: 0.8926 (ttpt) cc_final: 0.8502 (tptt) REVERT: G 46 GLU cc_start: 0.8268 (mp0) cc_final: 0.7996 (mp0) outliers start: 25 outliers final: 13 residues processed: 161 average time/residue: 0.2026 time to fit residues: 45.3239 Evaluate side-chains 143 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 190 TYR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 314 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 24 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 38 GLN S 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.154325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.111704 restraints weight = 12227.866| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.88 r_work: 0.3279 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9012 Z= 0.193 Angle : 0.540 7.036 12244 Z= 0.280 Chirality : 0.041 0.137 1393 Planarity : 0.004 0.055 1557 Dihedral : 4.952 49.096 1249 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.59 % Allowed : 16.40 % Favored : 81.01 % 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: 0.88 (0.25), residues: 1121 helix: 2.02 (0.25), residues: 410 sheet: 0.20 (0.31), residues: 279 loop : -0.50 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.006 0.001 HIS R 181 PHE 0.010 0.001 PHE B 246 TYR 0.013 0.001 TYR R 65 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: R 71 LYS cc_start: 0.7021 (mmmt) cc_final: 0.6698 (tptp) REVERT: R 78 ASN cc_start: 0.8723 (m-40) cc_final: 0.8486 (m110) REVERT: R 212 LEU cc_start: 0.8222 (mp) cc_final: 0.7934 (mp) REVERT: R 253 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6321 (ttp-170) REVERT: B 222 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.7024 (ptm) REVERT: B 273 ASN cc_start: 0.8670 (m-40) cc_final: 0.8411 (m110) REVERT: B 274 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7662 (pp) REVERT: S 66 ARG cc_start: 0.7738 (mtm-85) cc_final: 0.7380 (ttp-110) REVERT: S 86 ARG cc_start: 0.7360 (mtp85) cc_final: 0.6853 (mtm-85) REVERT: G 46 GLU cc_start: 0.8266 (mp0) cc_final: 0.7978 (mp0) outliers start: 24 outliers final: 17 residues processed: 156 average time/residue: 0.2132 time to fit residues: 46.2046 Evaluate side-chains 152 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 190 TYR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 213 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 20 optimal weight: 0.0020 chunk 18 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 83 ASN S 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.156347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.113825 restraints weight = 12266.477| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.90 r_work: 0.3306 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9012 Z= 0.151 Angle : 0.520 9.227 12244 Z= 0.267 Chirality : 0.041 0.135 1393 Planarity : 0.004 0.051 1557 Dihedral : 4.734 48.407 1249 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.37 % Allowed : 17.15 % Favored : 80.47 % 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: 0.98 (0.26), residues: 1121 helix: 2.16 (0.25), residues: 409 sheet: 0.18 (0.32), residues: 275 loop : -0.44 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.005 0.001 HIS R 181 PHE 0.009 0.001 PHE B 246 TYR 0.014 0.001 TYR A 237 ARG 0.006 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 71 LYS cc_start: 0.6998 (mmmt) cc_final: 0.6665 (tptp) REVERT: R 78 ASN cc_start: 0.8732 (m-40) cc_final: 0.8512 (m110) REVERT: R 212 LEU cc_start: 0.8086 (mp) cc_final: 0.7802 (mp) REVERT: R 253 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6358 (ttp-110) REVERT: B 222 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7162 (ptm) REVERT: B 273 ASN cc_start: 0.8650 (m-40) cc_final: 0.8335 (m110) REVERT: B 274 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7720 (pp) REVERT: S 86 ARG cc_start: 0.7380 (mtp85) cc_final: 0.6721 (mtt-85) REVERT: G 46 GLU cc_start: 0.8258 (mp0) cc_final: 0.7964 (mp0) outliers start: 22 outliers final: 16 residues processed: 163 average time/residue: 0.2165 time to fit residues: 49.1664 Evaluate side-chains 155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 261 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 0.0670 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 85 optimal weight: 0.0870 chunk 50 optimal weight: 4.