Starting phenix.real_space_refine on Fri Aug 22 17:35:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ge9_29961/08_2025/8ge9_29961.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ge9_29961/08_2025/8ge9_29961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ge9_29961/08_2025/8ge9_29961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ge9_29961/08_2025/8ge9_29961.map" model { file = "/net/cci-nas-00/data/ceres_data/8ge9_29961/08_2025/8ge9_29961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ge9_29961/08_2025/8ge9_29961.cif" } resolution = 3.5 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= -0.001 sd= 0.031 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 44 5.16 5 C 4201 2.51 5 N 1121 2.21 5 O 1153 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6519 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1705 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 10, 'ASN:plan1': 1, 'GLU:plan': 16, 'ASP:plan': 9, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 174 Chain: "B" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2393 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 8, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 123 Chain: "G" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 335 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "R" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2070 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 8, 'TRP:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ARG:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 1.34, per 1000 atoms: 0.21 Number of scatterers: 6519 At special positions: 0 Unit cell: (68.9, 96.46, 126.14, 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 44 16.00 O 1153 8.00 N 1121 7.00 C 4201 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 295.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 48.1% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.569A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.610A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.667A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.785A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.702A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.915A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 31 through 61 removed outlier: 3.611A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.757A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.560A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.420A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.867A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 236 Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.903A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.940A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.875A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.661A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.727A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.453A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 71 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.428A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.508A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.162A 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: 6.812A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.531A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.160A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1137 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: 0.98 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2101 1.34 - 1.46: 1560 1.46 - 1.58: 2937 1.58 - 1.70: 1 1.70 - 1.81: 60 Bond restraints: 6659 Sorted by residual: bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.594 -0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.451 -0.054 2.00e-02 2.50e+03 7.22e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.440 -0.046 2.00e-02 2.50e+03 5.33e+00 bond pdb=" CAF G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.558 -0.038 2.00e-02 2.50e+03 3.69e+00 ... (remaining 6654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 8756 1.25 - 2.49: 274 2.49 - 3.74: 63 3.74 - 4.99: 12 4.99 - 6.24: 6 Bond angle restraints: 9111 Sorted by residual: angle pdb=" N ILE A 257 " pdb=" CA ILE A 257 " pdb=" C ILE A 257 " ideal model delta sigma weight residual 106.21 110.10 -3.89 1.07e+00 8.73e-01 1.32e+01 angle pdb=" C GLY A 226 " pdb=" N GLN A 227 " pdb=" CA GLN A 227 " ideal model delta sigma weight residual 121.54 127.50 -5.96 1.91e+00 2.74e-01 9.75e+00 angle pdb=" C TYR B 59 " pdb=" N ALA B 60 " pdb=" CA ALA B 60 " ideal model delta sigma weight residual 122.37 118.41 3.96 1.72e+00 3.38e-01 5.29e+00 angle pdb=" CA GLY B 53 " pdb=" C GLY B 53 " pdb=" N HIS B 54 " ideal model delta sigma weight residual 116.69 121.22 -4.53 2.04e+00 2.40e-01 4.94e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 117.13 -6.24 3.00e+00 1.11e-01 4.32e+00 ... (remaining 9106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3565 17.97 - 35.94: 229 35.94 - 53.91: 39 53.91 - 71.87: 6 71.87 - 89.84: 5 Dihedral angle restraints: 3844 sinusoidal: 1220 harmonic: 2624 Sorted by residual: dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PRO B 194 " pdb=" C PRO B 194 " pdb=" N ASP B 195 " pdb=" CA ASP B 195 