Starting phenix.real_space_refine on Sun Jun 8 06:58:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w40_32298/06_2025/7w40_32298.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w40_32298/06_2025/7w40_32298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w40_32298/06_2025/7w40_32298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w40_32298/06_2025/7w40_32298.map" model { file = "/net/cci-nas-00/data/ceres_data/7w40_32298/06_2025/7w40_32298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w40_32298/06_2025/7w40_32298.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 57 5.16 5 C 5882 2.51 5 N 1573 2.21 5 O 1724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9236 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2280 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 14, 'TRANS': 286} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2330 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "C" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2409 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 5, 'TRANS': 309} Chain: "D" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 365 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "H" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "E" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 81 Unusual residues: {'BAL': 1} Classifications: {'peptide': 8, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'POST-BETA-TRANS': 1, 'PRE-BETA-TRANS': 1, 'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BAL:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.79, per 1000 atoms: 0.63 Number of scatterers: 9236 At special positions: 0 Unit cell: (111.54, 112.554, 128.778, 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 57 16.00 O 1724 8.00 N 1573 7.00 C 5882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.07 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 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: 2.26 Conformation dependent library (CDL) restraints added in 1.2 seconds 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN E 1 " Input volumes are d-peptide like pdb=" CB BAL E 6 " Number of C-beta restraints generated: 2222 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 39.2% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 37 through 69 Proline residue: A 44 - end of helix removed outlier: 4.306A pdb=" N VAL A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 103 removed outlier: 3.600A pdb=" N PHE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 108 through 144 removed outlier: 4.061A pdb=" N GLY A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Proline residue: A 117 - end of helix removed outlier: 3.523A pdb=" N THR A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 173 Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 219 through 243 removed outlier: 3.549A pdb=" N TYR A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 252 through 290 removed outlier: 3.717A pdb=" N LYS A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Proline residue: A 279 - end of helix removed outlier: 3.743A pdb=" N LEU A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 326 removed outlier: 3.593A pdb=" N ASN A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Proline residue: A 319 - end of helix removed outlier: 3.847A pdb=" N LEU A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 Processing helix chain 'B' and resid 12 through 38 removed outlier: 3.822A pdb=" N ARG B 38 " --> pdb=" O GLU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 54 through 64 Processing helix chain 'B' and resid 68 through 88 removed outlier: 4.687A pdb=" N LYS B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.750A pdb=" N GLU B 150 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 246 through 260 Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 275 through 286 removed outlier: 4.434A pdb=" N MET B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 removed outlier: 4.171A pdb=" N TYR B 291 " --> pdb=" O HIS B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 315 Processing helix chain 'B' and resid 335 through 356 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.509A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 197 removed outlier: 8.867A pdb=" N VAL A 294 " --> pdb=" O PRO A 183 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N