Starting phenix.real_space_refine on Wed Feb 12 14:18:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kh5_37237/02_2025/8kh5_37237.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kh5_37237/02_2025/8kh5_37237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kh5_37237/02_2025/8kh5_37237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kh5_37237/02_2025/8kh5_37237.map" model { file = "/net/cci-nas-00/data/ceres_data/8kh5_37237/02_2025/8kh5_37237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kh5_37237/02_2025/8kh5_37237.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.143 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 57 5.16 5 C 5034 2.51 5 N 1339 2.21 5 O 1407 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2214 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1778 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 2467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 338, 2460 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 116 Conformer: "B" Number of residues, atoms: 338, 2460 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 116 bond proxies already assigned to first conformer: 2496 Chain: "E" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 946 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 345 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {'CLR': 2, 'LPS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.58, per 1000 atoms: 0.84 Number of scatterers: 7838 At special positions: 0 Unit cell: (74.52, 97.2, 130.68, 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 57 16.00 P 1 15.00 O 1407 8.00 N 1339 7.00 C 5034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 91 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.3 seconds 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 43.3% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 15 through 51 removed outlier: 4.321A pdb=" N VAL A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 55 through 82 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 87 through 122 removed outlier: 3.630A pdb=" N LYS A 98 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 133 through 149 removed outlier: 3.526A pdb=" N CYS A 146 " --> pdb=" O TRP A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.699A pdb=" N LEU A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 213 Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 223 through 258 removed outlier: 3.623A pdb=" N LEU A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) Proline residue: A 245 - end of helix Proline residue: A 251 - end of helix Processing helix chain 'A' and resid 263 through 294 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'B' and resid 13 through 39 removed outlier: 3.595A pdb=" N ALA B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 39 " --> pdb=" O GLN B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 265 through 279 Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 307 through 312 removed outlier: 4.002A pdb=" N TYR B 311 " --> pdb=" O LYS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 318 Processing helix chain 'B' and resid 331 through 352 removed outlier: 3.651A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 391 Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.692A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 removed outlier: 3.836A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'B' and resid 209 through 214 removed outlier: 3.912A pdb=" N ALA B 243 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE B 244 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N PHE B 290 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE B 246 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN B 292 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 248 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.730A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.818A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.085A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.529A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.636A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.264A 