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 3841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 737 0.031 - 0.062: 235 0.062 - 0.093: 85 0.093 - 0.124: 37 0.124 - 0.155: 5 Chirality restraints: 1099 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CB ILE A 56 " pdb=" CA ILE A 56 " pdb=" CG1 ILE A 56 " pdb=" CG2 ILE A 56 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1096 not shown) Planarity restraints: 1145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C ILE R 205 " 0.024 2.00e-02 2.50e+03 pdb=" O ILE R 205 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL R 206 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO G 55 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 49 " -0.007 2.00e-02 2.50e+03 9.93e-03 1.73e+00 pdb=" CG PHE R 49 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE R 49 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE R 49 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE R 49 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 49 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE R 49 " -0.000 2.00e-02 2.50e+03 ... (remaining 1142 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 803 2.75 - 3.29: 6519 3.29 - 3.83: 11221 3.83 - 4.36: 12317 4.36 - 4.90: 22357 Nonbonded interactions: 53217 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.215 3.040 nonbonded pdb=" OG SER R 319 " pdb=" O HOH R 601 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.260 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" NH1 ARG B 314 " model vdw 2.285 3.120 ... (remaining 53212 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.470 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.003 0.071 6660 Z= 0.154 Angle : 0.561 6.237 9113 Z= 0.317 Chirality : 0.038 0.155 1099 Planarity : 0.003 0.034 1145 Dihedral : 13.036 89.842 2137 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.28), residues: 884 helix: 2.34 (0.26), residues: 396 sheet: 0.88 (0.41), residues: 168 loop : -0.93 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 283 TYR 0.010 0.001 TYR R 199 PHE 0.023 0.001 PHE R 49 TRP 0.009 0.001 TRP R 105 HIS 0.010 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6659) covalent geometry : angle 0.56054 ( 9111) SS BOND : bond 0.00163 ( 1) SS BOND : angle 1.14316 ( 2) hydrogen bonds : bond 0.15146 ( 391) hydrogen bonds : angle 5.84153 ( 1137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8277 (mtmt) cc_final: 0.8063 (mtpt) REVERT: B 243 THR cc_start: 0.8640 (p) cc_final: 0.8426 (p) REVERT: R 52 VAL cc_start: 0.9043 (t) cc_final: 0.8775 (m) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0568 time to fit residues: 8.8223 Evaluate side-chains 87 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.132621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.113062 restraints weight = 10471.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.116327 restraints weight = 6207.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.118502 restraints weight = 4345.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.120155 restraints weight = 3386.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.121040 restraints weight = 2802.876| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6660 Z= 0.159 Angle : 0.518 7.734 9113 Z= 0.286 Chirality : 0.041 0.161 1099 Planarity : 0.003 0.034 1145 Dihedral : 4.928 63.143 968 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.17 % Allowed : 8.54 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.28), residues: 884 helix: 2.68 (0.26), residues: 382 sheet: 0.46 (0.39), residues: 179 loop : -0.91 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.019 0.002 TYR A 318 PHE 0.016 0.002 PHE R 49 TRP 0.016 0.001 TRP B 339 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6659) covalent geometry : angle 0.51824 ( 9111) SS BOND : bond 0.00309 ( 1) SS BOND : angle 0.67179 ( 2) hydrogen bonds : bond 0.04328 ( 391) hydrogen bonds : angle 4.47966 ( 1137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8264 (tp40) cc_final: 0.8023 (tp-100) REVERT: A 309 GLU cc_start: 0.7782 (pm20) cc_final: 0.7549 (mp0) REVERT: B 147 SER cc_start: 0.8869 (m) cc_final: 0.8446 (t) outliers start: 7 outliers final: 5 residues processed: 96 average time/residue: 0.0627 time to fit residues: 8.4476 Evaluate side-chains 88 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain R residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 0.0270 chunk 40 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.132544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113097 restraints weight = 10309.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116337 restraints weight = 6145.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.118556 restraints weight = 4320.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.120114 restraints weight = 3364.