HIS A 185 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 196 removed outlier: 6.347A pdb=" N LEU B 40 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL B 204 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 42 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER B 225 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE B 226 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE B 272 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE B 228 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ASN B 274 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 230 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.739A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.697A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.072A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.660A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.895A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.286A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.595A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.730A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.327A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'H' and resid 147 through 148 removed outlier: 3.616A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2015 1.33 - 1.45: 2197 1.45 - 1.57: 5142 1.57 - 1.69: 0 1.69 - 1.82: 86 Bond restraints: 9440 Sorted by residual: bond pdb=" CG TRP E 3 " pdb=" CD2 TRP E 3 " ideal model delta sigma weight residual 1.433 1.333 0.100 1.80e-02 3.09e+03 3.07e+01 bond pdb=" CB PHE E 8 " pdb=" CG PHE E 8 " ideal model delta sigma weight residual 1.502 1.385 0.117 2.30e-02 1.89e+03 2.57e+01 bond pdb=" CG HIS E 7 " pdb=" ND1 HIS E 7 " ideal model delta sigma weight residual 1.378 1.324 0.054 1.10e-02 8.26e+03 2.37e+01 bond pdb=" CB DPN E 1 " pdb=" CG DPN E 1 " ideal model delta sigma weight residual 1.502 1.391 0.111 2.30e-02 1.89e+03 2.34e+01 bond pdb=" C VAL A 266 " pdb=" O VAL A 266 " ideal model delta sigma weight residual 1.237 1.292 -0.055 1.17e-02 7.31e+03 2.19e+01 ... (remaining 9435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 10547 1.64 - 3.28: 1904 3.28 - 4.92: 296 4.92 - 6.56: 40 6.56 - 8.20: 12 Bond angle restraints: 12799 Sorted by residual: angle pdb=" N ASP C 247 " pdb=" CA ASP C 247 " pdb=" C ASP C 247 " ideal model delta sigma weight residual 110.35 102.15 8.20 1.36e+00 5.41e-01 3.64e+01 angle pdb=" N ALA A 176 " pdb=" CA ALA A 176 " pdb=" C ALA A 176 " ideal model delta sigma weight residual 113.97 106.80 7.17 1.28e+00 6.10e-01 3.14e+01 angle pdb=" CA GLY H 114 " pdb=" C GLY H 114 " pdb=" O GLY H 114 " ideal model delta sigma weight residual 121.88 117.85 4.03 7.80e-01 1.64e+00 2.67e+01 angle pdb=" N LEU A 205 " pdb=" CA LEU A 205 " pdb=" C LEU A 205 " ideal model delta sigma weight residual 113.55 107.06 6.49 1.26e+00 6.30e-01 2.66e+01 angle pdb=" N ARG C 48 " pdb=" CA ARG C 48 " pdb=" C ARG C 48 " ideal model delta sigma weight residual 113.23 106.84 6.39 1.24e+00 6.50e-01 2.65e+01 ... (remaining 12794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 5102 16.73 - 33.46: 405 33.46 - 50.20: 78 50.20 - 66.93: 15 66.93 - 83.66: 2 Dihedral angle restraints: 5602 sinusoidal: 2154 harmonic: 3448 Sorted by residual: dihedral pdb=" C TYR H 235 " pdb=" N TYR H 235 " pdb=" CA TYR H 235 " pdb=" CB TYR H 235 " ideal model delta harmonic sigma weight residual -122.60 -140.20 17.60 0 2.50e+00 1.60e-01 4.96e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 36.36 56.64 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" N TYR H 235 " pdb=" C TYR H 235 " pdb=" CA TYR H 235 " pdb=" CB TYR H 235 " ideal model delta harmonic sigma weight residual 122.80 139.06 -16.26 0 2.50e+00 1.60e-01 4.23e+01 ... (remaining 5599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 1285 0.135 - 0.270: 145 0.270 - 0.405: 8 0.405 - 0.540: 0 0.540 - 0.675: 1 Chirality restraints: 1439 Sorted by residual: chirality pdb=" CA TYR H 235 " pdb=" N TYR H 235 " pdb=" C TYR H 235 " pdb=" CB TYR H 235 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CA LEU C 79 " pdb=" N LEU C 79 " pdb=" C LEU C 79 " pdb=" CB LEU C 79 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA LEU H 4 " pdb=" N LEU H 4 " pdb=" C LEU H 4 " pdb=" CB LEU H 4 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 1436 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 175 " 0.016 