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 181 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.155709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112848 restraints weight = 12366.259| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.95 r_work: 0.3293 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9012 Z= 0.170 Angle : 0.525 7.549 12244 Z= 0.270 Chirality : 0.041 0.137 1393 Planarity : 0.004 0.055 1557 Dihedral : 4.570 47.831 1247 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.59 % Allowed : 16.29 % Favored : 81.12 % 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: 1.00 (0.25), residues: 1121 helix: 2.21 (0.25), residues: 409 sheet: 0.19 (0.32), residues: 269 loop : -0.46 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.004 0.001 HIS R 181 PHE 0.009 0.001 PHE R 282 TYR 0.014 0.001 TYR R 190 ARG 0.007 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: R 71 LYS cc_start: 0.6985 (mmmt) cc_final: 0.6650 (tptp) REVERT: R 212 LEU cc_start: 0.8143 (mp) cc_final: 0.7864 (mp) REVERT: R 253 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6287 (ttp-110) REVERT: B 222 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7185 (ptm) REVERT: B 273 ASN cc_start: 0.8665 (m-40) cc_final: 0.8405 (m110) REVERT: B 274 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7674 (pp) REVERT: S 66 ARG cc_start: 0.7674 (mtm-85) cc_final: 0.7422 (ttp-110) REVERT: S 86 ARG cc_start: 0.7418 (mtp85) cc_final: 0.6742 (mtt-85) REVERT: G 46 GLU cc_start: 0.8264 (mp0) cc_final: 0.7970 (mp0) outliers start: 24 outliers final: 18 residues processed: 162 average time/residue: 0.2123 time to fit residues: 47.8487 Evaluate side-chains 159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 261 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 83 ASN R 181 HIS B 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.152605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.109284 restraints weight = 12507.948| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.95 r_work: 0.3227 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 9012 Z= 0.311 Angle : 0.597 9.798 12244 Z= 0.307 Chirality : 0.043 0.163 1393 Planarity : 0.004 0.053 1557 Dihedral : 4.810 46.960 1247 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.80 % Allowed : 17.26 % Favored : 79.94 % 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 (0.25), residues: 1121 helix: 2.10 (0.25), residues: 406 sheet: 0.01 (0.31), residues: 284 loop : -0.52 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 35 HIS 0.004 0.001 HIS R 309 PHE 0.013 0.001 PHE S 28 TYR 0.020 0.002 TYR B 64 ARG 0.006 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 71 LYS cc_start: 0.6932 (mmmt) cc_final: 0.6512 (tptp) REVERT: R 212 LEU cc_start: 0.8388 (mp) cc_final: 0.8142 (mp) REVERT: R 253 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6284 (ttp-110) REVERT: B 222 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7078 (ptm) REVERT: B 225 GLN cc_start: 0.8401 (mp10) cc_final: 0.8130 (mp10) REVERT: B 273 ASN cc_start: 0.8747 (m-40) cc_final: 0.8450 (m110) REVERT: B 274 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7730 (pp) REVERT: B 280 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8233 (m) REVERT: S 86 ARG cc_start: 0.7481 (mtp85) cc_final: 0.6766 (mtt-85) REVERT: G 46 GLU cc_start: 0.8266 (mp0) cc_final: 0.7972 (mp0) outliers start: 26 outliers final: 19 residues processed: 155 average time/residue: 0.2242 time to fit residues: 47.7367 Evaluate side-chains 153 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain S residue 10 LEU Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain A residue 261 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 15 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 78 ASN R 181 HIS S 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.153247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109984 restraints weight = 12525.452| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.96 r_work: 0.3254 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9012 Z= 0.234 Angle : 0.565 10.021 12244 Z= 0.288 Chirality : 0.042 0.164 1393 Planarity : 0.004 0.052 1557 Dihedral : 4.711 44.318 1247 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.59 % Allowed : 18.02 % Favored : 79.40 % 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: 0.84 (0.25), residues: 1121 helix: 2.13 (0.25), residues: 406 sheet: 0.07 (0.32), residues: 269 loop : -0.57 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.004 0.001 HIS R 181 PHE 0.009 0.001 PHE R 113 TYR 0.019 0.001 TYR B 64 ARG 0.007 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: R 71 LYS cc_start: 0.6944 (mmmt) cc_final: 0.6521 (tptp) REVERT: R 212 LEU cc_start: 0.8366 (mp) cc_final: 0.8151 (mp) REVERT: R 253 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6214 (ttp-110) REVERT: B 222 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7208 (ptm) REVERT: B 273 ASN cc_start: 0.8741 (m-40) cc_final: 0.8438 (m110) REVERT: B 274 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7665 (pp) REVERT: B 280 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8171 (m) REVERT: S 66 ARG cc_start: 0.7800 (mtm-85) cc_final: 0.7526 (ttp-110) REVERT: S 86 ARG cc_start: 0.7505 (mtp85) cc_final: 0.6831 (mtt-85) REVERT: S 220 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7130 (mp0) REVERT: G 46 GLU cc_start: 0.8275 (mp0) cc_final: 0.7992 (mp0) outliers start: 24 outliers final: 18 residues processed: 154 average time/residue: 0.2065 time to fit residues: 44.3912 Evaluate side-chains 157 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 261 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 