Starting phenix.real_space_refine on Fri Aug 22 18:50:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xzg_38795/08_2025/8xzg_38795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xzg_38795/08_2025/8xzg_38795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xzg_38795/08_2025/8xzg_38795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xzg_38795/08_2025/8xzg_38795.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xzg_38795/08_2025/8xzg_38795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xzg_38795/08_2025/8xzg_38795.map" } resolution = 3.2 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= -0.000 sd= 0.013 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 61 5.16 5 C 4572 2.51 5 N 1222 2.21 5 O 1317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 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: 7172 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1737 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2528 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "L" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 107 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 3, 'TRANS': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2356 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 1.90, per 1000 atoms: 0.26 Number of scatterers: 7172 At special positions: 0 Unit cell: (78.078, 120.666, 118.638, 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 61 16.00 O 1317 8.00 N 1222 7.00 C 4572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.02 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: 0.64 Conformation dependent library (CDL) restraints added in 461.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 44.8% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.941A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.524A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.114A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.509A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.019A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.703A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.899A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'G' and resid 6 through 22 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.717A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 27 through 53 Proline residue: R 32 - end of helix removed outlier: 3.942A pdb=" N GLY R 47 " --> pdb=" O THR R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 81 removed outlier: 3.841A pdb=" N THR R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 90 removed outlier: 3.517A pdb=" N TYR R 90 " --> pdb=" O ALA R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 132 removed outlier: 4.168A pdb=" N SER R 106 " --> pdb=" O CYS R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 144 removed outlier: 3.859A pdb=" N ARG R 141 " --> pdb=" O ASN R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 161 Processing helix chain 'R' and resid 162 through 165 Processing helix chain 'R' and resid 190 through 192 No H-bonds generated for 'chain 'R' and resid 190 through 192' Processing helix chain 'R' and resid 193 through 210 removed outlier: 3.522A pdb=" N TRP R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 232 Processing helix chain 'R' and resid 240 through 275 removed outlier: 4.072A pdb=" N ARG R 245 " --> pdb=" O ARG R 241 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU R 246 " --> pdb=" O LYS R 242 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU R 247 " --> pdb=" O ARG R 243 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE R 257 " --> pdb=" O LEU R 253 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET R 262 " --> pdb=" O ALA R 258 " (cutoff:3.500A) Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 283 through 298 Proline residue: R 292 - end of helix removed outlier: 4.224A pdb=" N CYS R 296 " --> pdb=" O PRO R 292 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER R 298 " --> pdb=" O CYS R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 305 Processing helix chain 'R' and resid 305 through 310 Processing helix chain 