Starting phenix.real_space_refine on Sun Jul 27 05:03:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sg1_40450/07_2025/8sg1_40450.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sg1_40450/07_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_40450/07_2025/8sg1_40450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sg1_40450/07_2025/8sg1_40450.map" model { file = "/net/cci-nas-00/data/ceres_data/8sg1_40450/07_2025/8sg1_40450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sg1_40450/07_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-5711/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: 5.84, per 1000 atoms: 0.66 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: 2.43 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: 1.06 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: 2.59 Time building geometry restraints manager: 2.86 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.320 Find NCS groups from input model: 0.100 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:13.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.550 ------------------------------------------------------------------------------- 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 9037 Z= 0.377 Angle : 0.890 19.854 12237 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 Details of bonding type rmsd hydrogen bonds : bond 0.19293 ( 401) hydrogen bonds : angle 6.68231 ( 1143) SS BOND : bond 0.00273 ( 3) SS BOND : angle 0.59027 ( 6) covalent geometry : bond 0.00534 ( 9034) covalent geometry : angle 0.88963 (12231) *********************** 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 : 0.907 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: 1.0808 time to fit residues: 148.8786 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 : 0.983 ------------------------------------------------------------------------------- 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 9037 Z= 0.115 Angle : 0.543 7.389 12237 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 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 401) hydrogen bonds : angle 4.62354 ( 1143) SS BOND : bond 0.00372 ( 3) SS BOND : angle 0.55549 ( 6) covalent geometry : bond 0.00248 ( 9034) covalent geometry : angle 0.54332 (12231) *********************** 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 : 1.067 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: 1.3342 time to fit residues: 163.9872 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 : 0.951 ------------------------------------------------------------------------------- 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 9037 Z= 0.111 Angle : 0.509 7.207 12237 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 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 401) hydrogen bonds : angle 4.32498 ( 1143) SS BOND : bond 0.00316 ( 3) SS BOND : angle 0.44064 ( 6) covalent geometry : bond 0.00247 ( 9034) covalent geometry : angle 0.50903 (12231) *********************** 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 : 1.030 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: 1.1847 time to fit residues: 167.2437 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 : 0.930 ------------------------------------------------------------------------------- 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 9037 Z= 0.113 Angle : 0.513 8.339 12237 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 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 401) hydrogen bonds : angle 4.18273 ( 1143) SS BOND : bond 0.00348 ( 3) SS BOND : angle 0.47493 ( 6) covalent geometry : bond 0.00258 ( 9034) covalent geometry : angle 0.51343 (12231) *********************** 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 : 1.450 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: 1.5103 time to fit residues: 206.0848 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 : 1.211 ------------------------------------------------------------------------------- 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 9037 Z= 0.164 Angle : 0.558 7.440 12237 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 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 401) hydrogen bonds : angle 4.24433 ( 1143) SS BOND : bond 0.00403 ( 3) SS BOND : angle 0.58690 ( 6) covalent geometry : bond 0.00395 ( 9034) covalent geometry : angle 0.55837 (12231) *********************** 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 : 0.926 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: 1.1952 time to fit residues: 162.6874 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 : 0.883 ------------------------------------------------------------------------------- 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: 2.9990 chunk 61 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.153960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106559 restraints weight = 10399.343| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.36 r_work: 0.3054 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9037 Z= 0.124 Angle : 0.537 9.836 12237 Z= 0.275 Chirality : 0.043 0.202 1395 Planarity : 0.004 0.053 1532 Dihedral : 5.469 55.870 1308 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.46 % Allowed : 18.22 % Favored : 78.32 % 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: 0.60 (0.25), residues: 1105 helix: 1.85 (0.29), residues: 368 sheet: 0.47 (0.30), residues: 282 loop : -0.85 (0.27), residues: 455 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 0.028 0.001 PHE R 169 TYR 0.017 0.001 TYR E 236 ARG 0.003 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 401) hydrogen bonds : angle 4.18572 ( 1143) SS BOND : bond 0.00330 ( 3) SS BOND : angle 0.52005 ( 6) covalent geometry : bond 0.00287 ( 9034) covalent geometry : angle 0.53660 (12231) *********************** 