Starting phenix.real_space_refine on Wed Sep 17 18:43:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xor_38538/09_2025/8xor_38538.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xor_38538/09_2025/8xor_38538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xor_38538/09_2025/8xor_38538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xor_38538/09_2025/8xor_38538.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xor_38538/09_2025/8xor_38538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xor_38538/09_2025/8xor_38538.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1900 atoms to isotropic. 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 58 5.16 5 C 5801 2.51 5 N 1478 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8979 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2481 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 5, 'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1848 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1729 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "R" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2400 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 11, 'TRANS': 293} Chain breaks: 1 Chain: "R" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'CLR': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 2.25, per 1000 atoms: 0.25 Number of scatterers: 8979 At special positions: 0 Unit cell: (116.739, 116.739, 103.887, 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 58 16.00 O 1642 8.00 N 1478 7.00 C 5801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 175 " - pdb=" SG CYS R 254 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 347.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 40.2% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 12 through 24 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.708A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 26 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 210 through 218 removed outlier: 4.212A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 245 removed outlier: 4.222A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 4.458A pdb=" N THR A 251 " --> pdb=" O TRP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 300 through 318 removed outlier: 3.544A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.807A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'R' and resid 89 through 98 Processing helix chain 'R' and resid 98 through 127 removed outlier: 5.016A pdb=" N VAL R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) Proline residue: R 106 - end of helix Proline residue: R 118 - end of helix Processing helix chain 'R' and resid 135 through 164 removed outlier: 3.699A pdb=" N VAL R 139 " --> pdb=" O LYS R 135 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL R 154 " --> pdb=" O LEU R 150 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU R 155 " --> pdb=" O PHE R 151 " (cutoff:3.500A) Proline residue: R 156 - end of helix Processing helix chain 'R' and resid 170 through 206 removed outlier: 4.360A pdb=" N LEU R 174 " --> pdb=" O PHE R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 214 removed outlier: 3.689A pdb=" N LEU R 211 " --> pdb=" O PRO R 207 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER R 212 " --> pdb=" O MET R 208 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TRP R 213 " --> pdb=" O GLN R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 240 Proline residue: R 236 - end of helix Processing helix chain 'R' and resid 260 through 265 Processing helix chain 'R' and resid 265 through 279 Processing helix chain 'R' and resid 279 through 299 Processing helix chain 'R' and resid 299 through 306 removed outlier: 4.055A pdb=" N SER R 306 " --> pdb=" O VAL R 302 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 339 Proline residue: R 328 - end of helix removed outlier: 3.757A pdb=" N PHE R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 361 removed outlier: 4.143A pdb=" N GLU R 347 " --> pdb=" O THR R 343 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ALA R 348 " --> pdb=" O SER R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 372 Proline residue: R 368 - end of helix Processing helix chain 'R' and resid 375 through 380 removed outlier: 4.274A pdb=" N ARG R 380 " --> pdb=" O SER R 376 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.560A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.601A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.937A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.674A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.962A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.498A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.763A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.617A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.125A pdb=" N TRP E 111 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ARG E 98 " --> pdb=" O TRP E 111 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLN E 113 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N CYS