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121128 restraints weight = 2800.618| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6660 Z= 0.130 Angle : 0.484 5.731 9113 Z= 0.265 Chirality : 0.040 0.164 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.762 58.629 968 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.01 % Allowed : 12.40 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.28), residues: 884 helix: 2.78 (0.26), residues: 382 sheet: 0.35 (0.39), residues: 179 loop : -0.92 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.014 0.001 TYR R 199 PHE 0.014 0.001 PHE B 241 TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6659) covalent geometry : angle 0.48404 ( 9111) SS BOND : bond 0.00200 ( 1) SS BOND : angle 0.38510 ( 2) hydrogen bonds : bond 0.04001 ( 391) hydrogen bonds : angle 4.21291 ( 1137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8277 (tp40) cc_final: 0.8025 (tp-100) REVERT: A 309 GLU cc_start: 0.7711 (pm20) cc_final: 0.7461 (mp0) REVERT: B 147 SER cc_start: 0.8780 (m) cc_final: 0.8389 (t) REVERT: B 188 MET cc_start: 0.8420 (mmm) cc_final: 0.7696 (mmm) REVERT: R 171 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7515 (mtm) REVERT: R 173 TRP cc_start: 0.7815 (m-10) cc_final: 0.6505 (m100) outliers start: 6 outliers final: 4 residues processed: 94 average time/residue: 0.0660 time to fit residues: 9.1296 Evaluate side-chains 86 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 171 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110833 restraints weight = 10475.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.114101 restraints weight = 6203.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.116320 restraints weight = 4322.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117767 restraints weight = 3363.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118761 restraints weight = 2818.317| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6660 Z= 0.158 Angle : 0.488 5.672 9113 Z= 0.270 Chirality : 0.040 0.159 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.705 53.892 968 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.18 % Allowed : 14.07 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.28), residues: 884 helix: 2.79 (0.26), residues: 382 sheet: 0.19 (0.38), residues: 186 loop : -0.92 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.016 0.001 TYR R 199 PHE 0.018 0.001 PHE R 49 TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6659) covalent geometry : angle 0.48804 ( 9111) SS BOND : bond 0.00229 ( 1) SS BOND : angle 0.35480 ( 2) hydrogen bonds : bond 0.04057 ( 391) hydrogen bonds : angle 4.16755 ( 1137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8322 (tp40) cc_final: 0.8026 (tp-100) REVERT: A 309 GLU cc_start: 0.7698 (pm20) cc_final: 0.7448 (mp0) REVERT: B 147 SER cc_start: 0.8825 (m) cc_final: 0.8601 (t) outliers start: 13 outliers final: 9 residues processed: 92 average time/residue: 0.0659 time to fit residues: 8.8572 Evaluate side-chains 87 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 7 optimal weight: 0.0170 chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 87 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112962 restraints weight = 10373.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.116157 restraints weight = 6147.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.118395 restraints weight = 4318.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119911 restraints weight = 3354.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.120928 restraints weight = 2799.372| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6660 Z= 0.109 Angle : 0.452 5.568 9113 Z= 0.248 Chirality : 0.039 0.154 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.471 46.394 968 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.18 % Allowed : 15.24 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.29), residues: 884 helix: 2.84 (0.26), residues: 385 sheet: 0.13 (0.38), residues: 184 loop : -0.87 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.022 0.001 TYR A 318 PHE 0.012 0.001 PHE R 289 TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 6659) covalent geometry : angle 0.45206 ( 9111) SS BOND : bond 0.00110 ( 1) SS BOND : angle 0.32956 ( 2) hydrogen bonds : bond 0.03689 ( 391) hydrogen bonds : angle 3.99021 ( 1137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8270 (tp40) cc_final: 0.7969 (tp-100) REVERT: A 309 GLU cc_start: 0.7734 (pm20) cc_final: 0.7514 (mp0) REVERT: B 147 SER cc_start: 0.8778 (m) cc_final: 0.8570 (t) REVERT: B 164 THR cc_start: 0.7861 (p) cc_final: 0.7643 (p) REVERT: B 188 MET cc_start: 0.8297 (mmm) cc_final: 0.7716 (mmm) REVERT: B 338 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8332 (mt) REVERT: R 86 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8737 (m) REVERT: R 173 TRP cc_start: 0.7639 (m-10) cc_final: 0.6557 (m100) outliers start: 13 outliers final: 9 residues processed: 104 average time/residue: 0.0621 time to fit residues: 9.5021 Evaluate side-chains 95 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 63 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111739 restraints weight = 10414.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114930 restraints weight = 6185.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.117186 restraints weight = 4353.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118652 restraints weight = 3372.