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 234 removed outlier: 6.482A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 254 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.759A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.046A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1234 1.30 - 1.43: 2168 1.43 - 1.55: 4530 1.55 - 1.68: 4 1.68 - 1.81: 78 Bond restraints: 8014 Sorted by residual: bond pdb=" C PRO A 123 " pdb=" O PRO A 123 " ideal model delta sigma weight residual 1.237 1.410 -0.173 1.26e-02 6.30e+03 1.88e+02 bond pdb=" C31 LPS A 402 " pdb=" O32 LPS A 402 " ideal model delta sigma weight residual 1.398 1.180 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" CA ALA A 140 " pdb=" C ALA A 140 " ideal model delta sigma weight residual 1.524 1.412 0.112 1.29e-02 6.01e+03 7.53e+01 bond pdb=" C ASP A 16 " pdb=" O ASP A 16 " ideal model delta sigma weight residual 1.235 1.314 -0.079 1.26e-02 6.30e+03 3.94e+01 bond pdb=" C PHE A 126 " pdb=" O PHE A 126 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.15e-02 7.56e+03 3.44e+01 ... (remaining 8009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 10812 3.42 - 6.85: 92 6.85 - 10.27: 18 10.27 - 13.70: 4 13.70 - 17.12: 1 Bond angle restraints: 10927 Sorted by residual: angle pdb=" N PHE A 126 " pdb=" CA PHE A 126 " pdb=" C PHE A 126 " ideal model delta sigma weight residual 111.07 123.34 -12.27 1.07e+00 8.73e-01 1.32e+02 angle pdb=" N CYS A 129 " pdb=" CA CYS A 129 " pdb=" C CYS A 129 " ideal model delta sigma weight residual 112.92 100.41 12.51 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N LYS A 130 " pdb=" CA LYS A 130 " pdb=" C LYS A 130 " ideal model delta sigma weight residual 112.57 102.29 10.28 1.13e+00 7.83e-01 8.28e+01 angle pdb=" CA PHE A 126 " pdb=" C PHE A 126 " pdb=" N HIS A 127 " ideal model delta sigma weight residual 117.07 126.17 -9.10 1.14e+00 7.69e-01 6.37e+01 angle pdb=" O PHE A 126 " pdb=" C PHE A 126 " pdb=" N HIS A 127 " ideal model delta sigma weight residual 122.07 114.52 7.55 1.03e+00 9.43e-01 5.37e+01 ... (remaining 10922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 4301 15.07 - 30.14: 382 30.14 - 45.21: 103 45.21 - 60.29: 19 60.29 - 75.36: 8 Dihedral angle restraints: 4813 sinusoidal: 1799 harmonic: 3014 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 147.71 -54.71 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" N PHE A 124 " pdb=" C PHE A 124 " pdb=" CA PHE A 124 " pdb=" CB PHE A 124 " ideal model delta harmonic sigma weight residual 122.80 110.88 11.92 0 2.50e+00 1.60e-01 2.27e+01 dihedral pdb=" CB CYS A 91 " pdb=" SG CYS A 91 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 131.85 -38.85 1 1.00e+01 1.00e-02 2.12e+01 ... (remaining 4810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.443: 1274 0.443 - 0.886: 1 0.886 - 1.329: 0 1.329 - 1.772: 0 1.772 - 2.214: 1 Chirality restraints: 1276 Sorted by residual: chirality pdb=" C31 LPS A 402 " pdb=" C32 LPS A 402 " pdb=" O31 LPS A 402 " pdb=" O32 LPS A 402 " both_signs ideal model delta sigma weight residual False -2.18 0.04 -2.21 2.00e-01 2.50e+01 1.23e+02 chirality pdb=" CA PHE A 126 " pdb=" N PHE A 126 " pdb=" C PHE A 126 " pdb=" CB PHE A 126 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.49e+00 chirality pdb=" C13 CLR A 401 " pdb=" C12 CLR A 401 " pdb=" C14 CLR A 401 " pdb=" C17 CLR A 401 " both_signs ideal model delta sigma weight residual False -2.93 -2.52 -0.41 2.00e-01 2.50e+01 4.14e+00 ... (remaining 1273 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 124 " 0.025 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C PHE A 124 " -0.085 2.00e-02 2.50e+03 pdb=" O PHE A 124 " 0.031 2.00e-02 2.50e+03 pdb=" N ARG A 125 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 126 " -0.025 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C PHE A 126 " 0.081 2.00e-02 2.50e+03 pdb=" O PHE A 126 " -0.028 2.00e-02 2.50e+03 