Starting phenix.real_space_refine on Thu Mar 13 17:50:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sg1_40450/03_2025/8sg1_40450.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sg1_40450/03_2025/8sg1_40450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sg1_40450/03_2025/8sg1_40450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sg1_40450/03_2025/8sg1_40450.map" model { file = "/net/cci-nas-00/data/ceres_data/8sg1_40450/03_2025/8sg1_40450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sg1_40450/03_2025/8sg1_40450.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5669 2.51 5 N 1490 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8846 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2172 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 3 Chain: "L" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 77 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "E" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'CLR': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.49, per 1000 atoms: 0.62 Number of scatterers: 8846 At special positions: 0 Unit cell: (94.976, 119.568, 125.504, 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 66 16.00 O 1621 8.00 N 1490 7.00 C 5669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 189 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " 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: 2.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 36.2% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'R' and resid 36 through 65 removed outlier: 3.929A pdb=" N ILE R 41 " --> pdb=" O ARG R 37 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 92 removed outlier: 3.830A pdb=" N TRP R 77 " --> pdb=" O VAL R 73 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE R 88 " --> pdb=" O ALA R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 101 Processing helix chain 'R' and resid 108 through 112 Processing helix chain 'R' and resid 114 through 126 Processing helix chain 'R' and resid 127 through 143 removed outlier: 3.802A pdb=" N SER R 134 " --> pdb=" O LEU R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 150 removed outlier: 3.641A pdb=" N ASN R 149 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 172 removed outlier: 3.648A pdb=" N ALA R 156 " --> pdb=" O SER R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 177 removed outlier: 3.921A pdb=" N VAL R 176 " --> pdb=" O SER R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 251 removed outlier: 5.043A pdb=" N VAL R 231 " --> pdb=" O CYS R 227 " (cutoff:3.500A) Proline residue: R 232 - end of helix Processing helix chain 'R' and resid 256 through 283 removed outlier: 3.617A pdb=" N ILE R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 284 through 286 No H-bonds generated for 'chain 'R' and resid 284 through 286' Processing helix chain 'R' and resid 291 through 307 removed outlier: 3.758A pdb=" N LEU R 296 " --> pdb=" O SER R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix removed outlier: 3.889A pdb=" N ALA R 307 " --> pdb=" O ALA R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 312 removed outlier: 3.692A pdb=" N MET R 311 " --> pdb=" O ALA R 307 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN R 312 " --> pdb=" O ASN R 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 307 through 312' Processing helix chain 'R' and resid 312 through 317 removed outlier: 3.522A pdb=" N VAL R 317 " --> pdb=" O PRO R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 327 removed outlier: 4.031A pdb=" N PHE R 326 " --> pdb=" O ASP R 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.566A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 21 removed outlier: 4.235A pdb=" N MET G 21 " --> pdb=" O GLN G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'A' and resid 6 through 30 removed outlier: 3.853A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.197A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.689A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.576A pdb=" N GLY A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 221 through 225 removed outlier: 4.121A pdb=" N VAL E 225 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 178 through 183 Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.403A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.678A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.910A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.645A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.611A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.580A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.637A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.286A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.419A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 