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.119820 restraints weight = 2826.717| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6660 Z= 0.138 Angle : 0.481 5.632 9113 Z= 0.263 Chirality : 0.040 0.153 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.462 41.376 968 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.01 % Allowed : 17.25 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.28), residues: 884 helix: 2.75 (0.26), residues: 385 sheet: 0.09 (0.38), residues: 184 loop : -0.87 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.015 0.001 TYR R 199 PHE 0.012 0.001 PHE R 289 TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6659) covalent geometry : angle 0.48081 ( 9111) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.31716 ( 2) hydrogen bonds : bond 0.03840 ( 391) hydrogen bonds : angle 4.08058 ( 1137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8307 (tp40) cc_final: 0.8003 (tp-100) REVERT: A 309 GLU cc_start: 0.7683 (pm20) cc_final: 0.7452 (mp0) REVERT: B 147 SER cc_start: 0.8898 (m) cc_final: 0.8689 (t) REVERT: B 164 THR cc_start: 0.7932 (p) cc_final: 0.7729 (p) REVERT: B 338 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8330 (mt) REVERT: R 173 TRP cc_start: 0.7543 (m-10) cc_final: 0.6501 (m100) outliers start: 12 outliers final: 10 residues processed: 94 average time/residue: 0.0660 time to fit residues: 9.0288 Evaluate side-chains 94 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 85 optimal weight: 0.2980 chunk 15 optimal weight: 0.0670 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.112130 restraints weight = 10345.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115409 restraints weight = 6112.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.117630 restraints weight = 4253.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.119162 restraints weight = 3303.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.120267 restraints weight = 2746.531| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6660 Z= 0.126 Angle : 0.465 5.641 9113 Z= 0.255 Chirality : 0.039 0.153 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.368 34.966 968 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.51 % Allowed : 17.42 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.28), residues: 884 helix: 2.80 (0.26), residues: 385 sheet: 0.01 (0.38), residues: 184 loop : -0.88 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.014 0.001 TYR R 199 PHE 0.021 0.001 PHE R 49 TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6659) covalent geometry : angle 0.46531 ( 9111) SS BOND : bond 0.00127 ( 1) SS BOND : angle 0.29080 ( 2) hydrogen bonds : bond 0.03751 ( 391) hydrogen bonds : angle 4.03091 ( 1137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8299 (tp40) cc_final: 0.8001 (tp-100) REVERT: A 309 GLU cc_start: 0.7720 (pm20) cc_final: 0.7497 (mp0) REVERT: B 147 SER cc_start: 0.8909 (m) cc_final: 0.8698 (t) REVERT: B 338 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8305 (mt) REVERT: R 86 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8577 (m) outliers start: 15 outliers final: 12 residues processed: 97 average time/residue: 0.0625 time to fit residues: 8.9685 Evaluate side-chains 100 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 259 GLN R 299 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.112111 restraints weight = 10445.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115344 restraints weight = 6148.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117610 restraints weight = 4273.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119153 restraints weight = 3298.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.120303 restraints weight = 2728.720| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6660 Z= 0.126 Angle : 0.467 5.618 9113 Z= 0.254 Chirality : 0.039 0.153 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.334 33.061 968 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.18 % Allowed : 16.75 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.29), residues: 884 helix: 2.76 (0.26), residues: 391 sheet: -0.04 (0.38), residues: 184 loop : -0.83 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.014 0.001 TYR R 199 PHE 0.012 0.001 PHE R 289 TRP 0.036 0.002 TRP R 173 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6659) covalent geometry : angle 0.46753 ( 9111) SS BOND : bond 0.00117 ( 1) SS BOND : angle 0.27747 ( 2) hydrogen bonds : bond 0.03730 ( 391) hydrogen bonds : angle 4.02371 ( 1137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8308 (tp40) cc_final: 0.8001 (tp-100) REVERT: A 309 GLU cc_start: 0.7718 (pm20) cc_final: 0.7489 (mp0) REVERT: B 59 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.7305 (m-80) REVERT: B 147 SER cc_start: 0.8913 (m) cc_final: 0.8694 (t) REVERT: B 338 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8296 (mt) REVERT: R 86 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8570 (m) REVERT: R 299 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7489 (pp30) outliers start: 19 outliers final: 13 residues processed: 99 average time/residue: 0.0620 time to fit residues: 9.1220 Evaluate side-chains 102 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 299 GLN Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 82 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 84 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 56 optimal weight: 0.0370 chunk 39 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 chunk 61 optimal weight: 0.0670 chunk 85 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.114423 restraints weight = 10391.