Starting phenix.real_space_refine on Fri Aug 22 23:24:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2k_38015/08_2025/8x2k_38015_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2k_38015/08_2025/8x2k_38015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x2k_38015/08_2025/8x2k_38015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2k_38015/08_2025/8x2k_38015.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2k_38015/08_2025/8x2k_38015_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2k_38015/08_2025/8x2k_38015_neut.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.086 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 56 5.16 5 C 5440 2.51 5 N 1472 2.21 5 O 1602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 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: 8570 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1896 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1795 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'LEU%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1803 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {'5YM': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 2.28, per 1000 atoms: 0.27 Number of scatterers: 8570 At special positions: 0 Unit cell: (88.4, 122.4, 124.95, 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 56 16.00 O 1602 8.00 N 1472 7.00 C 5440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 347.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 17 sheets defined 36.8% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 43 through 68 removed outlier: 3.614A pdb=" N THR A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 102 Processing helix chain 'A' and resid 105 through 140 removed outlier: 3.620A pdb=" N GLY A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 4.278A pdb=" N TYR A 145 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 167 removed outlier: 3.989A pdb=" N GLY A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 230 removed outlier: 3.973A pdb=" N ALA A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N PHE A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 removed outlier: 3.510A pdb=" N ALA A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 267 Proline residue: A 262 - end of helix Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.239A pdb=" N THR A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 298 removed outlier: 3.934A pdb=" N THR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Proline residue: A 294 - end of helix Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'B' and resid 13 through 38 removed outlier: 3.998A pdb=" N ALA B 18 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN B 29 " --> pdb=" O MET B 25 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 264 through 278 removed outlier: 4.388A pdb=" N GLU B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 4.005A pdb=" N ARG B 283 " --> pdb=" O ARG B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.536A pdb=" N LEU B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.931A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 391 removed outlier: 3.560A pdb=" N VAL B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 383 " --> pdb=" O CYS B 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 6 through 24 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.581A pdb=" N ALA D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.554A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 41 Processing sheet with id=AA2, first strand: chain 'B' and resid 43 through 47 removed outlier: 5.887A pdb=" N ILE B 244 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N PHE B 290 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE B 246 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN B 292 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B 248 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.520A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.578A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 105 removed outlier: 3.649A pdb=" N GLY C 115 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.782A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C 180 " --> pdb=" O CYS C 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 191 through 192 removed outlier: 4.007A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.485A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP C 254 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 275 removed outlier: 6.513A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 284 