2.00e-02 2.50e+03 2.45e-02 1.20e+01 pdb=" CG TYR H 175 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR H 175 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR H 175 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR H 175 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR H 175 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR H 175 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 175 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 127 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C LYS C 127 " -0.055 2.00e-02 2.50e+03 pdb=" O LYS C 127 " 0.021 2.00e-02 2.50e+03 pdb=" N THR C 128 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 315 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C VAL C 315 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL C 315 " -0.019 2.00e-02 2.50e+03 pdb=" N SER C 316 " -0.017 2.00e-02 2.50e+03 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1996 2.79 - 3.32: 8658 3.32 - 3.85: 14852 3.85 - 4.37: 18476 4.37 - 4.90: 31094 Nonbonded interactions: 75076 Sorted by model distance: nonbonded pdb=" O ASP C 333 " pdb=" OG SER C 334 " model vdw 2.266 3.040 nonbonded pdb=" OD1 ASP C 205 " pdb=" OG SER C 207 " model vdw 2.290 3.040 nonbonded pdb=" NE ARG C 283 " pdb=" OD1 ASP C 298 " model vdw 2.309 3.120 nonbonded pdb=" O SER C 67 " pdb=" OG SER C 67 " model vdw 2.322 3.040 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.341 3.040 ... (remaining 75071 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: 1.110 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.670 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 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 : 0.011 0.117 9443 Z= 0.716 Angle : 1.290 8.202 12805 Z= 0.929 Chirality : 0.085 0.675 1439 Planarity : 0.006 0.053 1630 Dihedral : 12.467 83.658 3371 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.58 % Favored : 97.25 % Rotamer: Outliers : 1.92 % Allowed : 3.84 % Favored : 94.24 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.23), residues: 1162 helix: 0.42 (0.25), residues: 411 sheet: 0.10 (0.31), residues: 286 loop : -1.08 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 82 HIS 0.009 0.002 HIS C 311 PHE 0.030 0.003 PHE C 199 TYR 0.056 0.003 TYR H 175 ARG 0.011 0.001 ARG A 259 Details of bonding type rmsd hydrogen bonds : bond 0.17159 ( 449) hydrogen bonds : angle 6.82059 ( 1272) SS BOND : bond 0.02111 ( 3) SS BOND : angle 3.05823 ( 6) covalent geometry : bond 0.01062 ( 9440) covalent geometry : angle 1.28847 (12799) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 SER cc_start: 0.5579 (t) cc_final: 0.5323 (m) REVERT: B 26 ASP cc_start: 0.7878 (m-30) cc_final: 0.7571 (m-30) REVERT: B 60 ARG cc_start: 0.6721 (ttp80) cc_final: 0.6093 (mmm160) REVERT: B 83 ILE cc_start: 0.6982 (mp) cc_final: 0.6749 (mp) REVERT: B 259 ILE cc_start: 0.7714 (pt) cc_final: 0.7487 (pt) REVERT: B 322 LYS cc_start: 0.7322 (mtpp) cc_final: 0.6755 (tptt) REVERT: B 332 THR cc_start: 0.7611 (t) cc_final: 0.7183 (m) REVERT: B 348 ILE cc_start: 0.6745 (mm) cc_final: 0.6509 (mt) outliers start: 19 outliers final: 3 residues processed: 246 average time/residue: 1.1825 time to fit residues: 310.5823 Evaluate side-chains 146 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 296 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 0.0020 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 HIS C 75 GLN H 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.212856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.174136 restraints weight = 9557.112| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.11 r_work: 0.4006 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3865 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9443 Z= 0.143 Angle : 0.640 9.305 12805 Z= 0.335 Chirality : 0.043 0.294 1439 Planarity : 0.004 0.049 1630 Dihedral : 5.378 46.068 1303 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.15 % Allowed : 13.85 % Favored : 82.