Starting phenix.real_space_refine on Thu Jul 2 13:44:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eo2_31225/07_2026/7eo2_31225_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eo2_31225/07_2026/7eo2_31225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7eo2_31225/07_2026/7eo2_31225_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eo2_31225/07_2026/7eo2_31225_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eo2_31225/07_2026/7eo2_31225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eo2_31225/07_2026/7eo2_31225.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.106 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 63 5.16 5 C 5665 2.51 5 N 1498 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8865 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2257 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 6, 'TRANS': 273} Chain breaks: 3 Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1769 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 2, 'TRANS': 217} Chain breaks: 2 Chain: "C" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'J89': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.68, per 1000 atoms: 0.19 Number of scatterers: 8865 At special positions: 0 Unit cell: (95.7, 121, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 1 15.00 O 1638 8.00 N 1498 7.00 C 5665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 338.0 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 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 12 sheets defined 37.3% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 removed outlier: 4.339A pdb=" N ILE A 25 " --> pdb=" O ASN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 71 Processing helix chain 'A' and resid 78 through 104 Processing helix chain 'A' and resid 105 through 111 removed outlier: 4.166A pdb=" N THR A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 146 removed outlier: 3.855A pdb=" N MET A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.742A pdb=" N GLY A 181 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 199 through 233 removed outlier: 3.774A pdb=" N ILE A 203 " --> pdb=" O HIS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 280 removed outlier: 3.611A pdb=" N VAL A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 288 through 292 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.939A pdb=" N VAL A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU A 299 " --> pdb=" O TYR A 295 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 315 through 322 Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.883A pdb=" N LYS B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.542A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.567A pdb=" N TRP B 211 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.766A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.570A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 329 through 351 removed outlier: 3.837A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 25 removed outlier: 3.731A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 6 through 24 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.794A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.522A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.606A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 3.768A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 7.059A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.954A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.924A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.906A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 158 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.152A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 232 removed outlier: 3.959A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 276 through 278 Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 6.288A pdb=" N GLY E 16 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.431A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.308A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1161 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2817 1.35 - 1.48: 2296 1.48 - 1.61: 3835 1.61 - 1.74: 1 1.74 - 1.87: 91 Bond restraints: 9040 Sorted by residual: bond pdb=" O21 J89 A 401 " pdb=" P22 J89 A 401 " ideal model delta sigma weight residual 1.716 1.866 -0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" C17 J89 A 401 " pdb=" C20 J89 A 401 " ideal model delta sigma weight residual 1.536 1.640 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C GLU E 222 " pdb=" N TYR E 223 " ideal model delta sigma weight residual 1.328 1.273 0.055 1.44e-02 