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 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: B 214 ARG cc_start: 0.8035 (mtt-85) cc_final: 0.7502 (mtm180) REVERT: B 215 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7728 (mm-30) REVERT: B 219 ARG cc_start: 0.7455 (ttm-80) cc_final: 0.7120 (mtt-85) REVERT: G 28 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.7080 (pp) REVERT: A 53 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.6397 (mtp) REVERT: E 62 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7239 (p0) REVERT: E 203 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.7085 (mtp180) REVERT: E 235 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7071 (mm-30) outliers start: 33 outliers final: 14 residues processed: 128 average time/residue: 1.6829 time to fit residues: 232.0321 Evaluate side-chains 120 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 27 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3741 r_free = 0.3741 target = 0.153819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106816 restraints weight = 10487.513| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.32 r_work: 0.3046 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9037 Z= 0.129 Angle : 0.541 9.545 12237 Z= 0.277 Chirality : 0.043 0.200 1395 Planarity : 0.004 0.053 1532 Dihedral : 5.504 57.853 1308 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.25 % Allowed : 18.95 % Favored : 77.80 % 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: 1.87 (0.28), residues: 368 sheet: 0.48 (0.30), residues: 282 loop : -0.84 (0.27), residues: 455 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 0.026 0.001 PHE R 169 TYR 0.019 0.001 TYR E 236 ARG 0.003 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 401) hydrogen bonds : angle 4.16047 ( 1143) SS BOND : bond 0.00344 ( 3) SS BOND : angle 0.41549 ( 6) covalent geometry : bond 0.00303 ( 9034) covalent geometry : angle 0.54147 (12231) *********************** 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: 31 poor density : 102 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: R 58 ASN cc_start: 0.5923 (m-40) cc_final: 0.5482 (m-40) REVERT: B 214 ARG cc_start: 0.8001 (mtt-85) cc_final: 0.7423 (mtm-85) REVERT: B 215 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7656 (mm-30) REVERT: B 219 ARG cc_start: 0.7439 (ttm-80) cc_final: 0.7091 (mtt-85) REVERT: G 28 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.7062 (pp) REVERT: E 62 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7199 (p0) REVERT: E 203 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.7197 (mtp180) REVERT: E 231 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.7147 (tpt) REVERT: E 235 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7014 (mm-30) REVERT: E 246 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6965 (mp) outliers start: 31 outliers final: 15 residues processed: 121 average time/residue: 1.1759 time to fit residues: 152.4779 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 : 0.949 ------------------------------------------------------------------------------- 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 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 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 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: 3.9990 chunk 48 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 75 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.152878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.105353 restraints weight = 10578.941| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.36 r_work: 0.3028 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9037 Z= 0.143 Angle : 0.560 11.156 12237 Z= 0.285 Chirality : 0.043 0.210 1395 Planarity : 0.004 0.053 1532 Dihedral : 5.586 58.759 1308 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.25 % Allowed : 19.06 % Favored : 77.70 % 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: 0.61 (0.25), residues: 1105 helix: 1.85 (0.28), residues: 368 sheet: 0.45 (0.30), residues: 282 loop : -0.82 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 77 HIS 0.004 0.001 HIS E 233 PHE 0.021 0.001 PHE R 169 TYR 0.022 0.001 TYR E 236 ARG 0.004 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 401) hydrogen bonds : angle 4.19862 ( 1143) SS BOND : bond 0.00360 ( 3) SS BOND : angle 0.58389 ( 6) covalent geometry : bond 0.00342 ( 9034) covalent geometry : angle 0.55992 (12231) *********************** 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: 31 poor density : 99 time to evaluate : 1.777 Fit side-chains REVERT: B 214 ARG cc_start: 0.7940 (mtt-85) cc_final: 0.7403 (mtm180) REVERT: B 215 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7616 (mm-30) REVERT: B 219 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.7024 (mtt-85) REVERT: G 28 ILE cc_start: 0.7228 (OUTLIER) cc_final: 0.6994 (pp) REVERT: E 62 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7189 (p0) REVERT: E 203 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7188 (mtp180) REVERT: E 231 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.6973 (tpt) REVERT: E 235 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7272 (mt-10) REVERT: E 246 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6989 (mp) outliers start: 31 outliers final: 21 residues processed: 122 average time/residue: 1.6299 time to fit residues: 212.1655 Evaluate side-chains 126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 262 MET Chi-restraints excluded: chain B residue 270 ILE 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 23 LEU 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 216 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 82 optimal weight: 0.0070 chunk 5 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 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: 