'R' and resid 313 through 327 removed outlier: 3.739A pdb=" N ARG R 317 " --> pdb=" O ASP R 313 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY R 327 " --> pdb=" O MET R 323 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190 removed outlier: 3.819A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.690A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 61 removed outlier: 6.844A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 114 removed outlier: 5.969A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 190 removed outlier: 6.543A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 231 removed outlier: 3.865A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.691A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 168 through 172 removed outlier: 3.533A pdb=" N THR R 169 " --> pdb=" O TYR R 182 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR R 182 " --> pdb=" O THR R 169 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 957 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.84 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: 2259 1.34 - 1.45: 1178 1.45 - 1.57: 3794 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 7319 Sorted by residual: bond pdb=" N PCA L 1 " pdb=" CD PCA L 1 " ideal model delta sigma weight residual 1.345 1.463 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N TRP R 279 " pdb=" CA TRP R 279 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.37e+01 bond pdb=" N ILE R 290 " pdb=" CA ILE R 290 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.09e-02 8.42e+03 1.23e+01 bond pdb=" N VAL R 79 " pdb=" CA VAL R 79 " ideal model delta sigma weight residual 1.458 1.496 -0.037 1.22e-02 6.72e+03 9.37e+00 bond pdb=" N VAL R 80 " pdb=" CA VAL R 80 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.12e+00 ... (remaining 7314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 9516 2.02 - 4.05: 355 4.05 - 6.07: 34 6.07 - 8.09: 6 8.09 - 10.11: 1 Bond angle restraints: 9912 Sorted by residual: angle pdb=" N HIS R 231 " pdb=" CA HIS R 231 " pdb=" C HIS R 231 " ideal model delta sigma weight residual 111.36 117.00 -5.64 1.09e+00 8.42e-01 2.68e+01 angle pdb=" N THR R 99 " pdb=" CA THR R 99 " pdb=" C THR R 99 " ideal model delta sigma weight residual 111.71 105.87 5.84 1.15e+00 7.56e-01 2.58e+01 angle pdb=" O ILE R 31 " pdb=" C ILE R 31 " pdb=" N PRO R 32 " ideal model delta sigma weight residual 120.42 123.50 -3.08 6.40e-01 2.44e+00 2.31e+01 angle pdb=" N LYS R 242 " pdb=" CA LYS R 242 " pdb=" C LYS R 242 " ideal model delta sigma weight residual 113.17 107.68 5.49 1.26e+00 6.30e-01 1.90e+01 angle pdb=" C TRP R 279 " pdb=" N PRO R 280 " pdb=" CA PRO R 280 " ideal model delta sigma weight residual 119.84 124.99 -5.15 1.25e+00 6.40e-01 1.70e+01 ... (remaining 9907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 3844 17.18 - 34.36: 419 34.36 - 51.53: 69 51.53 - 68.71: 7 68.71 - 85.89: 4 Dihedral angle restraints: 4343 sinusoidal: 1669 harmonic: 2674 Sorted by residual: dihedral pdb=" CA PHE B 199 " pdb=" C PHE B 199 " pdb=" N VAL B 200 " pdb=" CA VAL B 200 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA PHE B 241 " pdb=" C PHE B 241 " pdb=" N ALA B 242 " pdb=" CA ALA B 242 " ideal model delta harmonic sigma weight residual 180.00 156.67 23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 161.96 18.04 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 4340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 834 0.054 - 0.108: 226 0.108 - 0.162: 62 0.162 - 0.216: 12 0.216 - 0.270: 1 Chirality restraints: 1135 Sorted by residual: chirality pdb=" CA HIS R 231 " pdb=" N HIS R 231 " pdb=" C HIS R 231 " pdb=" CB HIS R 231 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA LEU R 71 " pdb=" N LEU R 71 " pdb=" C LEU R 71 " pdb=" CB LEU R 71 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA LEU R 120 " pdb=" N LEU R 120 " pdb=" C LEU R 120 " pdb=" CB LEU R 120 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 1132 not shown) Planarity restraints: 1247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY R 230 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLY R 230 " -0.056 2.00e-02 2.50e+03 pdb=" O GLY R 230 " 0.021 2.00e-02 2.50e+03 pdb=" N HIS R 231 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 60 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C ALA B 60 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA B 60 " -0.018 2.00e-02 2.50e+03 pdb=" N MET B 61 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 83 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.18e+00 pdb=" C ASP B 83 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP B 83 " 0.013 2.00e-02 2.50e+03 pdb=" N SER B 84 " 0.012 2.00e-02 2.50e+03 ... (remaining 1244 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 433 2.72 - 3.26: 6935 3.26 - 3.81: 10928 3.81 - 4.35: 13336 4.35 - 4.90: 23771 Nonbonded interactions: 55403 Sorted by model distance: nonbonded pdb=" ND2 ASN R 46 " pdb=" OD2 ASP R 75 " model vdw 2.173 3.120 nonbonded pdb=" O THR R 295 " pdb=" CE1 TYR R 299 " model vdw 2.209 3.340 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.229 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.234 3.040 nonbonded pdb=" NH2 ARG B 49 " pdb=" O PHE G 61 " model vdw 2.279 3.120 ... (remaining 55398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.810 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 0.118 7320 Z= 0.429 Angle : 1.021 51.330 9914 Z= 0.630 Chirality : 0.055 0.270 1135 Planarity : 0.005 0.047 1247 Dihedral : 14.038 85.891 2606 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.11 % Favored : 93.78 % Rotamer: Outliers : 1.56 % Allowed : 9.08 % Favored : 89.36 % 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: -2.72 (0.25), residues: 900 helix: -0.45 (0.25), residues: 382 sheet: -3.04 (0.29), residues: 169 loop : -2.59 (0.28), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 62 TYR 0.009 0.001 TYR B 124 PHE 0.017 0.002 PHE G 61 TRP 0.010 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00795 ( 7319) covalent geometry : angle 0.88125 ( 9912) SS BOND : bond 0.01131 ( 1) SS BOND : angle 36.32142 ( 2) hydrogen bonds : bond 0.17087 ( 331) hydrogen bonds : angle 6.65217 ( 957) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.285 Fit side-chains REVERT: A 35 LYS cc_start: 0.7726 (mttt) cc_final: 0.7488 (mttp) REVERT: A 251 ASP cc_start: 0.8791 (t70) cc_final: 0.8575 (t0) REVERT: A 260 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8104 (t) REVERT: B 118 ASP cc_start: 0.7505 (t0) cc_final: 0.7245 (t0) REVERT: B 129 ARG cc_start: 0.7139 (tpt90) cc_final: 0.6346 (mtp-110) REVERT: B 214 ARG cc_start: 0.7224 (mtt180) cc_final: 0.6712 (mmt180) REVERT: B 226 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7847 (mt-10) REVERT: R 31 ILE cc_start: 0.4786 (OUTLIER) cc_final: 0.4547 (mm) REVERT: R 323 MET cc_start: 0.6677 (mmm) cc_final: 0.5828 (mtt) outliers start: 12 outliers final: 3 residues processed: 120 average time/residue: 0.1215 time to fit residues: 18.4800 Evaluate side-chains 91 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 253 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 91 HIS B 155 ASN B 183 HIS G 24 ASN L 7 HIS ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 289 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.180994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.132337 restraints weight = 7696.417| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.41 r_work: 0.3328 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7320 Z= 0.180 Angle : 0.589 6.535 9914 Z= 0.313 Chirality : 0.044 0.147 1135 Planarity : 0.004 0.049 1247 Dihedral : 5.287 49.958 999 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.33 % Allowed : 14.40 % Favored : 83.27 % 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: -1.60 (0.27), residues: 900 helix: 0.50 (0.26), residues: 397 sheet: -2.64 (0.31), residues: 179 loop : -1.97 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 62 TYR 0.014 0.001 TYR R 35 PHE 0.025 0.002 PHE R 39 TRP 0.011 0.001 TRP R 95 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 7319) covalent geometry : angle 0.58764 ( 9912) SS BOND : bond 0.00196 ( 1) SS BOND : angle 