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.24), residues: 1162 helix: 1.76 (0.24), residues: 418 sheet: 0.46 (0.30), residues: 289 loop : -0.95 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 82 HIS 0.004 0.001 HIS C 91 PHE 0.015 0.002 PHE B 201 TYR 0.051 0.002 TYR H 235 ARG 0.007 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.04986 ( 449) hydrogen bonds : angle 4.72022 ( 1272) SS BOND : bond 0.00430 ( 3) SS BOND : angle 1.38632 ( 6) covalent geometry : bond 0.00306 ( 9440) covalent geometry : angle 0.63970 (12799) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.7744 (mptt) cc_final: 0.7209 (mttp) REVERT: B 60 ARG cc_start: 0.7034 (ttp80) cc_final: 0.5538 (mmp-170) REVERT: B 202 ARG cc_start: 0.7061 (mtp85) cc_final: 0.6426 (ptm160) REVERT: B 303 GLN cc_start: 0.6637 (tp40) cc_final: 0.6216 (tp40) REVERT: C 76 ASP cc_start: 0.7031 (p0) cc_final: 0.5888 (t0) REVERT: C 129 ARG cc_start: 0.7114 (mtt180) cc_final: 0.6756 (ttt90) REVERT: C 188 MET cc_start: 0.7147 (mmm) cc_final: 0.6913 (mmp) REVERT: C 197 ARG cc_start: 0.6879 (mtp85) cc_final: 0.6445 (mmp80) REVERT: H 244 LYS cc_start: 0.8080 (tttt) cc_final: 0.7839 (ttpp) outliers start: 41 outliers final: 17 residues processed: 177 average time/residue: 1.4440 time to fit residues: 271.0872 Evaluate side-chains 138 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 0.0370 chunk 87 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN H 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.211017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.172200 restraints weight = 9688.891| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 2.02 r_work: 0.3985 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9443 Z= 0.128 Angle : 0.597 8.270 12805 Z= 0.313 Chirality : 0.042 0.259 1439 Planarity : 0.004 0.047 1630 Dihedral : 5.695 86.193 1303 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.45 % Allowed : 16.38 % Favored : 79.17 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.24), residues: 1162 helix: 2.25 (0.25), residues: 413 sheet: 0.45 (0.30), residues: 280 loop : -0.87 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.002 PHE B 201 TYR 0.029 0.001 TYR H 235 ARG 0.008 0.000 ARG C 314 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 449) hydrogen bonds : angle 4.46162 ( 1272) SS BOND : bond 0.00464 ( 3) SS BOND : angle 2.92708 ( 6) covalent geometry : bond 0.00279 ( 9440) covalent geometry : angle 0.59382 (12799) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 216 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6915 (tt) REVERT: A 286 TYR cc_start: 0.6510 (OUTLIER) cc_final: 0.6274 (t80) REVERT: B 38 ARG cc_start: 0.7276 (mtp-110) cc_final: 0.7033 (mtp85) REVERT: B 60 ARG cc_start: 0.7094 (ttp80) cc_final: 0.5664 (mmp-170) REVERT: B 202 ARG cc_start: 0.7074 (mtp85) cc_final: 0.6504 (ptm160) REVERT: B 280 GLU cc_start: 0.7919 (tp30) cc_final: 0.7425 (tm-30) REVERT: B 322 LYS cc_start: 0.7578 (mtpt) cc_final: 0.7125 (mtpp) REVERT: C 52 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7532 (mtp85) REVERT: C 76 ASP cc_start: 0.7219 (p0) cc_final: 0.6724 (p0) REVERT: C 129 ARG cc_start: 0.7134 (mtt180) cc_final: 0.6826 (ttt90) REVERT: C 188 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6935 (mmp) REVERT: C 197 ARG cc_start: 0.6934 (mtp85) cc_final: 0.6500 (mmp80) REVERT: C 269 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6600 (mm) REVERT: H 6 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6110 (pm20) REVERT: H 192 MET cc_start: 0.7118 (ttp) cc_final: 0.6768 (ttp) REVERT: H 235 TYR cc_start: 0.4382 (OUTLIER) cc_final: 0.3976 (t80) REVERT: H 244 LYS cc_start: 0.8047 (tttt) cc_final: 0.7819 (ttpp) outliers start: 44 outliers final: 21 residues processed: 159 average time/residue: 1.3449 time to fit residues: 226.9334 Evaluate side-chains 144 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 286 TYR Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 76 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 99 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN C 110 ASN C 142 HIS H 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.209477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.173286 restraints weight = 9505.630| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 1.73 r_work: 0.3968 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9443 Z= 0.138 Angle : 0.598 7.711 12805 Z= 0.310 Chirality : 0.043 0.248 1439 Planarity : 0.004 0.045 1630 Dihedral : 5.372 68.086 1301 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.36 % Allowed : 17.19 % Favored : 77.45 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.24), residues: 1162 helix: 2.17 (0.25), residues: 420 sheet: 0.53 (0.31), residues: 275 loop : -0.77 