0.0870 chunk 104 optimal weight: 0.0980 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 = 0.3751 r_free = 0.3751 target = 0.154666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107644 restraints weight = 10527.594| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.35 r_work: 0.3049 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9037 Z= 0.109 Angle : 0.533 11.961 12237 Z= 0.270 Chirality : 0.042 0.190 1395 Planarity : 0.004 0.051 1532 Dihedral : 5.438 59.634 1307 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.93 % Allowed : 19.48 % 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: 0.68 (0.25), residues: 1105 helix: 1.89 (0.29), residues: 368 sheet: 0.51 (0.30), residues: 282 loop : -0.78 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 77 HIS 0.003 0.001 HIS E 233 PHE 0.021 0.001 PHE R 169 TYR 0.015 0.001 TYR E 236 ARG 0.003 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 401) hydrogen bonds : angle 4.14409 ( 1143) SS BOND : bond 0.00313 ( 3) SS BOND : angle 0.69767 ( 6) covalent geometry : bond 0.00245 ( 9034) covalent geometry : angle 0.53296 (12231) *********************** 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 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: B 214 ARG cc_start: 0.7944 (mtt-85) cc_final: 0.7448 (mmp80) REVERT: B 215 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7669 (mm-30) REVERT: B 219 ARG cc_start: 0.7429 (ttm-80) cc_final: 0.7040 (mtt-85) REVERT: G 28 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6997 (pp) REVERT: E 62 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7187 (p0) REVERT: E 203 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7204 (mtp180) REVERT: E 231 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.6891 (tpt) REVERT: E 235 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7206 (mt-10) REVERT: E 246 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6969 (mp) outliers start: 28 outliers final: 16 residues processed: 124 average time/residue: 1.4866 time to fit residues: 198.1166 Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 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 270 ILE 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 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 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: 8.9990 chunk 14 optimal weight: 10.0000 chunk 99 optimal weight: 0.0470 chunk 20 optimal weight: 2.9990 chunk 80 optimal weight: 0.0470 chunk 90 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 0.7978 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.154779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107341 restraints weight = 10423.280| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.35 r_work: 0.3062 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9037 Z= 0.104 Angle : 0.524 13.826 12237 Z= 0.264 Chirality : 0.042 0.174 1395 Planarity : 0.004 0.051 1532 Dihedral : 5.196 58.470 1306 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.51 % Allowed : 19.90 % 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: 0.76 (0.25), residues: 1105 helix: 2.03 (0.29), residues: 360 sheet: 0.58 (0.30), residues: 280 loop : -0.77 (0.27), residues: 465 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 0.021 0.001 PHE R 169 TYR 0.015 0.001 TYR E 236 ARG 0.003 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 401) hydrogen bonds : angle 4.08629 ( 1143) SS BOND : bond 0.00296 ( 3) SS BOND : angle 0.57708 ( 6) covalent geometry : bond 0.00234 ( 9034) covalent geometry : angle 0.52370 (12231) ********************** 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 128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: B 214 ARG cc_start: 0.7933 (mtt-85) cc_final: 0.7459 (mmp80) REVERT: B 215 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7681 (mm-30) REVERT: B 219 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.7115 (mtt-85) REVERT: G 28 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.7048 (pp) REVERT: E 203 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7264 (mtp180) REVERT: E 231 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7036 (tpt) REVERT: E 235 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7269 (mt-10) outliers start: 24 outliers final: 16 residues processed: 121 average time/residue: 1.1616 time to fit residues: 150.7469 Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 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 E residue 45 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 15 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 0.0470 overall best weight: 1.3482 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.154590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106968 restraints weight = 10542.730| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.37 r_work: 0.3053 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.255 9037 Z= 0.211 Angle : 0.928 59.197 12237 Z= 0.527 Chirality : 0.046 0.721 1395 Planarity : 0.004 0.051 1532 Dihedral : 5.194 58.452 1306 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.99 % Allowed : 20.52 % Favored : 77.49 % Cbeta Deviations : 0.09 % 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: 0.75 (0.25), residues: 1105 helix: 2.03 (0.29), residues: 360 sheet: 0.57 (0.30), residues: 280 loop : -0.76 (0.27), residues: 465 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 0.018 0.001 PHE R 169 TYR 0.015 0.001 TYR E 236 ARG 0.003 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 401) hydrogen bonds : angle 4.08698 ( 1143) SS BOND : bond 0.00312 ( 3) SS BOND : angle 0.56716 ( 6) covalent geometry : bond 0.00434 ( 9034) covalent geometry : angle 0.92824 (12231) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7637.44 seconds wall clock time: 139 minutes 27.95 seconds (8367.95 seconds total)