E 96 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 148 removed outlier: 5.896A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 87 through 88 removed outlier: 6.133A pdb=" N PHE R 43 " --> pdb=" O LEU R 258 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 243 through 245 453 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2811 1.34 - 1.46: 1740 1.46 - 1.58: 4561 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 9192 Sorted by residual: bond pdb=" CD2 HIS E 232 " pdb=" NE2 HIS E 232 " ideal model delta sigma weight residual 1.374 1.397 -0.023 1.10e-02 8.26e+03 4.54e+00 bond pdb=" ND1 HIS E 35 " pdb=" CE1 HIS E 35 " ideal model delta sigma weight residual 1.321 1.342 -0.021 1.00e-02 1.00e+04 4.49e+00 bond pdb=" C13 CLR R1405 " pdb=" C17 CLR R1405 " ideal model delta sigma weight residual 1.550 1.508 0.042 2.00e-02 2.50e+03 4.33e+00 bond pdb=" C13 CLR R1403 " pdb=" C17 CLR R1403 " ideal model delta sigma weight residual 1.550 1.509 0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" C13 CLR R1402 " pdb=" C17 CLR R1402 " ideal model delta sigma weight residual 1.550 1.509 0.041 2.00e-02 2.50e+03 4.26e+00 ... (remaining 9187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 11885 1.78 - 3.56: 544 3.56 - 5.34: 86 5.34 - 7.13: 18 7.13 - 8.91: 11 Bond angle restraints: 12544 Sorted by residual: angle pdb=" OE1 GLN E 231 " pdb=" CD GLN E 231 " pdb=" NE2 GLN E 231 " ideal model delta sigma weight residual 122.60 117.91 4.69 1.00e+00 1.00e+00 2.20e+01 angle pdb=" CB HIS E 35 " pdb=" CG HIS E 35 " pdb=" CD2 HIS E 35 " ideal model delta sigma weight residual 131.20 125.34 5.86 1.30e+00 5.92e-01 2.03e+01 angle pdb=" N PRO E 236 " pdb=" CA PRO E 236 " pdb=" C PRO E 236 " ideal model delta sigma weight residual 113.81 107.34 6.47 1.45e+00 4.76e-01 1.99e+01 angle pdb=" CA ASP E 137 " pdb=" CB ASP E 137 " pdb=" CG ASP E 137 " ideal model delta sigma weight residual 112.60 117.00 -4.40 1.00e+00 1.00e+00 1.93e+01 angle pdb=" CB HIS E 167 " pdb=" CG HIS E 167 " pdb=" CD2 HIS E 167 " ideal model delta sigma weight residual 131.20 125.78 5.42 1.30e+00 5.92e-01 1.74e+01 ... (remaining 12539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.31: 5346 21.31 - 42.61: 255 42.61 - 63.92: 56 63.92 - 85.23: 13 85.23 - 106.53: 6 Dihedral angle restraints: 5676 sinusoidal: 2289 harmonic: 3387 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 150.96 29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA LEU R 44 " pdb=" C LEU R 44 " pdb=" N LEU R 45 " pdb=" CA LEU R 45 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA THR B 249 " pdb=" C THR B 249 " pdb=" N CYS B 250 " pdb=" CA CYS B 250 " ideal model delta harmonic sigma weight residual 180.00 151.62 28.38 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 5673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1222 0.070 - 0.139: 217 0.139 - 0.209: 14 0.209 - 0.278: 8 0.278 - 0.348: 7 Chirality restraints: 1468 Sorted by residual: chirality pdb=" C13 CLR R1405 " pdb=" C12 CLR R1405 " pdb=" C14 CLR R1405 " pdb=" C17 CLR R1405 " both_signs ideal model delta sigma weight residual False -2.93 -2.58 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" C13 CLR R1402 " pdb=" C12 CLR R1402 " pdb=" C14 CLR R1402 " pdb=" C17 CLR R1402 " both_signs ideal model delta sigma weight residual False -2.93 -2.60 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C13 CLR R1401 " pdb=" C12 CLR R1401 " pdb=" C14 CLR R1401 " pdb=" C17 CLR R1401 " both_signs ideal model delta sigma weight residual False -2.93 -2.60 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 1465 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 101 " -0.087 2.00e-02 2.50e+03 5.04e-02 5.08e+01 pdb=" CG TYR E 101 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR E 101 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR E 101 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR E 101 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR E 101 " 0.026 2.00e-02 2.50e+03 pdb=" CZ TYR E 101 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR E 101 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 50 " 0.087 2.00e-02 2.50e+03 4.99e-02 4.99e+01 pdb=" CG TYR E 50 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR E 50 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR E 50 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR E 50 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR E 50 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR E 50 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR E 50 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 276 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C ALA R 276 " -0.065 2.00e-02 2.50e+03 pdb=" O ALA R 276 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL R 277 " 0.022 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1655 2.77 - 3.31: 9047 3.31 - 3.84: 15053 3.84 - 4.37: 18390 4.37 - 4.90: 31188 Nonbonded interactions: 75333 Sorted by model distance: nonbonded pdb=" OH TYR R 161 " pdb=" OD2 ASP R 256 " model vdw 2.242 3.040 nonbonded pdb=" OG SER