141 through 142 removed outlier: 3.714A pdb=" N VAL E 156 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 195 through 196 removed outlier: 6.674A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY E 226 " --> pdb=" O LEU E 246 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1143 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1412 1.31 - 1.44: 2497 1.44 - 1.56: 5028 1.56 - 1.69: 2 1.69 - 1.81: 95 Bond restraints: 9034 Sorted by residual: bond pdb=" C CYS R 272 " pdb=" O CYS R 272 " ideal model delta sigma weight residual 1.236 1.325 -0.089 1.15e-02 7.56e+03 5.93e+01 bond pdb=" C THR R 268 " pdb=" O THR R 268 " ideal model delta sigma weight residual 1.236 1.304 -0.068 1.15e-02 7.56e+03 3.45e+01 bond pdb=" C TRP R 273 " pdb=" O TRP R 273 " ideal model delta sigma weight residual 1.237 1.189 0.047 1.19e-02 7.06e+03 1.58e+01 bond pdb=" C PHE R 270 " pdb=" O PHE R 270 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.16e-02 7.43e+03 1.47e+01 bond pdb=" C ILE R 266 " pdb=" O ILE R 266 " ideal model delta sigma weight residual 1.237 1.277 -0.041 1.12e-02 7.97e+03 1.33e+01 ... (remaining 9029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 12136 3.97 - 7.94: 85 7.94 - 11.91: 9 11.91 - 15.88: 0 15.88 - 19.85: 1 Bond angle restraints: 12231 Sorted by residual: angle pdb=" CA PRO R 275 " pdb=" N PRO R 275 " pdb=" CD PRO R 275 " ideal model delta sigma weight residual 112.00 92.15 19.85 1.40e+00 5.10e-01 2.01e+02 angle pdb=" N MET R 111 " pdb=" CA MET R 111 " pdb=" C MET R 111 " ideal model delta sigma weight residual 112.88 103.50 9.38 1.29e+00 6.01e-01 5.29e+01 angle pdb=" N VAL R 73 " pdb=" CA VAL R 73 " pdb=" C VAL R 73 " ideal model delta sigma weight residual 113.42 105.36 8.06 1.17e+00 7.31e-01 4.75e+01 angle pdb=" N CYS R 112 " pdb=" CA CYS R 112 " pdb=" C CYS R 112 " ideal model delta sigma weight residual 114.56 106.02 8.54 1.27e+00 6.20e-01 4.52e+01 angle pdb=" CA TYR E 236 " pdb=" CB TYR E 236 " pdb=" CG TYR E 236 " ideal model delta sigma weight residual 113.90 103.37 10.53 1.80e+00 3.09e-01 3.42e+01 ... (remaining 12226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 4877 17.47 - 34.94: 408 34.94 - 52.41: 91 52.41 - 69.88: 14 69.88 - 87.34: 7 Dihedral angle restraints: 5397 sinusoidal: 2131 harmonic: 3266 Sorted by residual: dihedral pdb=" C TYR E 236 " pdb=" N TYR E 236 " pdb=" CA TYR E 236 " pdb=" CB TYR E 236 " ideal model delta harmonic sigma weight residual -122.60 -145.35 22.75 0 2.50e+00 1.60e-01 8.28e+01 dihedral pdb=" N TYR E 236 " pdb=" C TYR E 236 " pdb=" CA TYR E 236 " pdb=" CB TYR E 236 " ideal model delta harmonic sigma weight residual 122.80 144.39 -21.59 0 2.50e+00 1.60e-01 7.46e+01 dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 138.69 -45.69 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 5394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 1375 0.184 - 0.368: 19 0.368 - 0.552: 0 0.552 - 0.737: 0 0.737 - 0.921: 1 Chirality restraints: 1395 Sorted by residual: chirality pdb=" CA TYR E 236 " pdb=" N TYR E 236 " pdb=" C TYR E 236 " pdb=" CB TYR E 236 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb=" CA MET R 101 " pdb=" N MET R 101 " pdb=" C MET R 101 " pdb=" CB MET R 101 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA MET R 111 " pdb=" N MET R 111 " pdb=" C MET R 111 " pdb=" CB MET R 111 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 1392 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS R 274 " -0.127 5.00e-02 4.00e+02 1.73e-01 4.78e+01 pdb=" N PRO R 275 " 0.298 5.00e-02 4.00e+02 pdb=" CA PRO R 275 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO R 275 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 271 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C LEU R 271 " -0.074 2.00e-02 2.50e+03 pdb=" O LEU R 271 " 0.027 2.00e-02 2.50e+03 pdb=" N CYS R 272 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 275 " 0.021 2.00e-02 2.50e+03 4.21e-02 1.78e+01 pdb=" C PRO R 275 " -0.073 2.00e-02 2.50e+03 pdb=" O PRO R 275 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR R 276 " 0.025 2.00e-02 2.50e+03 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1528 2.77 - 3.30: 7933 3.30 - 3.83: 14018 3.83 - 4.37: 17055 4.37 - 4.90: 30530 Nonbonded interactions: 71064 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.235 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.246 