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.004 0.001 HIS B 218 PHE 0.014 0.002 PHE C 253 TYR 0.027 0.002 TYR H 235 ARG 0.006 0.000 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.04555 ( 449) hydrogen bonds : angle 4.35657 ( 1272) SS BOND : bond 0.00496 ( 3) SS BOND : angle 2.02230 ( 6) covalent geometry : bond 0.00312 ( 9440) covalent geometry : angle 0.59625 (12799) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 133 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.7823 (tptt) cc_final: 0.7567 (tptm) REVERT: B 38 ARG cc_start: 0.7267 (mtp-110) cc_final: 0.7039 (mtp85) REVERT: B 60 ARG cc_start: 0.7159 (ttp80) cc_final: 0.5614 (mmp-170) REVERT: B 202 ARG cc_start: 0.7021 (mtp85) cc_final: 0.6513 (ptm160) REVERT: B 280 GLU cc_start: 0.7927 (tp30) cc_final: 0.7412 (tm-30) REVERT: B 322 LYS cc_start: 0.7641 (mtpt) cc_final: 0.7208 (mtpp) REVERT: B 335 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6729 (tp30) REVERT: C 52 ARG cc_start: 0.7813 (mtt90) cc_final: 0.7581 (mtp85) REVERT: C 76 ASP cc_start: 0.7301 (p0) cc_final: 0.6882 (p0) REVERT: C 129 ARG cc_start: 0.7288 (mtt180) cc_final: 0.7002 (ttt90) REVERT: C 188 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6976 (mmp) REVERT: C 197 ARG cc_start: 0.6952 (mtp85) cc_final: 0.6618 (mmp80) REVERT: C 269 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6613 (mm) REVERT: H 235 TYR cc_start: 0.4607 (OUTLIER) cc_final: 0.4165 (t80) REVERT: H 244 LYS cc_start: 0.8206 (tttt) cc_final: 0.7983 (ttpp) outliers start: 53 outliers final: 26 residues processed: 167 average time/residue: 1.2880 time to fit residues: 228.8043 Evaluate side-chains 149 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 65 optimal weight: 0.0370 chunk 34 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 GLN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.209081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.169585 restraints weight = 9609.629| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.22 r_work: 0.3953 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9443 Z= 0.123 Angle : 0.579 7.924 12805 Z= 0.299 Chirality : 0.042 0.232 1439 Planarity : 0.004 0.044 1630 Dihedral : 5.096 55.280 1300 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.55 % Allowed : 18.81 % Favored : 76.64 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1162 helix: 2.27 (0.25), residues: 419 sheet: 0.65 (0.31), residues: 274 loop : -0.76 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS C 183 PHE 0.013 0.001 PHE C 199 TYR 0.025 0.001 TYR B 285 ARG 0.006 0.000 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 449) hydrogen bonds : angle 4.19425 ( 1272) SS BOND : bond 0.00442 ( 3) SS BOND : angle 1.64197 ( 6) covalent geometry : bond 0.00275 ( 9440) covalent geometry : angle 0.57847 (12799) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.7804 (tptt) cc_final: 0.7559 (tptm) REVERT: A 155 MET cc_start: 0.5858 (ttp) cc_final: 0.5583 (ttm) REVERT: A 298 MET cc_start: 0.6103 (tpp) cc_final: 0.5796 (tpt) REVERT: B 60 ARG cc_start: 0.7021 (ttp80) cc_final: 0.5619 (mmp-170) REVERT: B 202 ARG cc_start: 0.7018 (mtp85) cc_final: 0.6548 (ptm160) REVERT: B 261 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.6470 (m-80) REVERT: B 280 GLU cc_start: 0.7914 (tp30) cc_final: 0.7242 (tm-30) REVERT: B 281 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6212 (mp0) REVERT: B 335 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6679 (tp30) REVERT: C 52 ARG cc_start: 0.7891 (mtt90) cc_final: 0.7619 (mtp85) REVERT: C 76 ASP cc_start: 0.7157 (p0) cc_final: 0.6794 (p0) REVERT: C 101 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7443 (mtp) REVERT: C 129 ARG cc_start: 0.7359 (mtt180) cc_final: 0.7097 (ttt90) REVERT: C 188 MET cc_start: 0.7215 (mmm) cc_final: 0.6937 (mmp) REVERT: H 67 ARG cc_start: 0.4824 (ptt180) cc_final: 0.4595 (ptt90) REVERT: H 186 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7572 (pp30) REVERT: H 192 MET cc_start: 0.7460 (ttp) cc_final: 0.7238 (ttp) REVERT: H 235 TYR cc_start: 0.4670 (OUTLIER) cc_final: 0.4271 (t80) REVERT: H 244 LYS cc_start: 0.8197 (tttt) cc_final: 0.7974 (ttpp) outliers start: 45 outliers final: 27 residues processed: 159 average time/residue: 1.3875 time to fit residues: 233.7365 Evaluate side-chains 147 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 0.0070 