through 286 removed outlier: 6.442A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.948A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP E 36 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.948A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB7, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.424A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.573A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1128 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: 1.51 Time building geometry restraints manager: 1.13 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: 1392 1.30 - 1.43: 2297 1.43 - 1.56: 4964 1.56 - 1.69: 0 1.69 - 1.82: 81 Bond restraints: 8734 Sorted by residual: bond pdb=" C LEU A 212 " pdb=" O LEU A 212 " ideal model delta sigma weight residual 1.237 1.170 0.066 1.17e-02 7.31e+03 3.23e+01 bond pdb=" C18 5YM A 401 " pdb=" N20 5YM A 401 " ideal model delta sigma weight residual 1.344 1.450 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C TYR A 135 " pdb=" O TYR A 135 " ideal model delta sigma weight residual 1.236 1.172 0.064 1.29e-02 6.01e+03 2.49e+01 bond pdb=" C ILE A 208 " pdb=" O ILE A 208 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.13e-02 7.83e+03 1.97e+01 bond pdb=" C PHE A 263 " pdb=" O PHE A 263 " ideal model delta sigma weight residual 1.236 1.191 0.046 1.15e-02 7.56e+03 1.59e+01 ... (remaining 8729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 11636 2.39 - 4.77: 169 4.77 - 7.16: 24 7.16 - 9.55: 9 9.55 - 11.93: 4 Bond angle restraints: 11842 Sorted by residual: angle pdb=" N VAL A 160 " pdb=" CA VAL A 160 " pdb=" C VAL A 160 " ideal model delta sigma weight residual 111.81 100.78 11.03 8.60e-01 1.35e+00 1.64e+02 angle pdb=" N THR A 121 " pdb=" CA THR A 121 " pdb=" C THR A 121 " ideal model delta sigma weight residual 114.04 103.06 10.98 1.24e+00 6.50e-01 7.84e+01 angle pdb=" N PRO A 189 " pdb=" CA PRO A 189 " pdb=" CB PRO A 189 " ideal model delta sigma weight residual 103.25 95.34 7.91 1.05e+00 9.07e-01 5.68e+01 angle pdb=" CA LEU A 212 " pdb=" C LEU A 212 " pdb=" O LEU A 212 " ideal model delta sigma weight residual 120.55 113.11 7.44 1.06e+00 8.90e-01 4.93e+01 angle pdb=" N ALA A 129 " pdb=" CA ALA A 129 " pdb=" C ALA A 129 " ideal model delta sigma weight residual 113.12 104.57 8.55 1.25e+00 6.40e-01 4.68e+01 ... (remaining 11837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.81: 5065 33.81 - 67.62: 112 67.62 - 101.43: 10 101.43 - 135.24: 0 135.24 - 169.05: 1 Dihedral angle restraints: 5188 sinusoidal: 1981 harmonic: 3207 Sorted by residual: dihedral pdb=" C TYR A 135 " pdb=" N TYR A 135 " pdb=" CA TYR A 135 " pdb=" CB TYR A 135 " ideal model delta harmonic sigma weight residual -122.60 -109.21 -13.39 0 2.50e+00 1.60e-01 2.87e+01 dihedral pdb=" N20 5YM A 401 " pdb=" C21 5YM A 401 " pdb=" C22 5YM A 401 " pdb=" O23 5YM A 401 " ideal model delta sinusoidal sigma weight residual -61.92 107.13 -169.05 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" N ALA A 129 " pdb=" C ALA A 129 " pdb=" CA ALA A 129 " pdb=" CB ALA A 129 " ideal model delta harmonic sigma weight residual 122.90 111.87 11.03 0 2.50e+00 1.60e-01 1.95e+01 ... (remaining 5185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1246 0.083 - 0.165: 100 0.165 - 0.247: 13 0.247 - 0.330: 3 0.330 - 0.412: 1 Chirality restraints: 1363 Sorted by residual: chirality pdb=" CB VAL A 205 " pdb=" CA VAL A 205 " pdb=" CG1 VAL A 205 " pdb=" CG2 VAL A 205 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CA VAL A 160 " pdb=" N VAL A 160 " pdb=" C VAL A 160 " pdb=" CB VAL A 160 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ALA A 129 " pdb=" N ALA A 129 " pdb=" C ALA A 129 " pdb=" CB ALA A 129 " both_signs ideal model delta sigma weight residual False 2.48 2.78 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1360 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 200 " -0.026 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C ILE A 200 " 0.087 2.00e-02 2.50e+03 pdb=" O ILE A 200 " -0.033 2.00e-02 2.50e+03 pdb=" N ALA A 201 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 162 " -0.016 2.00e-02 2.50e+03 3.06e-02 9.39e+00 pdb=" C GLY A 162 " 0.053 2.00e-02 2.50e+03 pdb=" O GLY A 162 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY A 163 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 113 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C VAL A 113 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL A 113 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY A 114 " -0.017 2.00e-02 2.50e+03 