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR E 151 " pdb=" OE1 GLU E 154 " model vdw 2.263 3.040 nonbonded pdb=" O THR E 145 " pdb=" OG1 THR E 244 " model vdw 2.265 3.040 ... (remaining 71059 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.640 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 0.089 9034 Z= 0.342 Angle : 0.890 19.854 12231 Z= 0.605 Chirality : 0.063 0.921 1395 Planarity : 0.007 0.173 1532 Dihedral : 13.730 87.345 3276 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.78 % Allowed : 17.49 % Favored : 80.73 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1105 helix: 0.90 (0.30), residues: 351 sheet: 0.41 (0.31), residues: 281 loop : -0.79 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 273 HIS 0.013 0.001 HIS B 225 PHE 0.029 0.001 PHE L 154 TYR 0.061 0.002 TYR E 236 ARG 0.009 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 275 PRO cc_start: 0.6854 (OUTLIER) cc_final: 0.6601 (Cg_exo) REVERT: B 197 ARG cc_start: 0.7576 (mmt90) cc_final: 0.7074 (mpt180) REVERT: E 235 GLU cc_start: 0.7585 (mt-10) cc_final: 0.6745 (mm-30) outliers start: 17 outliers final: 15 residues processed: 128 average time/residue: 1.0805 time to fit residues: 149.0259 Evaluate side-chains 121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 275 PRO Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 74 ASN R 150 HIS B 175 GLN B 266 HIS B 340 ASN G 59 ASN A 331 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111839 restraints weight = 10371.068| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.38 r_work: 0.3072 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9034 Z= 0.164 Angle : 0.543 7.389 12231 Z= 0.286 Chirality : 0.042 0.208 1395 Planarity : 0.004 0.052 1532 Dihedral : 5.968 58.917 1324 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.09 % Allowed : 17.17 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1105 helix: 1.51 (0.29), residues: 362 sheet: 0.52 (0.30), residues: 280 loop : -0.79 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 77 HIS 0.003 0.001 HIS E 35 PHE 0.019 0.001 PHE R 259 TYR 0.018 0.001 TYR E 191 ARG 0.003 0.000 ARG R 249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 111 MET cc_start: 0.6888 (tpp) cc_final: 0.6611 (tpp) REVERT: B 215 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7639 (mm-30) REVERT: B 219 ARG cc_start: 0.7406 (ttm-80) cc_final: 0.7096 (mtt-85) REVERT: E 173 THR cc_start: 0.7980 (OUTLIER) cc_final: 0.7678 (t) REVERT: E 235 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7008 (mm-30) REVERT: E 236 TYR cc_start: 0.6493 (OUTLIER) cc_final: 0.5545 (t80) outliers start: 20 outliers final: 7 residues processed: 115 average time/residue: 1.1958 time to fit residues: 147.3307 Evaluate side-chains 104 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 236 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.155952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108482 restraints weight = 10550.918| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.39 r_work: 0.3082 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9034 Z= 0.164 Angle : 0.509 7.207 12231 Z= 0.266 Chirality : 0.042 0.208 1395 Planarity : 0.004 0.051 1532 Dihedral : 5.379 54.179 1308 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.14 % Allowed : 16.86 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.26), residues: 1105 helix: 1.82 (0.29), residues: 367 sheet: 0.52 (0.30), residues: 281 loop : -0.81 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 77 HIS 0.003 0.001 HIS E 233 PHE 0.025 0.001 PHE R 169 TYR 0.017 0.001 TYR E 236 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: R 271 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.7061 (mp) REVERT: B 214 ARG cc_start: 0.7975 (mtt-85) cc_final: 0.7440 (mtm180) REVERT: B 215 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7773 (mm-30) REVERT: B 219 ARG cc_start: 0.7409 (ttm-80) cc_final: 0.7140 (mtt-85) REVERT: G 28 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.7073 (pp) REVERT: A 53 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.6555 (mtp) REVERT: E 203 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6897 (mtp180) REVERT: E 235 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7117 (mm-30) REVERT: E 236 TYR cc_start: 0.5871 (OUTLIER) cc_final: 0.5015 (t80) outliers start: 30 outliers final: 11 residues processed: 131 average time/residue: 1.0963 time to fit residues: 154.4526 Evaluate side-chains 116 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 236 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 0.0570 