4.82e+03 1.45e+01 bond pdb=" N TRP C 82 " pdb=" CA TRP C 82 " ideal model delta sigma weight residual 1.455 1.499 -0.043 1.23e-02 6.61e+03 1.24e+01 bond pdb=" C16 J89 A 401 " pdb=" C17 J89 A 401 " ideal model delta sigma weight residual 1.540 1.603 -0.063 2.00e-02 2.50e+03 1.00e+01 ... (remaining 9035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 11989 2.17 - 4.34: 210 4.34 - 6.52: 24 6.52 - 8.69: 7 8.69 - 10.86: 2 Bond angle restraints: 12232 Sorted by residual: angle pdb=" N MET E 180 " pdb=" CA MET E 180 " pdb=" CB MET E 180 " ideal model delta sigma weight residual 114.17 108.88 5.29 1.14e+00 7.69e-01 2.15e+01 angle pdb=" N LEU A 151 " pdb=" CA LEU A 151 " pdb=" C LEU A 151 " ideal model delta sigma weight residual 111.14 116.03 -4.89 1.08e+00 8.57e-01 2.05e+01 angle pdb=" C LEU A 147 " pdb=" CA LEU A 147 " pdb=" CB LEU A 147 " ideal model delta sigma weight residual 110.45 103.07 7.38 1.73e+00 3.34e-01 1.82e+01 angle pdb=" C SER E 52 " pdb=" CA SER E 52 " pdb=" CB SER E 52 " ideal model delta sigma weight residual 110.36 103.50 6.86 1.78e+00 3.16e-01 1.49e+01 angle pdb=" N MET A 318 " pdb=" CA MET A 318 " pdb=" C MET A 318 " ideal model delta sigma weight residual 111.07 107.03 4.04 1.07e+00 8.73e-01 1.42e+01 ... (remaining 12227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.38: 5103 22.38 - 44.76: 232 44.76 - 67.14: 32 67.14 - 89.52: 15 89.52 - 111.90: 2 Dihedral angle restraints: 5384 sinusoidal: 2114 harmonic: 3270 Sorted by residual: dihedral pdb=" CA TRP C 82 " pdb=" C TRP C 82 " pdb=" N ASP C 83 " pdb=" CA ASP C 83 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA PHE C 235 " pdb=" C PHE C 235 " pdb=" N PRO C 236 " pdb=" CA PRO C 236 " ideal model delta harmonic sigma weight residual 180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TRP B 211 " pdb=" C TRP B 211 " pdb=" N ILE B 212 " pdb=" CA ILE B 212 " ideal model delta harmonic sigma weight residual 180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1203 0.059 - 0.118: 172 0.118 - 0.177: 29 0.177 - 0.236: 2 0.236 - 0.295: 2 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA TRP C 82 " pdb=" N TRP C 82 " pdb=" C TRP C 82 " pdb=" CB TRP C 82 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA ALA A 253 " pdb=" N ALA A 253 " pdb=" C ALA A 253 " pdb=" CB ALA A 253 " both_signs ideal model delta sigma weight residual False 2.48 2.73 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA HIS D 44 " pdb=" N HIS D 44 " pdb=" C HIS D 44 " pdb=" CB HIS D 44 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1405 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 177 " 0.046 5.00e-02 4.00e+02 6.97e-02 7.78e+00 pdb=" N PRO A 178 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.73e+00 pdb=" N PRO E 75 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO E 107 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " -0.030 5.00e-02 4.00e+02 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 232 2.70 - 3.25: 8556 3.25 - 3.80: 12782 3.80 - 4.35: 16597 4.35 - 4.90: 29144 Nonbonded interactions: 67311 Sorted by model distance: nonbonded pdb=" N GLY C 144 " pdb=" OD2 ASP C 163 " model vdw 2.152 3.120 nonbonded pdb=" OD1 ASN B 269 " pdb=" OG1 THR B 324 " model vdw 2.187 3.040 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.229 3.040 nonbonded pdb=" OG SER A 192 " pdb=" O LEU A 195 " model vdw 2.291 3.040 nonbonded pdb=" OE2 GLU B 318 " pdb=" OH TYR B 320 " model vdw 2.296 3.040 ... (remaining 67306 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: 0.010 Normalize map: mean=0, sd=1: 1.000 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.460 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 9043 Z= 0.224 Angle : 0.732 10.861 12238 Z= 0.429 Chirality : 0.045 0.295 1408 Planarity : 0.004 0.070 1520 Dihedral : 13.505 111.902 3263 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.25), residues: 1104 helix: 1.47 (0.27), residues: 367 sheet: -0.52 (0.31), residues: 265 loop : -1.86 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 78 TYR 0.013 0.001 TYR C 124 PHE 0.016 0.001 PHE C 199 TRP 0.017 0.002 TRP E 164 HIS 0.007 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.22 ( 9040) covalent geometry : angle 0.73183 / 0.43 (12232) SS BOND : bond 0.00466 / 0.17 ( 3) SS BOND : angle 0.75033 / 0.41 ( 6) hydrogen bonds : bond 0.14291 / 8.73 ( 422) hydrogen bonds : angle 5.58721 / 3.99 ( 1161) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 HIS cc_start: 0.6461 (m-70) cc_final: 0.5869 (m90) REVERT: E 18 ARG cc_start: 0.8095 (tpp80) cc_final: 0.7810 (mmt90) REVERT: E 218 MET cc_start: 0.8204 (ttp) cc_final: 0.7561 (ttt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.4051 