E 7 " pdb=" OG SER E 21 " model vdw 2.353 3.040 nonbonded pdb=" CE1 HIS R 143 " pdb=" C19 CLR R1405 " model vdw 2.363 3.680 nonbonded pdb=" OD2 ASP A 9 " pdb=" ND2 ASN E 169 " model vdw 2.400 3.120 nonbonded pdb=" OH TYR A 327 " pdb=" OD2 ASP A 348 " model vdw 2.401 3.040 ... (remaining 75328 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.770 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.005 0.042 9193 Z= 0.247 Angle : 0.901 8.907 12546 Z= 0.512 Chirality : 0.058 0.348 1468 Planarity : 0.007 0.056 1546 Dihedral : 14.200 106.534 3489 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.33 % Allowed : 4.67 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.23), residues: 1144 helix: -0.42 (0.23), residues: 407 sheet: 0.27 (0.30), residues: 276 loop : -0.52 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.008 ARG E 72 TYR 0.087 0.007 TYR E 101 PHE 0.030 0.002 PHE E 177 TRP 0.034 0.003 TRP E 47 HIS 0.011 0.002 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 9192) covalent geometry : angle 0.90075 (12544) SS BOND : bond 0.00010 ( 1) SS BOND : angle 2.48834 ( 2) hydrogen bonds : bond 0.11415 ( 453) hydrogen bonds : angle 6.15549 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 162 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8333 (pt0) cc_final: 0.8028 (pp30) REVERT: B 259 GLN cc_start: 0.7626 (pt0) cc_final: 0.7411 (pt0) REVERT: B 275 SER cc_start: 0.8846 (t) cc_final: 0.8361 (m) REVERT: B 280 LYS cc_start: 0.9250 (tttt) cc_final: 0.9034 (tttm) REVERT: A 25 LYS cc_start: 0.7565 (tptt) cc_final: 0.6934 (tmmm) REVERT: A 27 LYS cc_start: 0.7982 (tmtt) cc_final: 0.7568 (mmtt) REVERT: A 281 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8810 (mp0) REVERT: E 3 GLN cc_start: 0.8677 (tt0) cc_final: 0.8342 (tt0) REVERT: E 73 ASP cc_start: 0.7823 (t0) cc_final: 0.7278 (t0) REVERT: E 186 GLN cc_start: 0.8566 (tt0) cc_final: 0.8330 (tt0) REVERT: R 91 ASP cc_start: 0.8560 (p0) cc_final: 0.8269 (p0) REVERT: R 240 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7898 (mmtm) REVERT: R 245 GLN cc_start: 0.8573 (tp40) cc_final: 0.8339 (mm-40) REVERT: R 304 ASN cc_start: 0.9201 (m-40) cc_final: 0.8919 (m110) REVERT: R 347 GLU cc_start: 0.9067 (mp0) cc_final: 0.8678 (mp0) REVERT: R 377 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8117 (tp30) outliers start: 3 outliers final: 0 residues processed: 165 average time/residue: 0.7661 time to fit residues: 132.8814 Evaluate side-chains 116 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 62 HIS B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 24 GLN A 216 ASN E 194 ASN R 47 ASN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.054561 restraints weight = 22449.929| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 3.17 r_work: 0.2648 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9193 Z= 0.198 Angle : 0.681 8.232 12546 Z= 0.356 Chirality : 0.047 0.280 1468 Planarity : 0.005 0.050 1546 Dihedral : 8.972 56.359 1644 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.74 % Allowed : 10.42 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.25), residues: 1144 helix: 1.17 (0.27), residues: 410 sheet: 0.41 (0.30), residues: 261 loop : -0.24 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 18 TYR 0.025 0.002 TYR E 235 PHE 0.015 0.002 PHE B 253 TRP 0.017 0.002 TRP A 211 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 9192) covalent geometry : angle 0.68054 (12544) SS BOND : bond 0.00420 ( 1) SS BOND : angle 0.71057 ( 2) hydrogen bonds : bond 0.04618 ( 453) hydrogen bonds : angle 4.89230 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9509 (tppp) cc_final: 0.9260 (mppt) REVERT: B 175 GLN cc_start: 0.8731 (pt0) cc_final: 0.8307 (pp30) REVERT: B 228 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7848 (p0) REVERT: B 259 GLN cc_start: 0.8044 (pt0) cc_final: 0.7837 (pt0) REVERT: B 262 MET cc_start: 0.8627 (tpp) cc_final: 0.8387 (ttm) REVERT: B 275 SER cc_start: 0.8918 (t) cc_final: 0.8502 (m) REVERT: B 280 LYS cc_start: 0.9220 (tttt) cc_final: 0.8968 (tttm) REVERT: A 25 LYS cc_start: 0.7664 (tptt) cc_final: 0.7124 (tmmm) REVERT: A 27 LYS cc_start: 0.8020 (tmtt) cc_final: 0.7481 (mmtm) REVERT: A 52 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8712 (pp30) REVERT: A 281 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8888 (mp0) REVERT: E 3 GLN cc_start: 0.8792 (tt0) cc_final: 0.8556 (tt0) REVERT: E 13 GLN cc_start: 0.9315 (tp40) cc_final: 0.8740 (pp30) REVERT: E 38 ARG cc_start: 0.9190 (ptt180) cc_final: 0.8940 (ptp90) REVERT: E 73 ASP cc_start: 0.7786 (t0) cc_final: 0.7357 (t0) REVERT: E 74 ASP cc_start: 0.8417 (m-30) cc_final: 0.8163 (m-30) REVERT: E 113 GLN cc_start: 0.8488 (pm20) cc_final: 0.8285 (pm20) REVERT: E 186 GLN cc_start: 0.8840 (tt0) cc_final: 0.8578 (tt0) REVERT: E 223 ASP cc_start: 0.8576 (m-30) cc_final: 0.8205 (m-30) REVERT: E 230 MET cc_start: 0.9405 (ttp) cc_final: 0.9011 (ttp) REVERT: R 91 ASP cc_start: 0.8742 (p0) cc_final: 0.8523 (p0) REVERT: R 132 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8663 (mmmm) REVERT: R 245 GLN cc_start: 0.8703 (tp40) cc_final: 0.8484 (mm-40) REVERT: R 264 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8414 (mt-10) REVERT: R 347 GLU cc_start: 0.9269 (mp0) cc_final: 0.8676 (mp0) REVERT: R 362 ILE cc_start: 0.9273 (tt) cc_final: 0.9041 (pp) outliers start: 16 outliers final: 4 residues processed: 132 average time/residue: 0.7637 time to fit residues: 106.1335 Evaluate side-chains 115 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 36 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 75 GLN B 176 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 GLN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.075895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.055203 restraints weight = 21832.004| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.03 r_work: 0.2665 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9193 Z= 0.188 Angle : 0.626 7.937 12546 Z= 0.330 Chirality : 0.045 0.243 1468 Planarity : 0.004 0.049 1546 Dihedral : 8.031 55.965 1644 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.74 % Allowed : 12.70 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.25), residues: 1144 helix: 1.46 (0.27), residues: 410 sheet: 0.39 (0.30), residues: 262 loop : -0.17 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 18 TYR 0.017 0.002 TYR E 235 PHE 0.014 0.001 PHE B 199 TRP 0.017 0.002 TRP A 211 HIS 0.003 0.001 HIS R 336 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 9192) covalent geometry : angle 0.62565 (12544) SS BOND : bond 0.00312 ( 1) SS BOND : angle 0.37768 ( 2) hydrogen bonds : bond 0.04329 ( 453) hydrogen bonds : angle 4.64557 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 ARG cc_start: 0.7977 (mpt-90) cc_final: 0.7725 (mpt-90) REVERT: B 23 LYS cc_start: 0.9492 (tppp) cc_final: 0.9263 (mppt) REVERT: B 175 GLN cc_start: 0.8803 (pt0) cc_final: 0.8365 (pp30) REVERT: B 275 SER cc_start: 0.8964 (t) cc_final: 0.8581 (m) REVERT: B 280 LYS cc_start: 0.9187 (tttt) cc_final: 0.8944 (tttm) REVERT: C 29 LYS cc_start: 0.8961 (mttm) cc_final: 0.8713 (mmpt) REVERT: A 25 LYS cc_start: 0.7605 (tptt) cc_final: 0.7203 (tmmm) REVERT: A 27 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7439 (mmtm) REVERT: A 52 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8651 (pp30) REVERT: A 281 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8907 (mp0) REVERT: E 3 GLN cc_start: 0.8866 (tt0) cc_final: 0.8571 (tt0) REVERT: E 13 GLN cc_start: 0.9335 (tp40) cc_final: 0.8772 (pp30) REVERT: E 73 ASP cc_start: 0.7890 (t0) cc_final: 0.7412 (t0) REVERT: E 74 ASP cc_start: 0.8580 (m-30) cc_final: 0.8322 (m-30) REVERT: E 113 GLN cc_start: 0.8471 (pm20) cc_final: 0.8221 (pm20) REVERT: E 140 MET cc_start: 0.9211 (mmm) cc_final: 0.8959 (mmm) REVERT: E 183 GLN cc_start: 0.8495 (mp10) cc_final: 0.8167 (mm-40) REVERT: E 186 GLN cc_start: 0.8853 (tt0) cc_final: 0.8569 (tt0) REVERT: E 192 MET cc_start: 0.8994 (ttp) cc_final: 0.8602 (ttp) REVERT: E 223 ASP cc_start: 0.8737 (m-30) cc_final: 0.8284 (m-30) REVERT: E 230 MET cc_start: 0.9359 (ttp) cc_final: 0.8967 (ttp) REVERT: R 134 LYS cc_start: 0.9342 (mtmm) cc_final: 0.9112 (mtpp) REVERT: R 264 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8396 (mt-10) REVERT: R 347 GLU cc_start: 0.9264 (mp0) cc_final: 0.8568 (mp0) outliers start: 16 outliers final: 9 residues processed: 128 average time/residue: 0.7478 time to fit residues: 101.0068 Evaluate side-chains 119 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 131 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 32 GLN B 75 GLN A 352 GLN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.056515 restraints weight = 22262.569| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.09 r_work: 0.2703 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9193 Z= 0.130 Angle : 0.575 7.664 12546 Z= 0.304 Chirality : 0.043 0.216 1468 Planarity : 0.004 0.049 1546 Dihedral : 7.599 59.708 1644 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.28 % Allowed : 13.46 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.25), residues: 1144 helix: 1.63 (0.27), residues: 409 sheet: 0.37 (0.30), residues: 273 loop : 0.01 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 160 TYR 0.014 0.001 TYR E 235 PHE 0.011 0.001 PHE R 279 TRP 0.012 0.001 TRP A 211 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9192) covalent geometry : angle 0.57482 (12544) SS BOND : bond 0.00273 ( 1) SS BOND : angle 0.22852 ( 2) hydrogen bonds : bond 0.03795 ( 453) hydrogen bonds : angle 4.47333 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9521 (tppp) cc_final: 0.9296 (mppt) REVERT: B 175 GLN cc_start: 0.8819 (pt0) cc_final: 0.8435 (pp30) REVERT: B 220 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.9057 (mt0) REVERT: B 275 SER cc_start: 0.9000 (t) cc_final: 0.8672 (m) REVERT: C 29 LYS cc_start: 0.8916 (mttm) cc_final: 0.8571 (mmtt) REVERT: C 31 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8341 (m) REVERT: C 32 LYS cc_start: 0.8536 (mtmm) cc_final: 0.8294 (mtmm) REVERT: A 25 LYS cc_start: 0.7557 (tptt) cc_final: 0.7334 (tmmm) REVERT: A 27 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7341 (mmtm) REVERT: A 52 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8582 (pp30) REVERT: E 3 GLN cc_start: 0.8882 (tt0) cc_final: 0.8588 (tt0) REVERT: E 13 GLN cc_start: 0.9400 (tp40) cc_final: 0.8883 (pp30) REVERT: E 73 ASP cc_start: 0.8007 (t0) cc_final: 0.7570 (t0) REVERT: E 113 GLN cc_start: 0.8416 (pm20) cc_final: 0.8073 (pm20) REVERT: E 183 GLN cc_start: 0.8462 (mp10) cc_final: 0.8237 (mm-40) REVERT: E 186 GLN cc_start: 0.8864 (tt0) cc_final: 0.8601 (tt0) REVERT: E 223 ASP cc_start: 0.8749 (m-30) cc_final: 0.8228 (m-30) REVERT: E 230 MET cc_start: 0.9313 (ttp) cc_final: 0.8945 (ttp) REVERT: R 134 LYS cc_start: 0.9303 (mtmm) cc_final: 0.9074 (mtpp) REVERT: R 245 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8285 (tp-100) REVERT: R 264 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8369 (mt-10) REVERT: R 347 GLU cc_start: 0.9242 (mp0) cc_final: 0.8969 (mm-30) outliers start: 21 outliers final: 10 residues processed: 134 average time/residue: 0.7087 time to fit residues: 100.4173 Evaluate side-chains 124 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 13 optimal weight: 0.4980 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 18 optimal weight: 0.0970 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 32 GLN B 75 GLN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.077307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.056937 restraints weight = 21966.308| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.06 r_work: 0.2708 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9193 Z= 0.133 Angle : 0.576 7.695 12546 Z= 0.303 Chirality : 0.042 0.215 1468 Planarity : 0.004 0.049 1546 Dihedral : 7.340 59.955 1644 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.50 % Allowed : 13.90 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.25), residues: 1144 helix: 1.68 (0.27), residues: 411 sheet: 0.45 (0.31), residues: 262 loop : 0.04 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 160 TYR 0.016 0.001 TYR E 235 PHE 0.011 0.001 PHE B 199 TRP 0.013 0.001 TRP A 211 HIS 0.003 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9192) covalent geometry : angle 0.57583 (12544) SS BOND : bond 0.00300 ( 1) SS BOND : angle 0.18633 ( 2) hydrogen bonds : bond 0.03719 ( 453) hydrogen bonds : angle 4.41153 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8833 (pt0) cc_final: 0.8461 (pp30) REVERT: B 220 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.9018 (mt0) REVERT: B 275 SER cc_start: 0.8978 (t) cc_final: 0.8661 (m) REVERT: C 31 SER cc_start: 0.8849 (t) cc_final: 0.8389 (m) REVERT: C 52 THR cc_start: 0.8434 (m) cc_final: 0.7836 (p) REVERT: A 18 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8591 (mtm) REVERT: A 22 GLN cc_start: 0.8086 (tp40) cc_final: 0.7672 (tp40) REVERT: A 25 LYS cc_start: 0.7608 (tptt) cc_final: 0.7349 (tmmm) REVERT: A 27 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7294 (mmtm) REVERT: A 52 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8552 (pp30) REVERT: A 180 LYS cc_start: 0.8466 (mmpt) cc_final: 0.7971 (mptt) REVERT: E 3 GLN cc_start: 0.8872 (tt0) cc_final: 0.8573 (tt0) REVERT: E 13 GLN cc_start: 0.9387 (tp40) cc_final: 0.8889 (pp30) REVERT: E 73 ASP cc_start: 0.8013 (t0) cc_final: 0.7568 (t0) REVERT: E 113 GLN cc_start: 0.8397 (pm20) cc_final: 0.8051 (pm20) REVERT: E 140 MET cc_start: 0.9246 (mmm) cc_final: 0.9019 (OUTLIER) REVERT: E 183 GLN cc_start: 0.8496 (mp10) cc_final: 0.8224 (mm-40) REVERT: E 186 GLN cc_start: 0.8901 (tt0) cc_final: 0.8610 (tt0) REVERT: E 223 ASP cc_start: 0.8716 (m-30) cc_final: 0.8206 (m-30) REVERT: E 230 MET cc_start: 0.9312 (ttp) cc_final: 0.8964 (ttt) REVERT: R 134 LYS cc_start: 0.9289 (mtmm) cc_final: 0.9067 (mtpp) REVERT: R 242 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8206 (mm-40) REVERT: R 245 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8343 (tp-100) REVERT: R 264 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8394 (mt-10) REVERT: R 347 GLU cc_start: 0.9273 (mp0) cc_final: 0.9050 (mm-30) outliers start: 23 outliers final: 10 residues processed: 129 average time/residue: 0.6816 time to fit residues: 93.2247 Evaluate side-chains 123 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 97 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 79 optimal weight: 0.0870 chunk 68 optimal weight: 5.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 75 GLN B 230 ASN B 259 GLN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.075871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.055327 restraints weight = 22144.088| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.04 r_work: 0.2670 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9193 Z= 0.179 Angle : 0.591 8.036 12546 Z= 0.311 Chirality : 0.043 0.233 1468 Planarity : 0.004 0.052 1546 Dihedral : 7.244 59.447 1644 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.28 % Allowed : 15.