chunk 63 optimal weight: 0.0010 chunk 5 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN ** B 357 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 = 0.4514 r_free = 0.4514 target = 0.210245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.170253 restraints weight = 9465.033| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.24 r_work: 0.3977 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3834 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9443 Z= 0.112 Angle : 0.565 8.360 12805 Z= 0.291 Chirality : 0.041 0.222 1439 Planarity : 0.004 0.057 1630 Dihedral : 4.923 54.004 1300 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.45 % Allowed : 19.92 % Favored : 75.63 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.25), residues: 1162 helix: 2.45 (0.25), residues: 413 sheet: 0.66 (0.31), residues: 277 loop : -0.75 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS C 183 PHE 0.014 0.001 PHE C 199 TYR 0.022 0.001 TYR H 235 ARG 0.010 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 449) hydrogen bonds : angle 4.13498 ( 1272) SS BOND : bond 0.00410 ( 3) SS BOND : angle 1.49751 ( 6) covalent geometry : bond 0.00244 ( 9440) covalent geometry : angle 0.56385 (12799) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.7789 (tptt) cc_final: 0.7513 (tptm) REVERT: A 155 MET cc_start: 0.5895 (ttp) cc_final: 0.5610 (ttm) REVERT: A 298 MET cc_start: 0.5929 (tpp) cc_final: 0.5660 (tpt) REVERT: B 38 ARG cc_start: 0.7136 (mtp-110) cc_final: 0.6879 (mtp85) REVERT: B 60 ARG cc_start: 0.7042 (ttp80) cc_final: 0.5665 (mmp-170) REVERT: B 147 ARG cc_start: 0.7497 (ttm-80) cc_final: 0.7075 (pmt170) REVERT: B 202 ARG cc_start: 0.6981 (mtp85) cc_final: 0.6523 (ptm160) REVERT: B 280 GLU cc_start: 0.7881 (tp30) cc_final: 0.7221 (tm-30) REVERT: B 281 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6172 (mp0) REVERT: B 335 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6669 (tp30) REVERT: C 52 ARG cc_start: 0.7867 (mtt90) cc_final: 0.7606 (mtp85) REVERT: C 101 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7442 (mtp) REVERT: C 129 ARG cc_start: 0.7414 (mtt180) cc_final: 0.7155 (ttt90) REVERT: C 188 MET cc_start: 0.7155 (mmm) cc_final: 0.6866 (mmp) REVERT: C 234 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.6878 (m-80) REVERT: C 290 ASP cc_start: 0.6507 (OUTLIER) cc_final: 0.6200 (m-30) REVERT: D 52 THR cc_start: 0.6070 (t) cc_final: 0.5755 (m) REVERT: H 192 MET cc_start: 0.7517 (ttp) cc_final: 0.7252 (ttp) REVERT: H 235 TYR cc_start: 0.4572 (OUTLIER) cc_final: 0.4186 (t80) outliers start: 44 outliers final: 23 residues processed: 159 average time/residue: 1.5729 time to fit residues: 266.4610 Evaluate side-chains 148 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 1 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 0.0030 chunk 108 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN B 357 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.209737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.170688 restraints weight = 9565.601| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 1.87 r_work: 0.3985 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3851 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9443 Z= 0.116 Angle : 0.569 8.272 12805 Z= 0.293 Chirality : 0.041 0.222 1439 Planarity : 0.004 0.042 1630 Dihedral : 4.802 53.901 1300 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.94 % Allowed : 20.63 % Favored : 75.43 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1162 helix: 2.41 (0.25), residues: 413 sheet: 0.73 (0.31), residues: 277 loop : -0.74 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS C 183 PHE 0.017 0.001 PHE A 329 TYR 0.025 0.001 TYR B 285 ARG 0.007 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 449) hydrogen bonds : angle 4.11468 ( 1272) SS BOND : bond 0.00422 ( 3) SS BOND : angle 1.51138 ( 6) covalent geometry : bond 0.00258 ( 9440) covalent geometry : angle 0.56797 (12799) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.7789 (tptt) cc_final: 0.7496 (tptm) REVERT: A 155 MET cc_start: 0.5866 (ttp) cc_final: 0.5598 (ttm) REVERT: A 298 MET cc_start: 0.5953 (tpp) cc_final: 0.5719 (tpt) REVERT: B 38 ARG cc_start: 0.7217 (mtp-110) cc_final: 0.6914 (mtp85) REVERT: B 60 ARG cc_start: 0.7088 (ttp80) cc_final: 0.5754 (mmp-170) REVERT: B 147 ARG cc_start: 0.7447 (ttm-80) cc_final: 