time to fit residues: 54.2835 Evaluate side-chains 94 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.0010 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.0020 chunk 106 optimal weight: 0.8980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS E 171 GLN E 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.215521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.155310 restraints weight = 10766.257| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.13 r_work: 0.3783 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9043 Z= 0.120 Angle : 0.551 8.496 12238 Z= 0.296 Chirality : 0.042 0.145 1408 Planarity : 0.004 0.059 1520 Dihedral : 5.672 66.304 1241 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.75 % Allowed : 7.62 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.26), residues: 1104 helix: 2.36 (0.27), residues: 369 sheet: -0.01 (0.30), residues: 271 loop : -1.28 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 148 TYR 0.017 0.001 TYR A 98 PHE 0.022 0.002 PHE A 273 TRP 0.014 0.002 TRP C 211 HIS 0.007 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 ( 9040) covalent geometry : angle 0.55102 / 0.30 (12232) SS BOND : bond 0.00270 / 0.10 ( 3) SS BOND : angle 0.51004 / 0.25 ( 6) hydrogen bonds : bond 0.05119 / 3.38 ( 422) hydrogen bonds : angle 4.33451 / 3.12 ( 1161) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 HIS cc_start: 0.6433 (m-70) cc_final: 0.5991 (m90) REVERT: B 350 ASP cc_start: 0.6197 (OUTLIER) cc_final: 0.5995 (t70) REVERT: E 18 ARG cc_start: 0.7627 (tpp80) cc_final: 0.7408 (mmt90) REVERT: E 218 MET cc_start: 0.8431 (ttp) cc_final: 0.7926 (ttt) outliers start: 17 outliers final: 5 residues processed: 138 average time/residue: 0.4041 time to fit residues: 60.3010 Evaluate side-chains 110 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS E 113 GLN E 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.206181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.144412 restraints weight = 10596.169| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.10 r_work: 0.3653 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9043 Z= 0.216 Angle : 0.666 7.850 12238 Z= 0.357 Chirality : 0.045 0.177 1408 Planarity : 0.005 0.062 1520 Dihedral : 5.990 64.354 1241 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.99 % Allowed : 10.92 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.26), residues: 1104 helix: 2.24 (0.26), residues: 370 sheet: -0.04 (0.33), residues: 252 loop : -1.13 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 150 TYR 0.018 0.002 TYR A 202 PHE 0.025 0.003 PHE C 253 TRP 0.021 0.002 TRP B 211 HIS 0.007 0.002 HIS E 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 ( 9040) covalent geometry : angle 0.66559 / 0.36 (12232) SS BOND : bond 0.00593 / 0.22 ( 3) SS BOND : angle 0.73374 / 0.39 ( 6) hydrogen bonds : bond 0.07477 / 4.96 ( 422) hydrogen bonds : angle 4.62196 / 3.31 ( 1161) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 HIS cc_start: 0.6419 (m-70) cc_final: 0.5843 (m90) REVERT: A 141 GLU cc_start: 0.6770 (tp30) cc_final: 0.6567 (tt0) REVERT: C 304 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6377 (ttp80) REVERT: E 18 ARG cc_start: 0.7715 (tpp80) cc_final: 0.7430 (mmt90) REVERT: E 130 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.5997 (mm-40) REVERT: E 218 MET cc_start: 0.8495 (ttp) cc_final: 0.8012 (ttt) outliers start: 29 outliers final: 18 residues processed: 122 average time/residue: 0.4090 time to fit residues: 54.0464 Evaluate side-chains 114 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 130 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 100 optimal weight: 0.0000 chunk 92 optimal weight: 0.0980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 HIS E 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.212864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.151964 restraints weight = 10834.531| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.14 r_work: 0.3738 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9043 Z= 0.114 Angle : 0.521 8.069 12238 Z= 0.279 Chirality : 0.040 0.146 1408 Planarity : 0.004 0.059 1520 Dihedral : 5.034 47.309 1241 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.85 % Allowed : 12.98 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.26), residues: 1104 helix: 2.60 (0.27), residues: 376 sheet: 0.26 (0.31), residues: 268 loop : -1.08 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 148 TYR 0.016 0.001 TYR A 98 PHE 0.018 0.001 PHE A 273 TRP 0.015 0.001 TRP C 82 HIS 0.006 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 9040) covalent geometry : angle 0.52133 / 0.28 (12232) SS BOND : bond 0.00378 / 0.14 ( 3) SS BOND : angle 0.61459 / 0.30 ( 6) hydrogen bonds : bond 0.05070 / 3.35 ( 422) hydrogen bonds : angle 4.13561 / 2.98 ( 1161) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 HIS cc_start: 0.6454 (m90) cc_final: 0.5762 (m90) REVERT: C 45 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.6812 (mtp) REVERT: C 217 MET cc_start: 0.6097 (ptt) cc_final: 0.5661 (pmm) REVERT: C 304 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6740 (ttp80) REVERT: C 325 MET cc_start: 0.7786 (ttm) cc_final: 0.7544 (ttp) REVERT: E 211 ASP cc_start: 0.8047 (m-30) cc_final: 0.7424 (t0) REVERT: E 218 MET cc_start: 0.8459 (ttp) cc_final: 0.7994 (ttt) outliers start: 18 outliers final: 11 residues processed: 118 average time/residue: 0.4701 time to fit residues: 59.6792 Evaluate side-chains 110 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 80 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 94 optimal weight: 0.0670 chunk 83 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 241 ASN C 183 HIS E 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.212624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.151737 restraints weight = 10744.066| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 3.11 r_work: 0.3741 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9043 Z= 0.114 Angle : 0.516 6.800 12238 Z= 0.277 Chirality : 0.041 0.139 1408 Planarity : 0.004 0.059 1520 Dihedral : 4.798 49.785 1241 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.47 % Allowed : 14.32 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.26), residues: 1104 helix: 2.73 (0.27), residues: 376 sheet: 0.41 (0.31), residues: 267 loop : -1.00 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 208 TYR 0.013 0.001 TYR E 178 PHE 0.022 0.001 PHE A 273 TRP 0.014 0.001 TRP C 82 HIS 0.006 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 9040) covalent geometry : angle 0.51646 / 0.28 (12232) SS BOND : bond 0.00298 / 0.11 ( 3) SS BOND : angle 0.55984 / 0.31 ( 6) hydrogen bonds : bond 0.04939 / 3.26 ( 422) hydrogen bonds : angle 4.02285 / 2.90 ( 1161) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 HIS cc_start: 0.6234 (m90) cc_final: 0.5758 (m90) REVERT: C 45 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.6875 (mtp) REVERT: C 217 MET cc_start: 0.6095 (ptt) cc_final: 0.5663 (pmm) REVERT: C 226 GLU cc_start: 0.5728 (OUTLIER) cc_final: 0.5238 (mp0) REVERT: C 262 MET cc_start: 0.5942 (ttt) cc_final: 0.5016 (mpp) REVERT: C 325 MET cc_start: 0.7748 (ttm) cc_final: 0.7458 (ttp) REVERT: E 211 ASP cc_start: 0.7992 (m-30) cc_final: 0.7419 (t0) REVERT: E 218 MET cc_start: 0.8447 (ttp) cc_final: 0.7904 (ttt) outliers start: 24 outliers final: 15 residues processed: 113 average time/residue: 0.3998 time to fit residues: 48.6662 Evaluate side-chains 109 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.212794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.151824 restraints weight = 10661.753| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 3.11 r_work: 0.3741 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9043 Z= 0.113 Angle : 0.518 7.229 12238 Z= 0.274 Chirality : 0.040 0.137 1408 Planarity : 0.004 0.057 1520 Dihedral : 4.719 49.634 1241 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.16 % Allowed : 14.52 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.26), residues: 1104 helix: 2.74 (0.27), residues: 377 sheet: 0.56 (0.32), residues: 257 loop : -0.94 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 304 TYR 0.015 0.001 TYR A 81 PHE 0.022 0.001 PHE A 273 TRP 0.013 0.001 TRP C 82 HIS 0.006 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 9040) covalent geometry : angle 0.51785 / 0.27 (12232) SS BOND : bond 0.00327 / 0.12 ( 3) SS BOND : angle 0.63299 / 0.36 ( 6) hydrogen bonds : bond 0.04818 / 3.19 ( 422) hydrogen bonds : angle 3.97791 / 2.87 ( 1161) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 45 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.6938 (mtp) REVERT: C 217 MET cc_start: 0.6073 (ptt) cc_final: 0.5647 (pmm) REVERT: C 262 MET cc_start: 0.5877 (ttt) cc_final: 0.5025 (mpp) REVERT: C 325 MET cc_start: 0.7641 (ttm) cc_final: 0.7383 (ttp) REVERT: E 189 ASP cc_start: 0.7675 (m-30) cc_final: 0.7410 (t0) REVERT: E 211 ASP cc_start: 0.7960 (m-30) cc_final: 0.7391 (t0) REVERT: E 218 MET cc_start: 0.8443 (ttp) cc_final: 0.7854 (ttt) outliers start: 21 outliers final: 13 residues processed: 113 average time/residue: 0.4658 time to fit residues: 56.5651 Evaluate side-chains 110 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 37 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 chunk 73 