pdb=" N HIS A 127 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 122 " -0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 123 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.032 5.00e-02 4.00e+02 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 134 2.66 - 3.22: 7451 3.22 - 3.78: 12640 3.78 - 4.34: 17575 4.34 - 4.90: 29164 Nonbonded interactions: 66964 Sorted by model distance: nonbonded pdb=" OD1 ASP E 50 " pdb=" OG SER E 59 " model vdw 2.103 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.189 3.040 nonbonded pdb=" OH TYR A 78 " pdb=" OD2 ASP A 171 " model vdw 2.197 3.040 nonbonded pdb=" NH1 ARG B 228 " pdb=" OD1 ASP C 186 " model vdw 2.249 3.120 nonbonded pdb=" O CYS C 149 " pdb=" NH1 ARG C 150 " model vdw 2.254 3.120 ... (remaining 66959 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.890 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:15.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 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 : 0.008 0.218 8014 Z= 0.503 Angle : 0.852 17.124 10927 Z= 0.505 Chirality : 0.084 2.214 1276 Planarity : 0.005 0.060 1371 Dihedral : 12.854 75.356 2856 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.26 % Allowed : 0.77 % Favored : 98.97 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.27), residues: 1018 helix: 1.86 (0.27), residues: 402 sheet: 0.40 (0.34), residues: 218 loop : -0.56 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 142 HIS 0.011 0.002 HIS C 142 PHE 0.028 0.002 PHE A 239 TYR 0.031 0.002 TYR C 59 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 118 TRP cc_start: 0.6917 (t-100) cc_final: 0.6332 (t60) REVERT: A 250 PHE cc_start: 0.7690 (t80) cc_final: 0.7479 (t80) REVERT: B 317 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7440 (mtm-85) REVERT: B 378 ASP cc_start: 0.7929 (m-30) cc_final: 0.7619 (m-30) REVERT: C 277 SER cc_start: 0.8496 (t) cc_final: 0.8110 (m) outliers start: 2 outliers final: 2 residues processed: 206 average time/residue: 1.0753 time to fit residues: 235.8867 Evaluate side-chains 134 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain B residue 229 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN B 213 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS C 119 ASN C 156 GLN C 175 GLN C 176 GLN C 220 GLN C 259 GLN E 31 ASN D 44 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.161242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.126179 restraints weight = 11188.383| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.40 r_work: 0.3401 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8014 Z= 0.265 Angle : 0.611 7.708 10927 Z= 0.323 Chirality : 0.045 0.159 1276 Planarity : 0.005 0.059 1371 Dihedral : 7.141 107.944 1276 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.09 % Allowed : 11.20 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1018 helix: 1.92 (0.26), residues: 420 sheet: 0.54 (0.32), residues: 209 loop : -0.54 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 84 HIS 0.011 0.002 HIS B 220 PHE 0.027 0.002 PHE A 119 TYR 0.017 0.002 TYR C 59 ARG 0.009 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 118 TRP cc_start: 0.7848 (t-100) cc_final: 0.7227 (t-100) REVERT: A 155 LEU cc_start: 0.8296 (mm) cc_final: 0.8035 (mm) REVERT: A 185 MET cc_start: 0.7528 (tmm) cc_final: 0.7316 (tmm) REVERT: A 224 GLU cc_start: 0.8102 (mp0) cc_final: 0.7836 (mp0) REVERT: A 300 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7602 (mtp180) REVERT: A 301 ARG cc_start: 0.6921 (mtm-85) cc_final: 0.6434 (mtm-85) REVERT: B 223 ASP cc_start: 0.8554 (t0) cc_final: 0.8332 (t0) REVERT: B 274 LYS cc_start: 0.7794 (tttt) cc_final: 0.7458 (ttpt) REVERT: B 280 ARG cc_start: 0.8036 (ttt-90) cc_final: 0.7707 (ttt-90) REVERT: B 310 ASP cc_start: 0.8151 (t0) cc_final: 0.7604 (m-30) REVERT: B 317 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7696 (mtm-85) REVERT: B 330 GLU cc_start: 0.8092 (tt0) cc_final: 0.7812 (tt0) REVERT: C 188 MET cc_start: 0.8851 (mmm) cc_final: 0.8520 (mmm) REVERT: C 197 ARG cc_start: 0.7365 (mtp-110) cc_final: 0.6874 (mtp85) REVERT: C 214 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6337 (mpp80) REVERT: C 277 SER cc_start: 0.8534 (t) cc_final: 0.8146 (m) REVERT: E 80 TYR cc_start: 0.7162 (m-80) cc_final: 0.6419 (m-80) outliers start: 24 outliers final: 7 residues processed: 162 average time/residue: 1.3301 time to fit residues: 227.4511 Evaluate side-chains 139 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 99 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 93 optimal weight: 0.8980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN B 23 ASN B 213 GLN B 292 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 88 ASN C 175 GLN C 176 GLN C 220 GLN C 259 GLN E 31 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.161053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124308 restraints weight = 17380.468| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.01 r_work: 0.3369 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8014 Z= 0.178 Angle : 0.514 5.382 10927 Z= 0.276 Chirality : 0.041 0.136 1276 Planarity : 0.004 0.058 1371 Dihedral : 5.686 56.460 1272 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.96 % Allowed : 15.06 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1018 helix: 2.20 (0.26), residues: 420 sheet: 0.50 (0.32), residues: 212 loop : -0.58 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.007 0.001 HIS A 127 PHE 0.028 0.002 PHE A 119 TYR 0.012 0.001 TYR A 293 ARG 0.005 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.837 Fit side-chains REVERT: A 145 ILE cc_start: 0.7164 (OUTLIER) cc_final: 0.6696 (mp) REVERT: A 179 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7155 (tp) REVERT: A 185 MET cc_start: 0.7496 (tmm) cc_final: 0.7243 (tmm) REVERT: A 296 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7176 (t) REVERT: A 300 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7591 (mtp180) REVERT: B 218 ASN cc_start: 0.8231 (m-40) cc_final: 0.7871 (m110) REVERT: B 274 LYS cc_start: 0.7719 (tttt) cc_final: 0.7349 (ttpt) REVERT: B 280 ARG cc_start: 0.7939 (ttt-90) cc_final: 0.7604 (ttt-90) REVERT: B 310 ASP cc_start: 0.8262 (t0) cc_final: 0.7795 (m-30) REVERT: B 317 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7259 (ptp-110) REVERT: B 318 TYR cc_start: 0.8232 (t80) cc_final: 0.7786 (t80) REVERT: B 378 ASP cc_start: 0.8252 (m-30) cc_final: 0.8000 (m-30) REVERT: B 381 ASP cc_start: 0.8765 (t0) cc_final: 0.8565 (t0) REVERT: C 45 MET cc_start: 0.8564 (mtt) cc_final: 0.7931 (mtt) REVERT: C 197 ARG cc_start: 0.7387 (mtp-110) cc_final: 0.6934 (mtp85) REVERT: C 214 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6348 (mpp80) REVERT: E 80 TYR cc_start: 0.7169 (m-80) cc_final: 0.6500 (m-80) REVERT: E 87 LYS cc_start: 0.6816 (mtpt) cc_final: 0.6570 (ttmm) outliers start: 23 outliers final: 1 residues processed: 154 average time/residue: 1.2815 time to fit residues: 208.5084 Evaluate side-chains 126 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 214 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 156 GLN C 175 GLN C 176 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.152032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116078 restraints weight = 13112.772| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.56 r_work: 0.3254 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8014 Z= 0.318 Angle : 0.595 7.459 10927 Z= 0.317 Chirality : 0.045 0.149 1276 Planarity : 0.005 0.057 1371 Dihedral : 6.024 58.235 1272 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.96 % Allowed : 16.22 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.27), residues: 1018 helix: 2.09 (0.26), residues: 414 sheet: 0.35 (0.32), residues: 217 loop : -0.48 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 82 HIS 0.010 0.002 HIS B 357 PHE 0.028 0.002 PHE A 119 TYR 0.028 0.002 TYR C 59 ARG 0.006 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.7119 (mt) cc_final: 0.6899 (mt) REVERT: A 92 