chunk 103 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 250 ASN B 175 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.155059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107377 restraints weight = 10467.701| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.37 r_work: 0.3078 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9034 Z= 0.171 Angle : 0.513 8.339 12231 Z= 0.267 Chirality : 0.042 0.194 1395 Planarity : 0.004 0.050 1532 Dihedral : 5.328 53.789 1308 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.93 % Allowed : 17.59 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1105 helix: 1.83 (0.29), residues: 368 sheet: 0.51 (0.30), residues: 281 loop : -0.82 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 77 HIS 0.003 0.001 HIS E 35 PHE 0.025 0.001 PHE R 169 TYR 0.017 0.001 TYR E 236 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: R 111 MET cc_start: 0.6787 (tpp) cc_final: 0.6456 (tpp) REVERT: B 214 ARG cc_start: 0.7920 (mtt-85) cc_final: 0.7399 (mtm180) REVERT: B 215 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7623 (mm-30) REVERT: B 219 ARG cc_start: 0.7383 (ttm-80) cc_final: 0.7094 (mtt-85) REVERT: G 28 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.7055 (pp) REVERT: A 53 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.6357 (mtp) REVERT: E 203 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6864 (mtp180) REVERT: E 232 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8844 (tm-30) REVERT: E 235 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7052 (mm-30) REVERT: E 246 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6891 (mp) outliers start: 28 outliers final: 10 residues processed: 127 average time/residue: 1.1236 time to fit residues: 153.1758 Evaluate side-chains 114 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 106 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 250 ASN B 175 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.152600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105171 restraints weight = 10484.092| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.35 r_work: 0.3025 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9034 Z= 0.261 Angle : 0.558 7.440 12231 Z= 0.291 Chirality : 0.044 0.222 1395 Planarity : 0.004 0.055 1532 Dihedral : 5.565 54.696 1308 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.04 % Allowed : 18.43 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1105 helix: 1.80 (0.29), residues: 368 sheet: 0.45 (0.30), residues: 281 loop : -0.89 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 47 HIS 0.005 0.001 HIS E 233 PHE 0.016 0.001 PHE E 68 TYR 0.025 0.002 TYR E 236 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: B 214 ARG cc_start: 0.7963 (mtt-85) cc_final: 0.7413 (mtm180) REVERT: B 215 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7640 (mm-30) REVERT: B 219 ARG cc_start: 0.7477 (ttm-80) cc_final: 0.7117 (mtt-85) REVERT: G 28 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.7021 (pp) REVERT: A 53 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6338 (mtp) REVERT: E 62 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7214 (p0) REVERT: E 203 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6980 (mtp180) REVERT: E 235 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7119 (mm-30) REVERT: E 246 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6919 (mp) outliers start: 29 outliers final: 14 residues processed: 127 average time/residue: 1.1514 time to fit residues: 157.0776 Evaluate side-chains 120 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 93 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 61 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.155355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108530 restraints weight = 10401.131| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.33 r_work: 0.3064 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9034 Z= 0.154 Angle : 0.521 9.782 12231 Z= 0.265 Chirality : 0.042 0.189 1395 Planarity : 0.004 0.052 1532 Dihedral : 5.355 55.580 1308 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.14 % Allowed : 18.32 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1105 helix: 1.88 (0.29), residues: 368 sheet: 0.48 (0.30), residues: 283 loop : -0.82 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.027 0.001 PHE R 169 TYR 0.016 0.001 TYR E 236 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: R 58 ASN cc_start: 0.6023 (m-40) cc_final: 0.5525 (m-40) REVERT: B 214 ARG cc_start: 0.7983 (mtt-85) cc_final: 0.7439 (mtm180) REVERT: B 215 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7682 (mm-30) REVERT: B 219 ARG cc_start: 0.7422 (ttm-80) cc_final: 0.7111 (mtt-85) REVERT: G 28 ILE cc_start: 0.7276 (OUTLIER) cc_final: 0.7041 (pp) REVERT: A 53 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.6400 (mtp) REVERT: E 38 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8098 (ttp-170) REVERT: E 62 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7227 (p0) REVERT: E 203 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.7059 (mtp180) REVERT: E 216 THR cc_start: 0.7732 (OUTLIER) cc_final: 0.7505 (p) REVERT: E 235 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7000 (mm-30) outliers start: 30 outliers final: 14 residues processed: 127 average time/residue: 1.3909 time to fit residues: 189.6277 Evaluate side-chains 123 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 232 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 27 optimal weight: 30.0000 chunk 101 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.155515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108618 restraints weight = 10449.593| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.33 r_work: 0.3055 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9034 Z= 0.160 Angle : 0.518 9.753 12231 Z= 0.264 Chirality : 0.042 0.183 1395 Planarity : 0.004 0.051 1532 Dihedral : 5.291 57.008 1308 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.14 % Allowed : 18.74 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1105 helix: 1.90 (0.29), residues: 368 sheet: 0.53 (0.30), residues: 282 loop : -0.80 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 77 HIS 0.004 0.001 HIS E 233 PHE 0.025 0.001 PHE R 169 TYR 0.017 0.001 TYR E 236 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: R 58 ASN cc_start: 0.5787 (m-40) cc_final: 0.5357 (m-40) REVERT: B 214 ARG cc_start: 0.7978 (mtt-85) cc_final: 0.7418 (mtm180) REVERT: B 215 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7663 (mm-30) REVERT: B 219 ARG cc_start: 0.7367 (ttm-80) cc_final: 0.7024 (mtt-85) REVERT: G 28 ILE cc_start: 0.7251 (OUTLIER) cc_final: 0.7014 (pp) REVERT: E 38 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.8055 (ttp-170) REVERT: E 62 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7257 (p0) REVERT: E 203 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.7066 (mtp180) REVERT: E 235 GLU cc_start: 0.7598 (mt-10) cc_final: 0.6955 (mm-30) REVERT: E 246 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6878 (mp) outliers start: 30 outliers final: 16 residues processed: 122 average time/residue: 1.1473 time to fit residues: 150.0451 Evaluate side-chains 123 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 57 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 75 optimal weight: 0.0370 chunk 4 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.153459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105836 restraints weight = 10562.052| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.38 r_work: 0.3025 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9034 Z= 0.215 Angle : 0.552 11.100 12231 Z= 0.280 Chirality : 0.043 0.203 1395 Planarity : 0.004 0.052 1532 Dihedral : 5.400 58.293 1307 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.04 % Allowed : 18.85 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1105 helix: 1.87 (0.29), residues: 368 sheet: 0.51 (0.30), residues: 280 loop : -0.82 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 77 HIS 0.005 0.001 HIS E 233 PHE 0.020 0.001 PHE R 169 TYR 0.021 0.001 TYR E 236 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 1.589 Fit side-chains revert: symmetry clash REVERT: B 214 ARG cc_start: 0.7968 (mtt-85) cc_final: 0.7390 (mtm180) REVERT: B 215 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 219 ARG cc_start: 0.7447 (ttm-80) cc_final: 0.7082 (mtt-85) REVERT: G 28 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.7006 (pp) REVERT: E 11 LEU cc_start: 0.8118 (tt) cc_final: 0.7511 (mp) REVERT: E 62 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7234 (p0) REVERT: E 203 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7142 (mtp180) REVERT: E 216 THR cc_start: 0.7705 (OUTLIER) cc_final: 0.7498 (p) REVERT: E 231 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.6938 (tpt) REVERT: E 235 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7290 (mt-10) REVERT: E 246 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6954 (mp) outliers start: 29 outliers final: 16 residues processed: 121 average time/residue: 1.3975 time to fit residues: 