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 GLN E 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.213321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.152067 restraints weight = 10749.868| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 3.11 r_work: 0.3745 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9043 Z= 0.110 Angle : 0.511 6.960 12238 Z= 0.272 Chirality : 0.040 0.135 1408 Planarity : 0.004 0.058 1520 Dihedral : 4.617 53.080 1241 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.75 % Allowed : 15.65 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.26), residues: 1104 helix: 2.81 (0.27), residues: 377 sheet: 0.62 (0.32), residues: 257 loop : -0.89 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 304 TYR 0.013 0.001 TYR E 178 PHE 0.023 0.001 PHE A 273 TRP 0.013 0.001 TRP C 82 HIS 0.005 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9040) covalent geometry : angle 0.51124 / 0.27 (12232) SS BOND : bond 0.00323 / 0.12 ( 3) SS BOND : angle 0.48773 / 0.26 ( 6) hydrogen bonds : bond 0.04690 / 3.10 ( 422) hydrogen bonds : angle 3.94128 / 2.83 ( 1161) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 275 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6359 (tm) REVERT: C 45 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.6913 (mtp) REVERT: C 217 MET cc_start: 0.6070 (ptt) cc_final: 0.5645 (pmm) REVERT: C 262 MET cc_start: 0.5860 (ttt) cc_final: 0.5011 (mpp) REVERT: C 325 MET cc_start: 0.7648 (ttm) cc_final: 0.7327 (ttp) REVERT: E 130 GLN cc_start: 0.6477 (OUTLIER) cc_final: 0.5989 (mm110) REVERT: E 189 ASP cc_start: 0.7769 (m-30) cc_final: 0.7517 (t0) REVERT: E 211 ASP cc_start: 0.7928 (m-30) cc_final: 0.7408 (t0) REVERT: E 218 MET cc_start: 0.8441 (ttp) cc_final: 0.7973 (ttt) outliers start: 17 outliers final: 12 residues processed: 111 average time/residue: 0.4227 time to fit residues: 50.5210 Evaluate side-chains 112 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 130 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 33 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.213123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.152278 restraints weight = 10667.125| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.09 r_work: 0.3756 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9043 Z= 0.113 Angle : 0.526 8.499 12238 Z= 0.278 Chirality : 0.041 0.141 1408 Planarity : 0.004 0.057 1520 Dihedral : 4.624 54.647 1241 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.85 % Allowed : 16.89 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.26), residues: 1104 helix: 2.98 (0.27), residues: 371 sheet: 0.64 (0.32), residues: 257 loop : -0.84 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 304 TYR 0.012 0.001 TYR E 178 PHE 0.023 0.001 PHE A 273 TRP 0.013 0.001 TRP A 117 HIS 0.005 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 9040) covalent geometry : angle 0.52564 / 0.28 (12232) SS BOND : bond 0.00362 / 0.14 ( 3) SS BOND : angle 0.46726 / 0.23 ( 6) hydrogen bonds : bond 0.04703 / 3.11 ( 422) hydrogen bonds : angle 3.94671 / 2.83 ( 1161) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 275 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6382 (tm) REVERT: C 45 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.6929 (mtp) REVERT: C 262 MET cc_start: 0.5854 (ttt) cc_final: 0.5082 (mpp) REVERT: C 325 MET cc_start: 0.7639 (ttm) cc_final: 0.7308 (ttp) REVERT: E 189 ASP cc_start: 0.7778 (m-30) cc_final: 0.7536 (t0) REVERT: E 210 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7217 (mm-30) REVERT: E 211 ASP cc_start: 0.7916 (m-30) cc_final: 0.7387 (t0) REVERT: E 218 MET cc_start: 0.8445 (ttp) cc_final: 0.7669 (ttt) outliers start: 18 outliers final: 12 residues processed: 109 average time/residue: 0.3888 time to fit residues: 45.6551 Evaluate side-chains 106 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 GLN E 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.210234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.148741 restraints weight = 10649.350| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.09 r_work: 0.3714 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9043 Z= 0.144 Angle : 0.574 8.419 12238 Z= 0.303 Chirality : 0.042 0.134 1408 Planarity : 0.004 0.057 1520 Dihedral : 4.878 57.367 1241 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.37 % Allowed : 16.58 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1104 helix: 2.90 (0.27), residues: 370 sheet: 0.61 (0.32), residues: 257 loop : -0.96 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 304 TYR 0.017 0.002 TYR A 31 PHE 0.025 0.002 PHE A 273 TRP 0.012 0.002 TRP A 117 HIS 0.005 