2.89241 ( 2) hydrogen bonds : bond 0.04532 ( 331) hydrogen bonds : angle 4.56000 ( 957) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.268 Fit side-chains REVERT: B 52 ARG cc_start: 0.8731 (mtt90) cc_final: 0.8512 (mtt90) REVERT: B 118 ASP cc_start: 0.8057 (t0) cc_final: 0.7817 (t0) REVERT: B 129 ARG cc_start: 0.7245 (tpt90) cc_final: 0.6087 (mtp-110) REVERT: B 191 SER cc_start: 0.8872 (t) cc_final: 0.8589 (p) REVERT: B 200 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8321 (m) REVERT: B 214 ARG cc_start: 0.7775 (mtt180) cc_final: 0.6828 (mmt180) REVERT: B 226 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8416 (mt-10) REVERT: B 234 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: R 323 MET cc_start: 0.6653 (mmm) cc_final: 0.5871 (mtt) outliers start: 18 outliers final: 12 residues processed: 98 average time/residue: 0.1161 time to fit residues: 14.5629 Evaluate side-chains 91 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 253 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 86 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN R 46 ASN R 231 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.186663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134994 restraints weight = 7589.157| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.40 r_work: 0.3407 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7320 Z= 0.111 Angle : 0.488 5.536 9914 Z= 0.256 Chirality : 0.041 0.144 1135 Planarity : 0.004 0.040 1247 Dihedral : 4.443 49.085 994 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.95 % Allowed : 16.21 % Favored : 81.84 % 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: -0.93 (0.28), residues: 900 helix: 1.05 (0.27), residues: 399 sheet: -2.39 (0.32), residues: 183 loop : -1.56 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 62 TYR 0.008 0.001 TYR R 35 PHE 0.018 0.001 PHE R 39 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS R 231 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7319) covalent geometry : angle 0.48741 ( 9912) SS BOND : bond 0.00680 ( 1) SS BOND : angle 2.27194 ( 2) hydrogen bonds : bond 0.03503 ( 331) hydrogen bonds : angle 4.03611 ( 957) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.271 Fit side-chains REVERT: A 306 GLN cc_start: 0.7502 (tp40) cc_final: 0.7244 (tp40) REVERT: B 129 ARG cc_start: 0.7094 (tpt90) cc_final: 0.5889 (mtp-110) REVERT: B 152 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8096 (tt) REVERT: B 163 ASP cc_start: 0.7345 (t0) cc_final: 0.6769 (t0) REVERT: B 200 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8190 (m) REVERT: B 214 ARG cc_start: 0.7870 (mtt180) cc_final: 0.6804 (mmt180) REVERT: B 226 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8677 (mt-10) REVERT: B 234 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8510 (m-80) REVERT: B 258 ASP cc_start: 0.6654 (t70) cc_final: 0.5866 (t70) REVERT: R 323 MET cc_start: 0.6495 (mmm) cc_final: 0.5769 (mtt) outliers start: 15 outliers final: 8 residues processed: 105 average time/residue: 0.1013 time to fit residues: 13.9218 Evaluate side-chains 93 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 253 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 38 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 75 GLN B 230 ASN ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.185414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135351 restraints weight = 7681.745| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.50 r_work: 0.3374 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7320 Z= 0.113 Angle : 0.475 5.315 9914 Z= 0.249 Chirality : 0.040 0.173 1135 Planarity : 0.003 0.039 1247 Dihedral : 4.195 47.437 994 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.46 % Allowed : 18.55 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.64 (0.28), residues: 900 helix: 1.20 (0.27), residues: 408 sheet: -2.15 (0.33), residues: 184 loop : -1.41 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 62 TYR 0.007 0.001 TYR R 35 PHE 0.016 0.001 PHE R 39 TRP 0.011 0.001 TRP B 211 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7319) covalent