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 49 2.51 - 3.11: 6305 3.11 - 3.70: 12259 3.70 - 4.30: 18165 4.30 - 4.90: 31440 Nonbonded interactions: 68218 Sorted by model distance: nonbonded pdb=" OH TYR B 318 " pdb=" OD2 ASP B 343 " model vdw 1.909 3.040 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 1.957 3.040 nonbonded pdb=" O ASP C 228 " pdb=" OG SER C 245 " model vdw 1.979 3.040 nonbonded pdb=" OD1 ASP C 205 " pdb=" OG SER C 207 " model vdw 2.009 3.040 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.064 3.040 ... (remaining 68213 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: 2.700 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.120 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 8737 Z= 0.306 Angle : 0.734 11.933 11848 Z= 0.476 Chirality : 0.049 0.412 1363 Planarity : 0.004 0.056 1503 Dihedral : 14.074 169.051 3113 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.87 % Favored : 95.04 % Rotamer: Outliers : 0.77 % Allowed : 1.09 % Favored : 98.14 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 2.94 % 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: -0.74 (0.25), residues: 1089 helix: 0.30 (0.27), residues: 395 sheet: -0.78 (0.30), residues: 278 loop : -0.88 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 218 TYR 0.010 0.001 TYR C 105 PHE 0.029 0.002 PHE A 202 TRP 0.018 0.001 TRP C 339 HIS 0.003 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 8734) covalent geometry : angle 0.73361 (11842) SS BOND : bond 0.00493 ( 3) SS BOND : angle 1.48181 ( 6) hydrogen bonds : bond 0.16782 ( 400) hydrogen bonds : angle 5.83624 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.332 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. REVERT: B 238 PHE cc_start: 0.7600 (m-10) cc_final: 0.7388 (m-10) REVERT: C 197 ARG cc_start: 0.6720 (mmt90) cc_final: 0.6392 (mmp80) REVERT: E 180 ARG cc_start: 0.7663 (mtm110) cc_final: 0.7167 (mtt180) outliers start: 7 outliers final: 3 residues processed: 139 average time/residue: 0.1348 time to fit residues: 24.1089 Evaluate side-chains 115 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 205 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0470 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN C 88 ASN C 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.159764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115630 restraints weight = 10178.506| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.35 r_work: 0.3223 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8737 Z= 0.118 Angle : 0.528 6.612 11848 Z= 0.283 Chirality : 0.042 0.157 1363 Planarity : 0.004 0.055 1503 Dihedral : 7.214 179.972 1227 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.88 % Allowed : 6.46 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.15 (0.26), residues: 1089 helix: 0.97 (0.27), residues: 390 sheet: -0.47 (0.31), residues: 287 loop : -0.72 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 197 TYR 0.010 0.001 TYR E 60 PHE 0.014 0.001 PHE A 256 TRP 0.017 0.001 TRP C 339 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8734) covalent geometry : angle 0.52709 (11842) SS BOND : bond 0.00476 ( 3) SS BOND : angle 1.37119 ( 6) hydrogen bonds : bond 0.04235 ( 400) hydrogen bonds : angle 4.28058 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.366 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. REVERT: B 211 LYS cc_start: 0.8224 (mmtp) cc_final: 0.8015 (tppt) REVERT: C 197 ARG cc_start: 0.7232 (mmt90) cc_final: 0.6532 (mmp80) REVERT: E 17 SER cc_start: 0.8446 (m) cc_final: 0.8139 (p) REVERT: E 180 ARG cc_start: 0.7728 (mtm110) cc_final: 0.6932 (mtt180) outliers start: 8 outliers final: 4 residues processed: 129 average time/residue: 0.1325 time to fit residues: 22.1045 Evaluate side-chains 115 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 262 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.157669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.113482 restraints weight = 10154.107| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.33 r_work: 0.3183 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8737 Z= 0.139 Angle : 0.531 7.056 11848 Z= 0.283 Chirality : 0.042 0.174 1363 Planarity : 0.004 0.056 1503 Dihedral : 7.042 177.798 1223 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.42 % Allowed : 9.85 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.08 (0.26), residues: 1089 helix: 1.02 (0.27), residues: 396 sheet: -0.42 (0.30), residues: 296 loop : -0.71 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 197 TYR 0.013 0.001 