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117695 restraints weight = 5995.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.120019 restraints weight = 4146.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.121566 restraints weight = 3166.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.122388 restraints weight = 2611.884| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6660 Z= 0.098 Angle : 0.453 5.512 9113 Z= 0.245 Chirality : 0.039 0.156 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.230 33.023 968 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.51 % Allowed : 17.25 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.28), residues: 884 helix: 2.85 (0.26), residues: 391 sheet: -0.02 (0.38), residues: 179 loop : -0.84 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.011 0.001 TYR R 199 PHE 0.022 0.001 PHE R 49 TRP 0.038 0.002 TRP R 173 HIS 0.005 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 6659) covalent geometry : angle 0.45263 ( 9111) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.32849 ( 2) hydrogen bonds : bond 0.03480 ( 391) hydrogen bonds : angle 3.92071 ( 1137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8275 (tp40) cc_final: 0.7963 (tp-100) REVERT: A 309 GLU cc_start: 0.7699 (pm20) cc_final: 0.7496 (mp0) REVERT: B 59 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7201 (m-80) REVERT: B 188 MET cc_start: 0.8192 (mmm) cc_final: 0.7759 (mmm) REVERT: B 338 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8291 (mt) REVERT: R 299 GLN cc_start: 0.7568 (pp30) cc_final: 0.6986 (pp30) outliers start: 15 outliers final: 12 residues processed: 103 average time/residue: 0.0661 time to fit residues: 9.9389 Evaluate side-chains 99 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 33 optimal weight: 0.4980 chunk 79 optimal weight: 0.4980 chunk 85 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 32 optimal weight: 0.0020 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0470 chunk 8 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.3686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.114665 restraints weight = 10339.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117942 restraints weight = 6089.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.120221 restraints weight = 4255.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.121795 restraints weight = 3286.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.122759 restraints weight = 2727.385| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6660 Z= 0.101 Angle : 0.450 5.540 9113 Z= 0.244 Chirality : 0.039 0.156 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.185 33.459 968 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.35 % Allowed : 17.76 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.28), residues: 884 helix: 2.88 (0.26), residues: 391 sheet: 0.12 (0.40), residues: 163 loop : -0.87 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.012 0.001 TYR R 199 PHE 0.010 0.001 PHE R 289 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 6659) covalent geometry : angle 0.44984 ( 9111) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.40260 ( 2) hydrogen bonds : bond 0.03464 ( 391) hydrogen bonds : angle 3.89043 ( 1137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8286 (tp40) cc_final: 0.7973 (tp-100) REVERT: A 309 GLU cc_start: 0.7767 (pm20) cc_final: 0.7552 (mp0) REVERT: B 59 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7165 (m-80) REVERT: B 338 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8277 (mt) REVERT: R 299 GLN cc_start: 0.7632 (pp30) cc_final: 0.7344 (pp30) outliers start: 14 outliers final: 10 residues processed: 99 average time/residue: 0.0633 time to fit residues: 9.2425 Evaluate side-chains 98 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 48 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112569 restraints weight = 10433.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115810 restraints weight = 6179.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.118109 restraints weight = 4329.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119647 restraints weight = 3338.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.120631 restraints weight = 2777.430| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6660 Z= 0.127 Angle : 0.465 5.522 9113 Z= 0.254 Chirality : 0.039 0.153 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.246 33.832 968 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.68 % Allowed : 17.76 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.28), residues: 884 helix: 2.84 (0.26), residues: 391 sheet: -0.00 (0.38), residues: 177 loop : -0.86 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.015 0.001 TYR R 199 PHE 0.021 0.001 PHE R 49 TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6659) covalent geometry : angle 0.46545 ( 9111) SS BOND : bond 0.00113 ( 1) SS BOND : angle 0.32057 ( 2) hydrogen bonds : bond 0.03698 ( 391) hydrogen bonds : angle 3.96732 ( 1137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1217.59 seconds wall clock time: 21 minutes 47.25 seconds (1307.25 seconds total)