180.8164 Evaluate side-chains 124 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 82 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 88 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.148907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101623 restraints weight = 10639.315| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.34 r_work: 0.2975 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9034 Z= 0.392 Angle : 0.655 13.001 12231 Z= 0.336 Chirality : 0.047 0.266 1395 Planarity : 0.004 0.058 1532 Dihedral : 6.045 58.087 1307 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.14 % Allowed : 18.95 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1105 helix: 1.77 (0.28), residues: 361 sheet: 0.33 (0.29), residues: 282 loop : -0.83 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 47 HIS 0.006 0.001 HIS E 35 PHE 0.018 0.002 PHE E 68 TYR 0.032 0.002 TYR E 236 ARG 0.006 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.964 Fit side-chains REVERT: B 214 ARG cc_start: 0.7961 (mtt-85) cc_final: 0.7419 (mtm180) REVERT: B 215 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7749 (mm-30) REVERT: G 28 ILE cc_start: 0.7214 (OUTLIER) cc_final: 0.6979 (pp) REVERT: G 47 GLU cc_start: 0.8211 (pt0) cc_final: 0.7898 (pt0) REVERT: E 62 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7268 (p0) REVERT: E 203 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7177 (mtp180) REVERT: E 231 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8542 (tmm) REVERT: E 235 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7558 (mt-10) REVERT: E 246 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.7061 (mp) outliers start: 30 outliers final: 18 residues processed: 125 average time/residue: 1.4307 time to fit residues: 192.0758 Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 9 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.151553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.104248 restraints weight = 10500.895| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.34 r_work: 0.3012 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9034 Z= 0.220 Angle : 0.571 12.989 12231 Z= 0.292 Chirality : 0.043 0.224 1395 Planarity : 0.004 0.052 1532 Dihedral : 5.711 59.107 1306 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.41 % Allowed : 20.10 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1105 helix: 1.87 (0.29), residues: 362 sheet: 0.37 (0.30), residues: 282 loop : -0.79 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.012 0.001 PHE A 189 TYR 0.025 0.001 TYR E 236 ARG 0.003 0.000 ARG B 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.993 Fit side-chains REVERT: B 214 ARG cc_start: 0.7856 (mtt-85) cc_final: 0.7325 (mtm-85) REVERT: B 215 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7621 (mm-30) REVERT: B 219 ARG cc_start: 0.7462 (ttm-80) cc_final: 0.7056 (mtt-85) REVERT: G 28 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6950 (pp) REVERT: G 47 GLU cc_start: 0.8164 (pt0) cc_final: 0.7863 (pt0) REVERT: E 62 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7249 (p0) REVERT: E 203 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7216 (mtp180) REVERT: E 231 MET cc_start: 0.8764 (tpt) cc_final: 0.7040 (tpt) REVERT: E 235 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7377 (mt-10) REVERT: E 246 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.7043 (mp) outliers start: 23 outliers final: 16 residues processed: 120 average time/residue: 1.2347 time to fit residues: 158.9214 Evaluate side-chains 120 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 15 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 175 GLN A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.154398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.107127 restraints weight = 10580.433| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.37 r_work: 0.3050 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9034 Z= 0.158 Angle : 0.532 13.528 12231 Z= 0.269 Chirality : 0.042 0.177 1395 Planarity : 0.004 0.051 1532 Dihedral : 5.304 58.171 1306 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.20 % Allowed : 20.21 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1105 helix: 1.95 (0.29), residues: 366 sheet: 0.47 (0.30), residues: 282 loop : -0.84 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 77 HIS 0.003 0.001 HIS E 35 PHE 0.027 0.001 PHE R 169 TYR 0.014 0.001 TYR E 191 ARG 0.002 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7194.85 seconds wall clock time: 128 minutes 33.86 seconds (7713.86 seconds total)