geometry : angle 0.47527 ( 9912) SS BOND : bond 0.00404 ( 1) SS BOND : angle 1.03154 ( 2) hydrogen bonds : bond 0.03314 ( 331) hydrogen bonds : angle 3.85213 ( 957) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.302 Fit side-chains REVERT: B 129 ARG cc_start: 0.7136 (tpt90) cc_final: 0.6002 (mtp-110) REVERT: B 163 ASP cc_start: 0.7326 (t0) cc_final: 0.6858 (t70) REVERT: B 214 ARG cc_start: 0.7780 (mtt180) cc_final: 0.6832 (mmt180) REVERT: B 226 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8354 (mt-10) REVERT: B 234 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: B 258 ASP cc_start: 0.6465 (t70) cc_final: 0.5690 (t70) REVERT: R 323 MET cc_start: 0.6513 (mmm) cc_final: 0.5677 (mtt) outliers start: 19 outliers final: 14 residues processed: 102 average time/residue: 0.1108 time to fit residues: 14.7470 Evaluate side-chains 100 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 207 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 46 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 7 optimal weight: 0.0070 chunk 88 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 175 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 = 0.4133 r_free = 0.4133 target = 0.186719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136951 restraints weight = 7639.261| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.46 r_work: 0.3394 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7320 Z= 0.100 Angle : 0.469 9.130 9914 Z= 0.240 Chirality : 0.040 0.163 1135 Planarity : 0.003 0.038 1247 Dihedral : 3.724 17.022 992 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.72 % Allowed : 17.90 % Favored : 79.38 % 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: -0.31 (0.29), residues: 900 helix: 1.38 (0.27), residues: 409 sheet: -1.86 (0.35), residues: 184 loop : -1.20 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 62 TYR 0.007 0.001 TYR B 59 PHE 0.014 0.001 PHE R 39 TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS L 7 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 7319) covalent geometry : angle 0.46866 ( 9912) SS BOND : bond 0.00158 ( 1) SS BOND : angle 0.49727 ( 2) hydrogen bonds : bond 0.03088 ( 331) hydrogen bonds : angle 3.72961 ( 957) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.276 Fit side-chains REVERT: B 52 ARG cc_start: 0.8789 (mtt90) cc_final: 0.8569 (mtt90) REVERT: B 129 ARG cc_start: 0.7167 (tpt90) cc_final: 0.6083 (mtp-110) REVERT: B 163 ASP cc_start: 0.7259 (t0) cc_final: 0.6916 (t0) REVERT: B 214 ARG cc_start: 0.7743 (mtt180) cc_final: 0.6782 (mmt180) REVERT: B 217 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7516 (mtm) REVERT: B 219 ARG cc_start: 0.7869 (mtt90) cc_final: 0.7450 (mtt90) REVERT: B 226 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8353 (mt-10) REVERT: B 258 ASP cc_start: 0.6507 (t70) cc_final: 0.5759 (t70) REVERT: R 91 ARG cc_start: 0.4361 (OUTLIER) cc_final: 0.3174 (ptp-170) REVERT: R 120 LEU cc_start: 0.4693 (OUTLIER) cc_final: 0.4392 (tt) REVERT: R 183 MET cc_start: 0.7281 (mtp) cc_final: 0.7060 (ttm) REVERT: R 187 MET cc_start: 0.3860 (mmm) cc_final: 0.3546 (ttm) REVERT: R 323 MET cc_start: 0.6499 (mmm) cc_final: 0.5642 (mtt) outliers start: 21 outliers final: 12 residues processed: 100 average time/residue: 0.1054 time to fit residues: 13.6867 Evaluate side-chains 95 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 207 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.187808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.136616 restraints weight = 7679.110| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.49 r_work: 0.3357 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7320 Z= 0.125 Angle : 0.480 8.467 9914 Z= 0.247 Chirality : 0.041 0.161 1135 Planarity : 0.003 0.045 1247 Dihedral : 3.778 18.630 992 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.33 % Allowed : 19.46 % Favored : 78.21 % 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: -0.20 (0.29), residues: 900 helix: 1.46 (0.27), residues: 408 sheet: -1.74 (0.35), residues: 186 loop : -1.16 