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 9040) covalent geometry : angle 0.57390 / 0.30 (12232) SS BOND : bond 0.00422 / 0.17 ( 3) SS BOND : angle 0.59934 / 0.33 ( 6) hydrogen bonds : bond 0.05594 / 3.71 ( 422) hydrogen bonds : angle 4.13044 / 2.96 ( 1161) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 180 MET cc_start: 0.5664 (mmt) cc_final: 0.4180 (tmt) REVERT: C 45 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.6944 (mtp) REVERT: C 234 PHE cc_start: 0.6779 (OUTLIER) cc_final: 0.6432 (t80) REVERT: C 262 MET cc_start: 0.5959 (ttt) cc_final: 0.5075 (mpp) REVERT: C 325 MET cc_start: 0.7700 (ttm) cc_final: 0.7376 (ttp) REVERT: E 93 MET cc_start: 0.8216 (ttt) cc_final: 0.7882 (tpp) REVERT: E 130 GLN cc_start: 0.6348 (OUTLIER) cc_final: 0.5922 (mm-40) REVERT: E 211 ASP cc_start: 0.7922 (m-30) cc_final: 0.7397 (t0) REVERT: E 218 MET cc_start: 0.8498 (ttp) cc_final: 0.8034 (ttt) outliers start: 23 outliers final: 13 residues processed: 105 average time/residue: 0.4221 time to fit residues: 47.9750 Evaluate side-chains 106 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 130 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 101 optimal weight: 0.0010 chunk 98 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 0.1980 chunk 95 optimal weight: 0.6980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.213314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.152308 restraints weight = 10716.524| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.10 r_work: 0.3756 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9043 Z= 0.110 Angle : 0.532 9.175 12238 Z= 0.281 Chirality : 0.040 0.136 1408 Planarity : 0.004 0.057 1520 Dihedral : 4.639 57.026 1241 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.65 % Allowed : 17.30 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.26), residues: 1104 helix: 3.06 (0.27), residues: 371 sheet: 0.70 (0.32), residues: 257 loop : -0.88 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 304 TYR 0.012 0.001 TYR E 178 PHE 0.023 0.001 PHE A 273 TRP 0.021 0.001 TRP A 117 HIS 0.005 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 9040) covalent geometry : angle 0.53175 / 0.28 (12232) SS BOND : bond 0.00376 / 0.15 ( 3) SS BOND : angle 0.43650 / 0.20 ( 6) hydrogen bonds : bond 0.04640 / 3.08 ( 422) hydrogen bonds : angle 3.95956 / 2.84 ( 1161) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 180 MET cc_start: 0.5792 (mmt) cc_final: 0.4255 (tmt) REVERT: C 45 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.6903 (mtp) REVERT: C 217 MET cc_start: 0.5892 (pmt) cc_final: 0.5581 (pmm) REVERT: C 262 MET cc_start: 0.5873 (ttt) cc_final: 0.5120 (mpp) REVERT: C 325 MET cc_start: 0.7644 (ttm) cc_final: 0.7294 (ttp) REVERT: C 336 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7168 (mt) REVERT: D 38 MET cc_start: 0.6271 (tpt) cc_final: 0.5543 (ptp) REVERT: E 118 THR cc_start: 0.6657 (p) cc_final: 0.6291 (t) REVERT: E 210 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7201 (mm-30) REVERT: E 211 ASP cc_start: 0.7909 (m-30) cc_final: 0.7380 (t0) REVERT: E 218 MET cc_start: 0.8482 (ttp) cc_final: 0.7672 (ttt) outliers start: 16 outliers final: 11 residues processed: 106 average time/residue: 0.5555 time to fit residues: 63.1614 Evaluate side-chains 107 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 106 optimal weight: 0.0020 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 30.0000 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN E 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.213443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.152591 restraints weight = 10618.275| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 3.09 r_work: 0.3759 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9043 Z= 0.109 Angle : 0.520 8.463 12238 Z= 0.276 Chirality : 0.040 0.137 1408 Planarity : 0.004 0.057 1520 Dihedral : 4.539 58.865 1241 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.54 % Allowed : 17.30 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.26), residues: 1104 helix: 3.08 (0.27), residues: 371 sheet: 0.74 (0.32), residues: 257 loop : -0.85 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 304 TYR 0.013 0.001 TYR E 178 PHE 0.024 0.001 PHE A 273 TRP 0.017 0.001 TRP A 117 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 9040) covalent geometry : angle 0.52005 / 0.28 (12232) SS BOND : bond 0.00321 / 0.12 ( 3) SS BOND : angle 0.49269 / 0.25 ( 6) hydrogen bonds : bond 0.04522 / 2.98 ( 422) hydrogen bonds : angle 3.88398 / 2.80 ( 1161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2761.70 seconds wall clock time: 47 minutes 47.78 seconds (2867.78 seconds total)