TYR E 190 PHE 0.014 0.002 PHE C 199 TRP 0.017 0.001 TRP C 339 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8734) covalent geometry : angle 0.53013 (11842) SS BOND : bond 0.00466 ( 3) SS BOND : angle 1.50611 ( 6) hydrogen bonds : bond 0.04423 ( 400) hydrogen bonds : angle 4.14475 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.289 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. REVERT: B 211 LYS cc_start: 0.8184 (mmtp) cc_final: 0.7902 (tppt) REVERT: C 176 GLN cc_start: 0.8523 (mt0) cc_final: 0.8135 (mt0) REVERT: C 197 ARG cc_start: 0.7226 (mmt90) cc_final: 0.6515 (mmp80) REVERT: E 17 SER cc_start: 0.8447 (m) cc_final: 0.8107 (p) REVERT: E 180 ARG cc_start: 0.7701 (mtm110) cc_final: 0.6833 (mtt180) outliers start: 13 outliers final: 9 residues processed: 124 average time/residue: 0.1225 time to fit residues: 19.8914 Evaluate side-chains 121 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 84 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.157387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.113368 restraints weight = 10347.708| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.34 r_work: 0.3181 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8737 Z= 0.137 Angle : 0.521 6.281 11848 Z= 0.277 Chirality : 0.042 0.161 1363 Planarity : 0.004 0.056 1503 Dihedral : 6.959 174.702 1223 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.64 % Allowed : 12.04 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.13 (0.26), residues: 1089 helix: 1.40 (0.28), residues: 377 sheet: -0.35 (0.30), residues: 301 loop : -0.70 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 197 TYR 0.013 0.001 TYR E 190 PHE 0.014 0.002 PHE B 222 TRP 0.015 0.001 TRP C 339 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8734) covalent geometry : angle 0.52056 (11842) SS BOND : bond 0.00482 ( 3) SS BOND : angle 1.36902 ( 6) hydrogen bonds : bond 0.04295 ( 400) hydrogen bonds : angle 4.04607 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.319 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. REVERT: D 21 MET cc_start: 0.6953 (ttp) cc_final: 0.6176 (tmm) REVERT: E 17 SER cc_start: 0.8471 (m) cc_final: 0.8133 (p) REVERT: E 180 ARG cc_start: 0.7710 (mtm110) cc_final: 0.6956 (mtt180) outliers start: 15 outliers final: 12 residues processed: 121 average time/residue: 0.1115 time to fit residues: 17.7532 Evaluate side-chains 119 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.159429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.115288 restraints weight = 10234.461| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.34 r_work: 0.3213 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8737 Z= 0.108 Angle : 0.480 5.864 11848 Z= 0.258 Chirality : 0.041 0.145 1363 Planarity : 0.004 0.055 1503 Dihedral : 6.681 167.883 1223 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.97 % Allowed : 13.02 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.30 (0.26), residues: 1089 helix: 1.57 (0.28), residues: 377 sheet: -0.22 (0.30), residues: 303 loop : -0.67 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.011 0.001 TYR E 190 PHE 0.012 0.001 PHE C 199 TRP 0.012 0.001 TRP C 339 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8734) covalent geometry : angle 0.47983 (11842) SS BOND : bond 0.00410 ( 3) SS BOND : angle 1.14674 ( 6) hydrogen bonds : bond 0.03799 ( 400) hydrogen bonds : angle 3.86676 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.337 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 197 ARG cc_start: 0.7196 (mmt90) cc_final: 0.6474 (mmp80) REVERT: D 21 MET cc_start: 0.6988 (ttp) cc_final: 0.6196 (tmm) REVERT: E 17 SER cc_start: 0.8473 (m) cc_final: 0.8126 (p) REVERT: E 180 ARG cc_start: 0.7695 (mtm110) cc_final: 0.6906 (mtt180) outliers start: 18 outliers final: 13 residues processed: 125 average time/residue: 0.1143 time to fit residues: 18.9351 Evaluate side-chains 123 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 9 GLN Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 97 optimal weight: 0.0980 chunk 63 optimal weight: 0.8980 chunk 95 optimal weight: 0.0980 chunk 54 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.160635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121620 restraints weight = 10222.279| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.48 r_work: 0.3230 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8737 Z= 0.094 Angle : 0.461 6.318 11848 Z= 0.248 Chirality : 0.040 0.134 1363 Planarity : 0.004 0.054 1503 Dihedral : 6.301 154.046 1223 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.75 % Allowed : 13.57 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.52 (0.26), residues: 1089 helix: 1.89 (0.27), residues: 372 sheet: -0.17 (0.30), residues: 303 loop : -0.61 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 197 TYR 0.010 0.001 TYR E 190 PHE 0.012 0.001 PHE B 208 TRP 0.010 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 8734) covalent geometry : angle 0.46041 (11842) SS BOND : bond 0.00338 ( 3) SS BOND : angle 1.16047 ( 6) hydrogen bonds : bond 0.03395 ( 400) hydrogen bonds : angle 3.71499 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.337 Fit side-chains TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. REVERT: A 225 GLN cc_start: 0.7514 (mt0) cc_final: 0.7076 (pt0) REVERT: B 381 ASP cc_start: 0.7582 (p0) cc_final: 0.7378 (m-30) REVERT: D 21 MET cc_start: 0.6921 (ttp) cc_final: 0.6134 (tmm) REVERT: E 17 SER cc_start: 0.8362 (m) cc_final: 0.8041 (p) REVERT: E 180 ARG cc_start: 0.7592 (mtm110) cc_final: 0.6936 (mtt180) outliers start: 16 outliers final: 13 residues processed: 128 average time/residue: 0.1045 time to fit residues: 17.7770 Evaluate side-chains 126 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.156395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.111997 restraints weight = 10345.290| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.36 r_work: 0.3166 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8737 Z= 0.186 Angle : 0.573 7.703 11848 Z= 0.301 Chirality : 0.043 0.179 1363 Planarity : 0.004 0.056 1503 Dihedral : 6.565 151.000 1223 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.86 % Allowed : 14.77 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.18 (0.26), residues: 1089 helix: 1.48 (0.27), residues: 377 sheet: -0.39 (0.30), residues: 290 loop : -0.65 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.018 0.002 TYR E 190 PHE 0.017 0.002 PHE C 199 TRP 0.017 0.002 TRP C 339 HIS 0.005 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 8734) covalent geometry : angle 0.57184 (11842) SS BOND : bond 0.00587 ( 3) SS BOND : angle 1.51555 ( 6) hydrogen bonds : bond 0.04704 ( 400) hydrogen bonds : angle 4.06477 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.333 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. REVERT: C 197 ARG cc_start: 0.7269 (mmt90) cc_final: 0.6470 (mmp80) REVERT: D 21 MET cc_start: 0.6966 (ttp) cc_final: 0.6217 (tmm) REVERT: E 180 ARG cc_start: 0.7737 (mtm110) cc_final: 0.6894 (mtt180) outliers start: 17 outliers final: 11 residues processed: 119 average time/residue: 0.1240 time to fit residues: 19.3126 Evaluate side-chains 115 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 90 optimal weight: 0.0870 chunk 105 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.159660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115622 restraints weight = 10184.703| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.35 r_work: 0.3216 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8737 Z= 0.107 Angle : 0.486 6.537 11848 Z= 0.260 Chirality : 0.041 0.136 1363 Planarity : 0.004 0.052 1503 Dihedral : 5.950 129.653 1223 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.20 % Allowed : 15.32 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.43 (0.26), residues: 1089 helix: 1.82 (0.27), residues: 371 sheet: -0.25 (0.30), residues: 297 loop : -0.63 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.010 0.001 TYR E 190 PHE 0.011 0.001 PHE B 222 TRP 0.010 0.001 TRP C 339 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8734) covalent geometry : angle 0.48522 (11842) SS BOND : bond 0.00431 ( 3) SS BOND : angle 1.16921 ( 6) hydrogen bonds : bond 0.03698 ( 400) hydrogen bonds : angle 3.79140 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.348 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. REVERT: A 72 ARG cc_start: 0.7774 (mpt180) cc_final: 0.7554 (mpt180) REVERT: C 197 ARG cc_start: 0.7215 (mmt90) cc_final: 0.6473 (mmp80) REVERT: D 21 MET cc_start: 0.6957 (ttp) cc_final: 0.6229 (tmm) REVERT: E 17 SER cc_start: 0.8455 (m) cc_final: 0.8147 (p) REVERT: E 180 ARG cc_start: 0.7699 (mtm110) cc_final: 0.6938 (mtt180) outliers start: 11 outliers final: 11 residues processed: 119 average time/residue: 0.1100 time to fit residues: 17.2033 Evaluate side-chains 121 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 104 optimal weight: 0.0010 chunk 30 optimal weight: 0.0050 chunk 89 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.160694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116798 restraints weight = 10173.997| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.35 r_work: 0.3231 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8737 Z= 0.098 Angle : 0.479 6.646 11848 Z= 0.255 Chirality : 0.040 0.144 1363 Planarity : 0.004 0.055 1503 Dihedral : 5.457 102.341 1223 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.53 % Allowed : 14.99 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.57 (0.26), residues: 1089 helix: 1.98 (0.27), residues: 372 sheet: -0.19 (0.30), residues: 296 loop : -0.58 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.010 0.001 TYR E 190 PHE 0.011 0.001 PHE C 199 TRP 0.010 0.001 TRP C 169 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 8734) covalent geometry : angle 0.47816 (11842) SS BOND : bond 0.00374 ( 3) SS BOND : angle 1.12308 ( 6) hydrogen bonds : bond 0.03467 ( 400) hydrogen bonds : angle 3.70206 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.325 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. REVERT: A 65 ILE cc_start: 0.6017 (OUTLIER) cc_final: 0.5784 (mp) REVERT: A 225 GLN cc_start: 0.7643 (mt0) cc_final: 0.7153 (pt0) REVERT: B 381 ASP cc_start: 0.7951 (p0) cc_final: 0.7492 (m-30) REVERT: C 197 ARG cc_start: 0.7212 (mmt90) cc_final: 0.6478 (mmp80) REVERT: D 21 MET cc_start: 0.6903 (ttp) cc_final: 0.6183 (tmm) REVERT: E 17 SER cc_start: 0.8449 (m) cc_final: 0.8125 (p) REVERT: E 180 ARG cc_start: 0.7696 (mtm110) cc_final: 0.6957 (mtt180) outliers start: 14 outliers final: 10 residues processed: 119 average time/residue: 0.1145 time to fit residues: 17.7220 Evaluate side-chains 122 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.157929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.113742 restraints weight = 10244.645| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.36 r_work: 0.3183 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8737 Z= 0.143 Angle : 0.541 7.772 11848 Z= 0.284 Chirality : 0.042 0.169 1363 Planarity : 0.004 0.057 1503 Dihedral : 5.333 77.215 1223 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.31 % Allowed : 15.21 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.34 (0.26), residues: 1089 helix: 1.69 (0.27), residues: 378 sheet: -0.30 (0.30), residues: 293 loop : -0.66 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 197 TYR 0.015 0.001 TYR E 190 PHE 0.014 0.001 PHE C 199 TRP 0.015 0.001 TRP C 339 HIS 0.004 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8734) covalent geometry : angle 0.54012 (11842) SS BOND : bond 0.00500 ( 3) SS BOND : angle 1.34914 ( 6) hydrogen bonds : bond 0.04135 ( 400) hydrogen bonds : angle 3.87216 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.278 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 394 " (corrupted residue). Skipping it. REVERT: A 65 ILE cc_start: 0.6060 (OUTLIER) cc_final: 0.5793 (mp) REVERT: A 72 ARG cc_start: 0.7793 (mpt180) cc_final: 0.7585 (mpt180) REVERT: C 197 ARG cc_start: 0.7265 (mmt90) cc_final: 0.6495 (mmp80) REVERT: D 21 MET cc_start: 0.6910 (ttp) cc_final: 0.6230 (tmm) REVERT: E 17 SER cc_start: 0.8458 (m) cc_final: 0.8132 (p) REVERT: E 180 ARG cc_start: 0.7724 (mtm110) cc_final: 0.6904 (mtt180) outliers start: 12 outliers final: 10 residues processed: 115 average time/residue: 0.1028 time to fit residues: 15.5761 Evaluate side-chains 119 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 56 optimal weight: 0.0000 chunk 68 optimal weight: 0.3980 chunk 98 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.161387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.123117 restraints weight = 10136.977| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.46 r_work: 0.3227 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8737 Z= 0.095 Angle : 0.479 7.595 11848 Z= 0.254 Chirality : 0.040 0.134 1363 Planarity : 0.004 0.056 1503 Dihedral : 4.812 57.720 1223 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.42 % Allowed : 14.99 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.66 (0.26), residues: 1089 helix: 2.05 (0.27), residues: 373 sheet: -0.16 (0.30), residues: 296 loop : -0.52 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.009 0.001 TYR E 190 PHE 0.010 0.001 PHE C 199 TRP 0.010 0.001 TRP C 169 HIS 0.002 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 8734) covalent geometry : angle 0.47837 (11842) SS BOND : bond 0.00376 ( 3) SS BOND : angle 1.06692 ( 6) hydrogen bonds : bond 0.03352 ( 400) hydrogen bonds : angle 3.65626 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2572.09 seconds wall clock time: 44 minutes 40.86 seconds (2680.86 seconds total)