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 62 TYR 0.008 0.001 TYR B 59 PHE 0.013 0.001 PHE R 39 TRP 0.011 0.001 TRP R 261 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7319) covalent geometry : angle 0.48004 ( 9912) SS BOND : bond 0.00209 ( 1) SS BOND : angle 0.37978 ( 2) hydrogen bonds : bond 0.03237 ( 331) hydrogen bonds : angle 3.72458 ( 957) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.187 Fit side-chains REVERT: B 17 GLN cc_start: 0.7811 (tm-30) cc_final: 0.7248 (tm-30) REVERT: B 129 ARG cc_start: 0.7135 (tpt90) cc_final: 0.6146 (mtp-110) REVERT: B 163 ASP cc_start: 0.7425 (t0) cc_final: 0.7176 (t0) REVERT: B 214 ARG cc_start: 0.7749 (mtt180) cc_final: 0.6780 (mmt180) REVERT: B 217 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7505 (mtm) REVERT: B 226 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8318 (mt-10) REVERT: R 91 ARG cc_start: 0.4475 (OUTLIER) cc_final: 0.3299 (ptp-170) REVERT: R 183 MET cc_start: 0.7297 (mtp) cc_final: 0.7008 (ttm) REVERT: R 187 MET cc_start: 0.3800 (mmm) cc_final: 0.3512 (ttm) REVERT: R 323 MET cc_start: 0.6447 (mmm) cc_final: 0.5592 (mtt) outliers start: 18 outliers final: 13 residues processed: 98 average time/residue: 0.1212 time to fit residues: 15.0630 Evaluate side-chains 98 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 207 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 12 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 75 optimal weight: 0.0050 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 45 optimal weight: 0.1980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.187997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.138068 restraints weight = 7616.564| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.35 r_work: 0.3405 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7320 Z= 0.101 Angle : 0.459 7.621 9914 Z= 0.236 Chirality : 0.040 0.159 1135 Planarity : 0.003 0.040 1247 Dihedral : 3.651 18.523 992 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.33 % Allowed : 19.84 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.00 (0.29), residues: 900 helix: 1.57 (0.27), residues: 408 sheet: -1.60 (0.36), residues: 186 loop : -1.01 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 62 TYR 0.016 0.001 TYR A 287 PHE 0.012 0.001 PHE R 39 TRP 0.013 0.001 TRP R 261 HIS 0.003 0.001 HIS L 7 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 7319) covalent geometry : angle 0.45885 ( 9912) SS BOND : bond 0.00211 ( 1) SS BOND : angle 0.27220 ( 2) hydrogen bonds : bond 0.02977 ( 331) hydrogen bonds : angle 3.62955 ( 957) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.286 Fit side-chains REVERT: B 129 ARG cc_start: 0.7090 (tpt90) cc_final: 0.5998 (mtp-110) REVERT: B 163 ASP cc_start: 0.7538 (t0) cc_final: 0.7255 (t0) REVERT: B 217 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7590 (mtm) REVERT: B 226 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8423 (mt-10) REVERT: B 258 ASP cc_start: 0.6535 (t70) cc_final: 0.6152 (t70) REVERT: B 325 MET cc_start: 0.8711 (tpp) cc_final: 0.8475 (mmp) REVERT: R 91 ARG cc_start: 0.4467 (OUTLIER) cc_final: 0.3263 (ptp-170) REVERT: R 120 LEU cc_start: 0.5080 (OUTLIER) cc_final: 0.4705 (tt) REVERT: R 183 MET cc_start: 0.7285 (mtp) cc_final: 0.6987 (ttm) REVERT: R 187 MET cc_start: 0.3777 (mmm) cc_final: 0.3525 (ttm) REVERT: R 323 MET cc_start: 0.6413 (mmm) cc_final: 0.5529 (mtt) outliers start: 18 outliers final: 13 residues processed: 94 average time/residue: 0.0942 time to fit residues: 11.6452 Evaluate side-chains 95 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 207 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 88 optimal weight: 7.9990 chunk 80 optimal weight: 0.0980 chunk 17 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 175 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 = 0.4132 r_free = 0.4132 target = 0.186632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.136011 restraints weight = 7719.793| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.33 r_work: 0.3382 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7320 Z= 0.119 Angle : 0.469 7.728 