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6579 (mmp) REVERT: A 145 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7217 (mm) REVERT: A 179 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7125 (tp) REVERT: A 188 ILE cc_start: 0.7004 (mt) cc_final: 0.6727 (mt) REVERT: A 276 VAL cc_start: 0.8159 (t) cc_final: 0.7912 (m) REVERT: A 296 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7539 (p) REVERT: A 300 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7803 (mtp180) REVERT: B 211 LYS cc_start: 0.8570 (mttp) cc_final: 0.7675 (mttm) REVERT: B 274 LYS cc_start: 0.7764 (tttt) cc_final: 0.7393 (ttpt) REVERT: B 280 ARG cc_start: 0.8115 (ttt-90) cc_final: 0.7748 (ttt-90) REVERT: B 314 GLU cc_start: 0.7601 (pm20) cc_final: 0.7305 (pm20) REVERT: B 317 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7293 (ptp-110) REVERT: B 330 GLU cc_start: 0.8161 (tt0) cc_final: 0.7599 (tt0) REVERT: C 45 MET cc_start: 0.8772 (mtt) cc_final: 0.8177 (mtt) REVERT: C 197 ARG cc_start: 0.7531 (mtp-110) cc_final: 0.6942 (mtp85) REVERT: C 213 VAL cc_start: 0.6888 (m) cc_final: 0.6609 (m) REVERT: C 214 ARG cc_start: 0.6930 (mpp80) cc_final: 0.6455 (mpp80) REVERT: E 83 MET cc_start: 0.8204 (mtp) cc_final: 0.7838 (mtp) outliers start: 23 outliers final: 7 residues processed: 160 average time/residue: 1.1509 time to fit residues: 195.8794 Evaluate side-chains 140 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 0.1980 chunk 99 optimal weight: 0.0470 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 0.0170 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN B 227 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 175 GLN C 176 GLN C 220 GLN E 31 ASN E 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.156617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123223 restraints weight = 9339.383| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.17 r_work: 0.3361 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8014 Z= 0.158 Angle : 0.505 6.953 10927 Z= 0.269 Chirality : 0.041 0.135 1276 Planarity : 0.004 0.057 1371 Dihedral : 5.546 59.228 1272 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.09 % Allowed : 17.76 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.27), residues: 1018 helix: 2.23 (0.26), residues: 418 sheet: 0.36 (0.32), residues: 222 loop : -0.54 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.007 0.001 HIS A 127 PHE 0.027 0.001 PHE A 119 TYR 0.012 0.001 TYR B 391 ARG 0.005 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.841 Fit side-chains REVERT: A 27 THR cc_start: 0.7556 (m) cc_final: 0.7217 (p) REVERT: A 31 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.8094 (p) REVERT: A 92 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6851 (mmt) REVERT: A 179 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7190 (tp) REVERT: A 185 MET cc_start: 0.7564 (tmm) cc_final: 0.7166 (tmm) REVERT: A 296 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7544 (p) REVERT: B 211 LYS cc_start: 0.8487 (mttp) cc_final: 0.7410 (mmtm) REVERT: B 218 ASN cc_start: 0.8246 (m-40) cc_final: 0.7961 (m110) REVERT: B 274 LYS cc_start: 0.7744 (tttt) cc_final: 0.7393 (ttpt) REVERT: B 314 GLU cc_start: 0.7606 (pm20) cc_final: 0.7319 (pm20) REVERT: B 317 ARG cc_start: 0.7936 (mtm-85) cc_final: 0.7409 (ptp-110) REVERT: B 318 TYR cc_start: 0.8414 (t80) cc_final: 0.8052 (t80) REVERT: B 330 GLU cc_start: 0.8152 (tt0) cc_final: 0.7532 (tt0) REVERT: C 59 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: C 188 MET cc_start: 0.8894 (mmm) cc_final: 0.8607 (mmm) REVERT: C 197 ARG cc_start: 0.7445 (mtp-110) cc_final: 0.6837 (mtp85) REVERT: C 214 ARG cc_start: 0.6893 (mpp80) cc_final: 0.6486 (mpp80) REVERT: E 83 MET cc_start: 0.8109 (mtp) cc_final: 0.7881 (mtp) outliers start: 24 outliers final: 5 residues processed: 155 average time/residue: 1.1288 time to fit residues: 186.1346 Evaluate side-chains 137 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN C 175 GLN C 176 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.149901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114981 