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.25), residues: 1144 helix: 1.76 (0.27), residues: 409 sheet: 0.44 (0.32), residues: 261 loop : 0.02 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 160 TYR 0.018 0.002 TYR E 235 PHE 0.013 0.001 PHE B 199 TRP 0.015 0.001 TRP A 211 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 9192) covalent geometry : angle 0.59115 (12544) SS BOND : bond 0.00245 ( 1) SS BOND : angle 0.18851 ( 2) hydrogen bonds : bond 0.03962 ( 453) hydrogen bonds : angle 4.43118 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8865 (pt0) cc_final: 0.8426 (pp30) REVERT: B 220 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8951 (mt0) REVERT: B 275 SER cc_start: 0.8986 (t) cc_final: 0.8653 (m) REVERT: C 29 LYS cc_start: 0.8884 (mttm) cc_final: 0.8576 (mmpt) REVERT: C 31 SER cc_start: 0.8949 (t) cc_final: 0.8519 (m) REVERT: C 32 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8420 (mtmm) REVERT: C 48 ASP cc_start: 0.8814 (t0) cc_final: 0.8571 (t0) REVERT: C 52 THR cc_start: 0.8572 (m) cc_final: 0.7999 (p) REVERT: A 18 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8610 (mtm) REVERT: A 25 LYS cc_start: 0.7668 (tptt) cc_final: 0.7433 (tmmm) REVERT: A 27 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7460 (mmtm) REVERT: A 52 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8554 (pp30) REVERT: E 3 GLN cc_start: 0.8890 (tt0) cc_final: 0.8593 (tt0) REVERT: E 13 GLN cc_start: 0.9394 (tp40) cc_final: 0.8919 (pp30) REVERT: E 73 ASP cc_start: 0.8054 (t0) cc_final: 0.7603 (t0) REVERT: E 113 GLN cc_start: 0.8438 (pm20) cc_final: 0.8050 (pm20) REVERT: E 183 GLN cc_start: 0.8543 (mp10) cc_final: 0.8299 (mm-40) REVERT: E 186 GLN cc_start: 0.8914 (tt0) cc_final: 0.8619 (tt0) REVERT: E 223 ASP cc_start: 0.8755 (m-30) cc_final: 0.8188 (m-30) REVERT: E 230 MET cc_start: 0.9353 (ttp) cc_final: 0.9140 (ttm) REVERT: R 134 LYS cc_start: 0.9286 (mtmm) cc_final: 0.9064 (mtpp) REVERT: R 245 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8349 (tp-100) REVERT: R 264 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8350 (mt-10) outliers start: 21 outliers final: 9 residues processed: 125 average time/residue: 0.6757 time to fit residues: 89.4219 Evaluate side-chains 120 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 75 GLN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.076008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.054894 restraints weight = 22264.563| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.10 r_work: 0.2666 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9193 Z= 0.175 Angle : 0.597 7.865 12546 Z= 0.316 Chirality : 0.043 0.225 1468 Planarity : 0.004 0.051 1546 Dihedral : 7.162 58.859 1644 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.61 % Allowed : 16.29 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.25), residues: 1144 helix: 1.94 (0.27), residues: 397 sheet: 0.42 (0.32), residues: 261 loop : 0.09 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 160 TYR 0.017 0.001 TYR A 230 PHE 0.013 0.001 PHE B 253 TRP 0.014 0.001 TRP A 211 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9192) covalent geometry : angle 0.59695 (12544) SS BOND : bond 0.00263 ( 1) SS BOND : angle 0.14157 ( 2) hydrogen bonds : bond 0.03936 ( 453) hydrogen bonds : angle 4.45876 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8866 (pt0) cc_final: 0.8477 (pp30) REVERT: B 220 GLN cc_start: 0.9235 (mt0) cc_final: 0.8901 (mt0) REVERT: B 275 SER cc_start: 0.9004 (t) cc_final: 0.8690 (m) REVERT: C 29 LYS cc_start: 0.8939 (mttm) cc_final: 0.8628 (mmtt) REVERT: C 31 SER cc_start: 0.8992 (t) cc_final: 0.8596 (m) REVERT: C 32 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8457 (mtmm) REVERT: C 41 CYS cc_start: 0.8977 (m) cc_final: 0.8744 (m) REVERT: C 48 ASP cc_start: 0.8836 (t0) cc_final: 0.8611 (t0) REVERT: C 52 THR cc_start: 0.8583 (m) cc_final: 0.8025 (p) REVERT: A 18 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8635 (mtm) REVERT: A 22 GLN cc_start: 0.8033 (tp40) cc_final: 0.7582 (tp40) REVERT: A 25 LYS cc_start: 0.7720 (tptt) cc_final: 0.7452 (tmmm) REVERT: A 27 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7475 (mmtm) REVERT: A 52 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8568 (pp30) REVERT: A 180 LYS cc_start: 0.8488 (mmpt) cc_final: 0.8003 (mptt) REVERT: A 251 THR cc_start: 0.9540 (OUTLIER) cc_final: 0.9221 (t) REVERT: E 3 GLN cc_start: 0.8865 (tt0) cc_final: 0.8575 (tt0) REVERT: E 73 ASP cc_start: 0.8106 (t0) cc_final: 0.7653 (t0) REVERT: E 113 GLN cc_start: 0.8425 (pm20) cc_final: 0.8002 (pm20) REVERT: E 183 GLN cc_start: 0.8567 (mp10) cc_final: 0.8286 (mm-40) REVERT: E 186 GLN cc_start: 0.8907 (tt0) cc_final: 0.8608 (tt0) REVERT: E 223 ASP cc_start: 0.8744 (m-30) cc_final: 0.8162 (m-30) REVERT: E 230 MET cc_start: 0.9337 (ttp) cc_final: 0.8959 (ttp) REVERT: R 134 LYS cc_start: 0.9277 (mtmm) cc_final: 0.9061 (mtpp) REVERT: R 245 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8351 (tp-100) REVERT: R 264 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8415 (mt-10) REVERT: R 347 GLU cc_start: 0.9305 (mp0) cc_final: 0.9092 (mm-30) outliers start: 24 