13 optimal weight: 0.3980 chunk 81 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 181 HIS S 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.154268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.112099 restraints weight = 12696.254| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.91 r_work: 0.3272 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9012 Z= 0.167 Angle : 0.549 10.145 12244 Z= 0.278 Chirality : 0.041 0.172 1393 Planarity : 0.004 0.053 1557 Dihedral : 4.567 42.941 1247 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.37 % Allowed : 18.23 % Favored : 79.40 % 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: 0.93 (0.26), residues: 1121 helix: 2.16 (0.25), residues: 409 sheet: 0.10 (0.32), residues: 274 loop : -0.48 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.004 0.001 HIS R 181 PHE 0.011 0.001 PHE L 220 TYR 0.015 0.001 TYR B 64 ARG 0.008 0.000 ARG A 302 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: R 71 LYS cc_start: 0.6959 (mmmt) cc_final: 0.6561 (tptp) REVERT: R 212 LEU cc_start: 0.8281 (mp) cc_final: 0.8075 (mp) REVERT: R 253 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.6224 (ttp-110) REVERT: B 222 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.7151 (ptm) REVERT: B 225 GLN cc_start: 0.8368 (mp10) cc_final: 0.8130 (mp10) REVERT: B 273 ASN cc_start: 0.8723 (m-40) cc_final: 0.8423 (m110) REVERT: B 274 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7696 (pp) REVERT: B 280 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8108 (m) REVERT: S 66 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7532 (ttp-110) REVERT: S 86 ARG cc_start: 0.7515 (mtp85) cc_final: 0.6878 (mtt-85) REVERT: S 220 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7138 (mp0) REVERT: A 262 THR cc_start: 0.8447 (m) cc_final: 0.8184 (t) outliers start: 22 outliers final: 17 residues processed: 157 average time/residue: 0.2034 time to fit residues: 44.7328 Evaluate side-chains 164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 261 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 78 ASN R 181 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.153169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.111072 restraints weight = 12683.880| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.90 r_work: 0.3252 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9012 Z= 0.216 Angle : 0.558 10.929 12244 Z= 0.284 Chirality : 0.042 0.161 1393 Planarity : 0.004 0.054 1557 Dihedral : 4.572 42.210 1247 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.27 % Allowed : 18.77 % Favored : 78.96 % 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: 0.91 (0.25), residues: 1121 helix: 2.16 (0.25), residues: 408 sheet: 0.13 (0.33), residues: 263 loop : -0.52 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.003 0.001 HIS R 181 PHE 0.012 0.001 PHE L 220 TYR 0.015 0.001 TYR B 64 ARG 0.007 0.000 ARG A 302 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: R 71 LYS cc_start: 0.6946 (mmmt) cc_final: 0.6527 (tptp) REVERT: R 253 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.6202 (ttp-110) REVERT: B 222 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7121 (ptm) REVERT: B 225 GLN cc_start: 0.8371 (mp10) cc_final: 0.8118 (mp10) REVERT: B 273 ASN cc_start: 0.8738 (m-40) cc_final: 0.8432 (m110) REVERT: B 274 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7662 (pp) REVERT: B 280 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8135 (m) REVERT: S 66 ARG cc_start: 0.7777 (mtm-85) cc_final: 0.7525 (ttp-110) REVERT: S 86 ARG cc_start: 0.7464 (mtp85) cc_final: 0.6869 (mtt-85) REVERT: A 262 THR cc_start: 0.8425 (m) cc_final: 0.7863 (p) outliers start: 21 outliers final: 17 residues processed: 151 average time/residue: 0.2096 time to fit residues: 44.0817 Evaluate side-chains 159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 200 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 261 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 181 HIS S 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.154544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.112664 restraints weight = 12634.548| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.89 r_work: 0.3267 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9012 Z= 0.172 Angle : 0.550 10.287 12244 Z= 0.280 Chirality : 0.041 0.158 1393 Planarity : 0.004 0.052 1557 Dihedral : 4.504 41.141 1247 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.16 % Allowed : 18.99 % Favored : 78.86 % 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: 0.96 (0.26), residues: 1121 helix: 2.20 (0.25), residues: 408 sheet: 0.17 (0.32), residues: 263 loop : -0.49 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.004 0.001 HIS R 181 PHE 0.012 0.001 PHE L 220 TYR 0.014 0.001 TYR B 64 ARG 0.007 0.000 ARG A 302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4626.07 seconds wall clock time: 83 minutes 8.59 seconds (4988.59 seconds total)