restraints weight = 11150.496| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.36 r_work: 0.3235 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8014 Z= 0.367 Angle : 0.619 7.696 10927 Z= 0.328 Chirality : 0.046 0.157 1276 Planarity : 0.005 0.057 1371 Dihedral : 6.062 56.202 1272 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.09 % Allowed : 18.40 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1018 helix: 2.04 (0.26), residues: 414 sheet: 0.18 (0.33), residues: 216 loop : -0.40 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 63 HIS 0.011 0.002 HIS B 357 PHE 0.029 0.002 PHE A 119 TYR 0.018 0.002 TYR E 95 ARG 0.010 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7321 (mmp) REVERT: A 145 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7417 (mm) REVERT: A 188 ILE cc_start: 0.7096 (mt) cc_final: 0.6796 (mt) REVERT: A 296 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.7746 (p) REVERT: A 300 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7881 (mtp180) REVERT: B 32 LYS cc_start: 0.7999 (ttmm) cc_final: 0.7697 (mttm) REVERT: B 274 LYS cc_start: 0.8045 (tttt) cc_final: 0.7617 (ttpt) REVERT: B 317 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7464 (ptp-110) REVERT: C 59 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: C 197 ARG cc_start: 0.7423 (mtp-110) cc_final: 0.7187 (mtp85) REVERT: E 80 TYR cc_start: 0.8059 (m-80) cc_final: 0.7588 (m-80) REVERT: E 83 MET cc_start: 0.8327 (mtp) cc_final: 0.8108 (mtp) outliers start: 24 outliers final: 10 residues processed: 148 average time/residue: 1.1177 time to fit residues: 176.4994 Evaluate side-chains 145 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 176 GLN C 220 GLN E 31 ASN E 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.151382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.118202 restraints weight = 12716.674| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.64 r_work: 0.3236 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8014 Z= 0.270 Angle : 0.573 7.416 10927 Z= 0.301 Chirality : 0.044 0.147 1276 Planarity : 0.004 0.056 1371 Dihedral : 5.875 53.140 1272 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.60 % Allowed : 18.79 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 1018 helix: 2.04 (0.26), residues: 414 sheet: 0.22 (0.33), residues: 224 loop : -0.46 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.008 0.001 HIS B 357 PHE 0.029 0.002 PHE A 119 TYR 0.014 0.002 TYR B 391 ARG 0.011 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.7260 (mt) cc_final: 0.7043 (mt) REVERT: A 79 TYR cc_start: 0.7755 (m-80) cc_final: 0.7307 (m-80) REVERT: A 92 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7351 (mmp) REVERT: A 145 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7455 (mm) REVERT: A 185 MET cc_start: 0.7762 (tmm) cc_final: 0.7474 (ttp) REVERT: A 188 ILE cc_start: 0.7164 (mt) cc_final: 0.6857 (mt) REVERT: A 296 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.7814 (p) REVERT: A 300 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7931 (mtp180) REVERT: B 211 LYS cc_start: 0.8744 (mttp) cc_final: 0.7941 (mttm) REVERT: B 213 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8492 (tm-30) REVERT: B 274 LYS cc_start: 0.8134 (tttt) cc_final: 0.7742 (ttpt) REVERT: B 314 GLU cc_start: 0.7796 (pm20) cc_final: 0.7591 (pm20) REVERT: B 317 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7634 (ptp-110) REVERT: B 330 GLU cc_start: 0.8222 (tt0) cc_final: 0.7756 (tt0) REVERT: C 197 ARG cc_start: 0.7608 (mtp-110) cc_final: 0.7308 (mtp85) REVERT: E 80 TYR cc_start: 0.8089 (m-80) cc_final: 0.7698 (m-80) outliers start: 28 outliers final: 12 residues processed: 148 average time/residue: 1.0314 time to fit residues: 163.5138 Evaluate side-chains 149 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 176 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.153732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121335 restraints weight = 