9914 Z= 0.242 Chirality : 0.040 0.158 1135 Planarity : 0.003 0.039 1247 Dihedral : 3.697 17.788 992 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.85 % Allowed : 19.07 % Favored : 78.08 % 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: 0.06 (0.29), residues: 900 helix: 1.60 (0.27), residues: 408 sheet: -1.59 (0.36), residues: 186 loop : -0.93 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 62 TYR 0.010 0.001 TYR A 287 PHE 0.011 0.001 PHE R 39 TRP 0.015 0.001 TRP R 261 HIS 0.003 0.001 HIS L 7 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7319) covalent geometry : angle 0.46926 ( 9912) SS BOND : bond 0.00224 ( 1) SS BOND : angle 0.21768 ( 2) hydrogen bonds : bond 0.03111 ( 331) hydrogen bonds : angle 3.63469 ( 957) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.290 Fit side-chains REVERT: B 17 GLN cc_start: 0.7671 (tm-30) cc_final: 0.7119 (tm-30) REVERT: B 129 ARG cc_start: 0.7067 (tpt90) cc_final: 0.5991 (mtp-110) REVERT: B 163 ASP cc_start: 0.7605 (t0) cc_final: 0.7345 (t0) REVERT: B 217 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7539 (mtm) REVERT: B 226 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8425 (mt-10) REVERT: B 258 ASP cc_start: 0.6502 (t70) cc_final: 0.6123 (t70) REVERT: R 91 ARG cc_start: 0.4639 (OUTLIER) cc_final: 0.3401 (ptp-170) REVERT: R 120 LEU cc_start: 0.5103 (OUTLIER) cc_final: 0.4690 (tt) REVERT: R 183 MET cc_start: 0.7226 (mtp) cc_final: 0.6958 (ttm) REVERT: R 187 MET cc_start: 0.3516 (mmm) cc_final: 0.3251 (ttm) REVERT: R 242 LYS cc_start: 0.8101 (mmtt) cc_final: 0.6740 (mtmt) REVERT: R 323 MET cc_start: 0.6495 (mmm) cc_final: 0.5565 (mtt) outliers start: 22 outliers final: 17 residues processed: 104 average time/residue: 0.0934 time to fit residues: 12.7139 Evaluate side-chains 108 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 207 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 6 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 0.0170 chunk 86 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 74 optimal weight: 10.0000 chunk 56 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 175 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 = 0.4146 r_free = 0.4146 target = 0.188441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.138339 restraints weight = 7511.122| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.26 r_work: 0.3409 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7320 Z= 0.097 Angle : 0.452 7.230 9914 Z= 0.233 Chirality : 0.040 0.158 1135 Planarity : 0.003 0.038 1247 Dihedral : 3.566 15.831 992 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.59 % Allowed : 19.58 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.22 (0.29), residues: 900 helix: 1.72 (0.27), residues: 407 sheet: -1.47 (0.37), residues: 184 loop : -0.84 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 62 TYR 0.010 0.001 TYR A 287 PHE 0.011 0.001 PHE R 39 TRP 0.016 0.001 TRP R 261 HIS 0.002 0.001 HIS L 7 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 7319) covalent geometry : angle 0.45251 ( 9912) SS BOND : bond 0.00226 ( 1) SS BOND : angle 0.17356 ( 2) hydrogen bonds : bond 0.02868 ( 331) hydrogen bonds : angle 3.55515 ( 957) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.291 Fit side-chains REVERT: B 17 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7156 (tm-30) REVERT: B 129 ARG cc_start: 0.7053 (tpt90) cc_final: 0.5988 (mtp-110) REVERT: B 163 ASP cc_start: 0.7513 (t0) cc_final: 0.7251 (t0) REVERT: B 217 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7560 (mtm) REVERT: B 226 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8390 (mt-10) REVERT: B 258 ASP cc_start: 0.6539 (t70) cc_final: 0.6151 (t70) REVERT: G 21 MET cc_start: 0.7957 (tmm) cc_final: 0.7707 (tmm) REVERT: R 91 ARG cc_start: 0.4703 (OUTLIER) cc_final: 0.3574 (ptp-170) REVERT: R 120 LEU cc_start: 0.5013 (OUTLIER) cc_final: 0.4537 (tt) REVERT: R 183 MET cc_start: 0.7262 (mtp) cc_final: 0.6988 (ttm) REVERT: R 242 LYS cc_start: 0.8099 (mmtt) cc_final: 0.6775 (mtmt) REVERT: R 309 TYR cc_start: 0.7520 (m-80) cc_final: 0.7221 (m-80) REVERT: R 323 MET cc_start: 0.6545 (mmm) cc_final: 0.5588 (mtt) outliers start: 20 outliers final: 16 residues processed: 102 average time/residue: 0.0923 time to fit residues: 12.3186 Evaluate side-chains 103 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 22 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.188922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.138255 restraints weight = 7622.099| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.41 r_work: 0.3395 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7320 Z= 0.106 Angle : 0.460 7.169 9914 Z= 0.236 Chirality : 0.040 0.158 1135 Planarity : 0.003 0.039 1247 Dihedral : 3.587 17.265 992 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.72 % Allowed : 19.20 % Favored : 78.08 % 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: 0.26 (0.29), residues: 900 helix: 1.71 (0.27), residues: 408 sheet: -1.46 (0.36), residues: 186 loop : -0.77 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 62 TYR 0.009 0.001 TYR R 221 PHE 0.011 0.001 PHE R 39 TRP 0.014 0.001 TRP R 261 HIS 0.002 0.001 HIS L 7 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 7319) covalent geometry : angle 0.46046 ( 9912) SS BOND : bond 0.00218 ( 1) SS BOND : angle 0.14898 ( 2) hydrogen bonds : bond 0.02952 ( 331) hydrogen bonds : angle 3.56077 ( 957) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.334 Fit side-chains REVERT: B 17 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7146 (tm-30) REVERT: B 129 ARG cc_start: 0.7059 (tpt90) cc_final: 0.6008 (mtp-110) REVERT: B 163 ASP cc_start: 0.7577 (t0) cc_final: 0.7325 (t0) REVERT: B 217 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7568 (mtm) REVERT: B 226 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8390 (mt-10) REVERT: B 258 ASP cc_start: 0.6597 (t70) cc_final: 0.6156 (t70) REVERT: B 259 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7776 (mm-40) REVERT: G 21 MET cc_start: 0.7978 (tmm) cc_final: 0.7698 (tmm) REVERT: G 58 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7154 (tm-30) REVERT: R 91 ARG cc_start: 0.4821 (OUTLIER) cc_final: 0.3660 (ptp-170) REVERT: R 120 LEU cc_start: 0.5065 (OUTLIER) cc_final: 0.4669 (tt) REVERT: R 183 MET cc_start: 0.7269 (mtp) cc_final: 0.6985 (ttm) REVERT: R 242 LYS cc_start: 0.8128 (mmtt) cc_final: 0.6814 (mtmt) REVERT: R 309 TYR cc_start: 0.7435 (m-80) cc_final: 0.7202 (m-80) REVERT: R 323 MET cc_start: 0.6558 (mmm) cc_final: 0.5636 (mtt) outliers start: 21 outliers final: 16 residues processed: 104 average time/residue: 0.0996 time to fit residues: 13.6676 Evaluate side-chains 111 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 91 ARG Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 85 optimal weight: 0.0270 chunk 34 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 chunk 29 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 0.0070 chunk 18 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN R 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.189768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.139843 restraints weight = 7606.365| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.36 r_work: 0.3431 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7320 Z= 0.087 Angle : 0.446 6.712 9914 Z= 0.229 Chirality : 0.039 0.158 1135 Planarity : 0.003 0.037 1247 Dihedral : 3.496 15.921 992 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.95 % Allowed : 20.23 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.36 (0.30), residues: 900 helix: 1.76 (0.27), residues: 408 sheet: -1.31 (0.37), residues: 182 loop : -0.75 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 62 TYR 0.008 0.001 TYR A 287 PHE 0.011 0.001 PHE R 39 TRP 0.018 0.001 TRP R 261 HIS 0.002 0.001 HIS L 7 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 7319) covalent geometry : angle 0.44649 ( 9912) SS BOND : bond 0.00189 ( 1) SS BOND : angle 0.11744 ( 2) hydrogen bonds : bond 0.02732 ( 331) hydrogen bonds : angle 3.50467 ( 957) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2031.36 seconds wall clock time: 35 minutes 29.18 seconds (2129.18 seconds total)