outliers final: 10 residues processed: 126 average time/residue: 0.6471 time to fit residues: 86.5314 Evaluate side-chains 121 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 86 optimal weight: 0.0010 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.076230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.055142 restraints weight = 22080.621| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.10 r_work: 0.2673 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9193 Z= 0.167 Angle : 0.608 7.803 12546 Z= 0.321 Chirality : 0.043 0.223 1468 Planarity : 0.004 0.051 1546 Dihedral : 7.080 58.869 1644 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.28 % Allowed : 17.16 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.25), residues: 1144 helix: 1.84 (0.27), residues: 397 sheet: 0.45 (0.32), residues: 261 loop : 0.10 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 160 TYR 0.017 0.001 TYR A 230 PHE 0.012 0.001 PHE B 253 TRP 0.014 0.001 TRP A 211 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9192) covalent geometry : angle 0.60830 (12544) SS BOND : bond 0.00233 ( 1) SS BOND : angle 0.27880 ( 2) hydrogen bonds : bond 0.03905 ( 453) hydrogen bonds : angle 4.47303 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8870 (pt0) cc_final: 0.8475 (pp30) REVERT: B 220 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.9058 (mt0) REVERT: B 275 SER cc_start: 0.9032 (t) cc_final: 0.8724 (m) REVERT: C 29 LYS cc_start: 0.8901 (mttm) cc_final: 0.8548 (mmpt) REVERT: C 31 SER cc_start: 0.8986 (t) cc_final: 0.8617 (m) REVERT: C 32 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8447 (mtmm) REVERT: C 41 CYS cc_start: 0.8890 (m) cc_final: 0.8686 (m) REVERT: C 42 GLU cc_start: 0.8468 (pp20) cc_final: 0.8267 (pp20) REVERT: C 48 ASP cc_start: 0.8902 (t0) cc_final: 0.8692 (t0) REVERT: C 52 THR cc_start: 0.8606 (m) cc_final: 0.8064 (p) REVERT: A 18 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8625 (mtm) REVERT: A 22 GLN cc_start: 0.8074 (tp40) cc_final: 0.7591 (tp40) REVERT: A 25 LYS cc_start: 0.7709 (tptt) cc_final: 0.7442 (tmmm) REVERT: A 27 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7463 (mmtm) REVERT: A 52 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8569 (pp30) REVERT: A 180 LYS cc_start: 0.8476 (mmpt) cc_final: 0.8033 (mptt) REVERT: A 251 THR cc_start: 0.9532 (OUTLIER) cc_final: 0.9214 (t) REVERT: E 3 GLN cc_start: 0.8854 (tt0) cc_final: 0.8565 (tt0) REVERT: E 73 ASP cc_start: 0.8122 (t0) cc_final: 0.7662 (t0) REVERT: E 113 GLN cc_start: 0.8343 (pm20) cc_final: 0.7912 (pm20) REVERT: E 183 GLN cc_start: 0.8556 (mp10) cc_final: 0.8317 (mm-40) REVERT: E 186 GLN cc_start: 0.8881 (tt0) cc_final: 0.8579 (tt0) REVERT: E 223 ASP cc_start: 0.8742 (m-30) cc_final: 0.8153 (m-30) REVERT: E 230 MET cc_start: 0.9334 (ttp) cc_final: 0.8959 (ttp) REVERT: R 91 ASP cc_start: 0.8935 (p0) cc_final: 0.8597 (p0) REVERT: R 134 LYS cc_start: 0.9276 (mtmm) cc_final: 0.9061 (mtpp) REVERT: R 245 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8329 (tp-100) outliers start: 21 outliers final: 10 residues processed: 125 average time/residue: 0.5899 time to fit residues: 78.2098 Evaluate side-chains 122 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 40 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 32 GLN B 75 GLN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.077771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.057006 restraints weight = 21775.174| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.09 r_work: 0.2717 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9193 Z= 0.122 Angle : 0.591 8.070 12546 Z= 0.311 Chirality : 0.042 0.193 1468 Planarity : 0.004 0.050 1546 Dihedral : 6.749 57.737 1644 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.85 % Allowed : 17.81 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.25), residues: 1144 helix: 1.78 (0.27), residues: 405 sheet: 0.60 (0.33), residues: 250 loop : 0.06 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 160 TYR 0.016 0.001 TYR A 230 PHE 0.011 0.001 PHE R 279 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9192) covalent geometry : angle 0.59087 (12544) SS BOND : bond 0.00319 ( 1) SS BOND : angle 0.21744 ( 2) hydrogen bonds : bond 0.03625 ( 453) hydrogen bonds : angle 4.38225 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8856 (pt0) cc_final: 0.8469 (pp30) REVERT: B 275 SER cc_start: 0.9043 (t) cc_final: 0.8792 (m) REVERT: B 301 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7716 (mtpp) REVERT: C 29 LYS cc_start: 0.8896 (mttm) cc_final: 0.8538 (mmpt) REVERT: C 31 SER cc_start: 0.9028 (t) cc_final: 0.8672 (m) REVERT: C 32 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8293 (mtmm) REVERT: C 41 CYS cc_start: 0.8938 (m) cc_final: 0.8418 (m) REVERT: C 42 GLU cc_start: 0.8454 (pp20) cc_final: 0.8212 (pp20) REVERT: C 52 THR cc_start: 0.8675 (m) cc_final: 0.8194 (p) REVERT: A 22 GLN cc_start: 0.8127 (tp40) cc_final: 0.7672 (tp40) REVERT: A 25 LYS cc_start: 0.7645 (tptt) cc_final: 0.7402 (tmmm) REVERT: A 27 LYS cc_start: 0.7923 (tmtt) cc_final: 0.7453 (mptm) REVERT: A 52 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8556 (pp30) REVERT: A 180 LYS cc_start: 0.8570 (mmpt) cc_final: 0.8159 (mptt) REVERT: A 251 THR cc_start: 0.9511 (OUTLIER) cc_final: 0.9214 (t) REVERT: A 325 ILE cc_start: 0.9097 (mt) cc_final: 0.8621 (tp) REVERT: E 3 GLN cc_start: 0.8828 (tt0) cc_final: 0.8594 (tt0) REVERT: E 73 ASP cc_start: 0.8112 (t0) cc_final: 0.7679 (t0) REVERT: E 183 GLN cc_start: 0.8515 (mp10) cc_final: 0.8250 (mm-40) REVERT: E 186 GLN cc_start: 0.8889 (tt0) cc_final: 0.8577 (tt0) REVERT: E 223 ASP cc_start: 0.8746 (m-30) cc_final: 0.8138 (m-30) REVERT: E 230 MET cc_start: 0.9308 (ttp) cc_final: 0.8964 (ttp) REVERT: R 134 LYS cc_start: 0.9248 (mtmm) cc_final: 0.9046 (mtpp) REVERT: R 173 GLU cc_start: 0.8334 (mp0) cc_final: 0.7407 (mm-30) REVERT: R 245 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8319 (tp-100) outliers start: 17 outliers final: 8 residues processed: 121 average time/residue: 0.6297 time to fit residues: 80.9527 Evaluate side-chains 114 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 8.9990 chunk 0 optimal weight: 60.0000 chunk 27 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 125 ASN A 352 GLN R 169 GLN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.073797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.052626 restraints weight = 22383.613| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.10 r_work: 0.2613 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 9193 Z= 0.304 Angle : 0.714 8.992 12546 Z= 0.374 Chirality : 0.047 0.279 1468 Planarity : 0.005 0.057 1546 Dihedral : 7.082 59.272 1644 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.30 % Allowed : 18.68 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.25), residues: 1144 helix: 1.71 (0.27), residues: 404 sheet: 0.41 (0.33), residues: 261 loop : -0.07 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 160 TYR 0.022 0.002 TYR A 230 PHE 0.019 0.002 PHE B 253 TRP 0.019 0.002 TRP A 211 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00709 ( 9192) covalent geometry : angle 0.71391 (12544) SS BOND : bond 0.00194 ( 1) SS BOND : angle 0.33318 ( 2) hydrogen bonds : bond 0.04576 ( 453) hydrogen bonds : angle 4.60408 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8887 (pt0) cc_final: 0.8426 (pp30) REVERT: B 215 GLU cc_start: 0.8312 (pp20) cc_final: 0.8109 (pp20) REVERT: B 275 SER cc_start: 0.8987 (t) cc_final: 0.8660 (m) REVERT: B 301 LYS cc_start: 0.8254 (mtpp) cc_final: 0.7802 (mtpp) REVERT: C 29 LYS cc_start: 0.8972 (mttm) cc_final: 0.8662 (mmtt) REVERT: C 31 SER cc_start: 0.9000 (t) cc_final: 0.8667 (m) REVERT: C 42 GLU cc_start: 0.8567 (pp20) cc_final: 0.8324 (pp20) REVERT: C 52 THR cc_start: 0.8928 (m) cc_final: 0.8416 (p) REVERT: A 27 LYS cc_start: 0.8023 (tmtt) cc_final: 0.7504 (mmtm) REVERT: A 180 LYS cc_start: 0.8593 (mmpt) cc_final: 0.8247 (mptt) REVERT: A 251 THR cc_start: 0.9560 (OUTLIER) cc_final: 0.9224 (t) REVERT: E 3 GLN cc_start: 0.8873 (tt0) cc_final: 0.8609 (tt0) REVERT: E 73 ASP cc_start: 0.8171 (t0) cc_final: 0.7680 (t0) REVERT: E 183 GLN cc_start: 0.8611 (mp10) cc_final: 0.8272 (mm110) REVERT: E 186 GLN cc_start: 0.8890 (tt0) cc_final: 0.8566 (tt0) REVERT: E 223 ASP cc_start: 0.8768 (m-30) cc_final: 0.8124 (m-30) REVERT: E 230 MET cc_start: 0.9386 (ttp) cc_final: 0.9003 (ttp) REVERT: R 91 ASP cc_start: 0.8966 (p0) cc_final: 0.8681 (p0) REVERT: R 134 LYS cc_start: 0.9257 (mtmm) cc_final: 0.9027 (mtpp) REVERT: R 141 MET cc_start: 0.9031 (mtp) cc_final: 0.8809 (mtm) REVERT: R 173 GLU cc_start: 0.8446 (mp0) cc_final: 0.7562 (mm-30) REVERT: R 199 ASP cc_start: 0.9031 (t70) cc_final: 0.8507 (t70) REVERT: R 245 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8286 (tp-100) outliers start: 12 outliers final: 7 residues processed: 111 average time/residue: 0.6463 time to fit residues: 76.3255 Evaluate side-chains 109 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 65 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.076571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.055749 restraints weight = 21829.983| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.08 r_work: 0.2687 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9193 Z= 0.141 Angle : 0.610 7.962 12546 Z= 0.321 Chirality : 0.043 0.193 1468 Planarity : 0.004 0.054 1546 Dihedral : 6.771 58.803 1644 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.87 % Allowed : 19.54 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.26), residues: 1144 helix: 1.73 (0.27), residues: 406 sheet: 0.48 (0.33), residues: 255 loop : -0.01 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 160 TYR 0.014 0.001 TYR A 230 PHE 0.011 0.001 PHE R 279 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9192) covalent geometry : angle 0.60964 (12544) SS BOND : bond 0.00271 ( 1) SS BOND : angle 0.37538 ( 2) hydrogen bonds : bond 0.03829 ( 453) hydrogen bonds : angle 4.44806 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3022.17 seconds wall clock time: 52 minutes 27.73 seconds (3147.73 seconds total)