13091.169| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.56 r_work: 0.3285 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8014 Z= 0.192 Angle : 0.531 7.208 10927 Z= 0.280 Chirality : 0.042 0.141 1276 Planarity : 0.004 0.056 1371 Dihedral : 5.660 51.538 1272 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.45 % Allowed : 19.95 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.27), residues: 1018 helix: 2.15 (0.26), residues: 412 sheet: 0.28 (0.33), residues: 224 loop : -0.46 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.006 0.001 HIS B 220 PHE 0.028 0.002 PHE A 119 TYR 0.011 0.001 TYR B 339 ARG 0.007 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7772 (m-80) cc_final: 0.7355 (m-80) REVERT: A 92 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7288 (mmp) REVERT: A 94 CYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7677 (t) REVERT: A 145 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7353 (mm) REVERT: A 185 MET cc_start: 0.7742 (tmm) cc_final: 0.7402 (ttp) REVERT: A 296 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.7787 (p) REVERT: A 300 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7885 (mtp180) REVERT: B 211 LYS cc_start: 0.8719 (mttp) cc_final: 0.7914 (mttm) REVERT: B 213 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8372 (tm-30) REVERT: B 274 LYS cc_start: 0.8127 (tttt) cc_final: 0.7760 (ttpt) REVERT: B 317 ARG cc_start: 0.8131 (mtm-85) cc_final: 0.7789 (ptp-110) REVERT: B 330 GLU cc_start: 0.8245 (tt0) cc_final: 0.7655 (tt0) REVERT: B 370 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7187 (mm-30) REVERT: C 188 MET cc_start: 0.8983 (mmm) cc_final: 0.8730 (mmm) REVERT: C 197 ARG cc_start: 0.7578 (mtp-110) cc_final: 0.7184 (mtp85) REVERT: E 80 TYR cc_start: 0.8045 (m-80) cc_final: 0.7624 (m-80) REVERT: E 83 MET cc_start: 0.8331 (mtp) cc_final: 0.8048 (mtp) outliers start: 19 outliers final: 9 residues processed: 143 average time/residue: 1.0558 time to fit residues: 161.5677 Evaluate side-chains 143 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 30.0000 chunk 0 optimal weight: 8.9990 chunk 93 optimal weight: 0.4980 chunk 53 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 175 GLN C 176 GLN C 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.154330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.122669 restraints weight = 15955.583| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.96 r_work: 0.3263 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8014 Z= 0.184 Angle : 0.535 7.516 10927 Z= 0.280 Chirality : 0.042 0.144 1276 Planarity : 0.004 0.056 1371 Dihedral : 5.594 51.787 1272 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.57 % Allowed : 19.43 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 1018 helix: 2.22 (0.26), residues: 411 sheet: 0.38 (0.33), residues: 222 loop : -0.44 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.006 0.001 HIS B 220 PHE 0.028 0.002 PHE A 119 TYR 0.011 0.001 TYR B 339 ARG 0.013 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7658 (m-80) cc_final: 0.7297 (m-80) REVERT: A 92 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7256 (mmp) REVERT: A 94 CYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7628 (t) REVERT: A 145 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7324 (mm) REVERT: A 185 MET cc_start: 0.7669 (tmm) cc_final: 0.7245 (tmm) REVERT: A 296 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.7777 (p) REVERT: A 300 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7809 (mtp180) REVERT: B 211 LYS cc_start: 0.8694 (mttp) cc_final: 0.7901 (mttm) REVERT: B 213 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8368 (tm-30) REVERT: B 274 LYS cc_start: 0.8071 (tttt) cc_final: 0.7706 (ttpt) REVERT: B 317 ARG cc_start: 0.8044 (mtm-85) cc_final: 0.7728 (ptp-110) REVERT: B 330 GLU cc_start: 0.8230 (tt0) cc_final: 0.7801 (tt0) REVERT: B 370 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7071 (mm-30) REVERT: C 137 ARG cc_start: 0.7232 (mtp-110) cc_final: 0.7009 (mtp85) REVERT: C 188 MET cc_start: 0.8914 (mmm) cc_final: 0.8681 (mmm) REVERT: C 197 ARG cc_start: 0.7480 (mtp-110) cc_final: 0.7103 (mtp85) REVERT: E 80 TYR cc_start: 0.8016 (m-80) cc_final: 0.7581 (m-80) REVERT: E 83 MET cc_start: 0.8312 (mtp) cc_final: 0.8019 (mtp) outliers start: 20 outliers final: 11 residues processed: 141 average time/residue: 1.0968 time to fit residues: 165.0051 Evaluate side-chains 144 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 175 GLN C 176 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.152747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120311 restraints weight = 13105.903| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.52 r_work: 0.3273 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8014 Z= 0.243 Angle : 0.558 7.264 10927 Z= 0.291 Chirality : 0.043 0.148 1276 Planarity : 0.004 0.055 1371 Dihedral : 5.657 51.313 1272 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.45 % Allowed : 19.56 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.27), residues: 1018 helix: 2.18 (0.26), residues: 411 sheet: 0.31 (0.33), residues: 224 loop : -0.45 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.007 0.001 HIS B 357 PHE 0.029 0.002 PHE A 119 TYR 0.013 0.001 TYR E 95 ARG 0.013 0.001 ARG C 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7731 (m-80) cc_final: 0.7400 (m-80) REVERT: A 92 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7390 (mmp) REVERT: A 145 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7346 (mm) REVERT: A 185 MET cc_start: 0.7680 (tmm) cc_final: 0.7358 (ttp) REVERT: A 296 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.7982 (p) REVERT: A 300 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7862 (mtp180) REVERT: B 25 LYS cc_start: 0.8369 (ttpp) cc_final: 0.8061 (tttt) REVERT: B 211 LYS cc_start: 0.8738 (mttp) cc_final: 0.7938 (mttm) REVERT: B 213 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8410 (tm-30) REVERT: B 274 LYS cc_start: 0.8171 (tttt) cc_final: 0.7803 (ttpt) REVERT: B 314 GLU cc_start: 0.7739 (pm20) cc_final: 0.7533 (pm20) REVERT: B 317 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7773 (ptp-110) REVERT: B 330 GLU cc_start: 0.8274 (tt0) cc_final: 0.7648 (tt0) REVERT: B 370 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7248 (mm-30) REVERT: C 188 MET cc_start: 0.8983 (mmm) cc_final: 0.8685 (mmm) REVERT: C 197 ARG cc_start: 0.7547 (mtp-110) cc_final: 0.7150 (mtp85) REVERT: E 80 TYR cc_start: 0.8126 (m-80) cc_final: 0.7673 (m-80) REVERT: E 83 MET cc_start: 0.8337 (mtp) cc_final: 0.8027 (mtp) outliers start: 19 outliers final: 13 residues processed: 136 average time/residue: 1.0890 time to fit residues: 158.1934 Evaluate side-chains 142 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 0.4980 chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 7 optimal weight: 0.0000 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.0000 chunk 71 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 57 optimal weight: 0.0980 overall best weight: 0.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 175 GLN C 176 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.157691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.121526 restraints weight = 17243.239| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.95 r_work: 0.3318 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8014 Z= 0.148 Angle : 0.514 7.199 10927 Z= 0.271 Chirality : 0.041 0.137 1276 Planarity : 0.004 0.056 1371 Dihedral : 5.343 49.249 1272 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.54 % Allowed : 20.59 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.27), residues: 1018 helix: 2.14 (0.26), residues: 420 sheet: 0.46 (0.33), residues: 220 loop : -0.49 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 234 HIS 0.007 0.001 HIS A 127 PHE 0.028 0.001 PHE A 119 TYR 0.012 0.001 TYR B 339 ARG 0.009 0.000 ARG C 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6525.95 seconds wall clock time: 115 minutes 44.10 seconds (6944.10 seconds total)