0.7128 (pmt170) REVERT: B 202 ARG cc_start: 0.6937 (mtp85) cc_final: 0.6531 (ptm160) REVERT: B 261 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.7402 (m-10) REVERT: B 280 GLU cc_start: 0.7868 (tp30) cc_final: 0.7298 (tm-30) REVERT: B 281 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6271 (mp0) REVERT: B 335 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6691 (tp30) REVERT: C 52 ARG cc_start: 0.7867 (mtt90) cc_final: 0.7609 (mtp85) REVERT: C 101 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7368 (mtp) REVERT: C 188 MET cc_start: 0.7147 (mmm) cc_final: 0.6879 (mmp) REVERT: C 197 ARG cc_start: 0.7612 (ttt90) cc_final: 0.7373 (tpp-160) REVERT: C 234 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.6902 (m-80) REVERT: D 52 THR cc_start: 0.6191 (t) cc_final: 0.5906 (m) REVERT: H 235 TYR cc_start: 0.4486 (OUTLIER) cc_final: 0.4120 (t80) REVERT: H 244 LYS cc_start: 0.8403 (ttpp) cc_final: 0.7861 (ttpp) outliers start: 39 outliers final: 25 residues processed: 155 average time/residue: 1.2490 time to fit residues: 206.5264 Evaluate side-chains 147 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 99 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 0.0770 chunk 107 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 45 optimal weight: 0.0370 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN B 336 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.210738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.171686 restraints weight = 9772.317| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.25 r_work: 0.3970 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3824 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9443 Z= 0.112 Angle : 0.573 10.100 12805 Z= 0.292 Chirality : 0.041 0.215 1439 Planarity : 0.004 0.042 1630 Dihedral : 4.590 53.530 1298 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.04 % Allowed : 20.63 % Favored : 75.33 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1162 helix: 2.43 (0.25), residues: 413 sheet: 0.79 (0.31), residues: 277 loop : -0.80 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS A 206 PHE 0.012 0.001 PHE C 199 TYR 0.022 0.001 TYR H 235 ARG 0.006 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 449) hydrogen bonds : angle 4.07756 ( 1272) SS BOND : bond 0.00392 ( 3) SS BOND : angle 1.40178 ( 6) covalent geometry : bond 0.00247 ( 9440) covalent geometry : angle 0.57197 (12799) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 1.510 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.7789 (tptt) cc_final: 0.7509 (tptm) REVERT: A 155 MET cc_start: 0.5975 (ttp) cc_final: 0.5688 (ttm) REVERT: B 60 ARG cc_start: 0.7046 (ttp80) cc_final: 0.5651 (mmp-170) REVERT: B 147 ARG cc_start: 0.7489 (ttm-80) cc_final: 0.7053 (pmt170) REVERT: B 202 ARG cc_start: 0.6957 (mtp85) cc_final: 0.6517 (ptm160) REVERT: B 280 GLU cc_start: 0.7878 (tp30) cc_final: 0.7156 (tm-30) REVERT: B 281 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6128 (mp0) REVERT: B 335 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6616 (tp30) REVERT: C 52 ARG cc_start: 0.7904 (mtt90) cc_final: 0.7619 (mtp85) REVERT: C 101 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7408 (mtp) REVERT: C 175 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7806 (mm-40) REVERT: C 188 MET cc_start: 0.7106 (mmm) cc_final: 0.6855 (mmp) REVERT: C 197 ARG cc_start: 0.7685 (ttt90) cc_final: 0.7417 (tpp-160) REVERT: C 234 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.6921 (m-80) REVERT: C 290 ASP cc_start: 0.6775 (OUTLIER) cc_final: 0.6383 (m-30) REVERT: D 52 THR cc_start: 0.6076 (t) cc_final: 0.5841 (m) REVERT: H 67 ARG cc_start: 0.5065 (ptt90) cc_final: 0.4684 (ptt90) REVERT: H 192 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7177 (ttp) REVERT: H 235 TYR cc_start: 0.4542 (OUTLIER) cc_final: 0.4143 (t80) REVERT: H 244 LYS cc_start: 0.8264 (ttpp) cc_final: 0.7791 (ttpp) outliers start: 40 outliers final: 26 residues processed: 158 average time/residue: 1.4573 time to fit residues: 245.4058 Evaluate side-chains 152 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 56 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 82 optimal weight: 0.0970 chunk 59 optimal weight: 0.0980 chunk 114 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.209824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.173236 restraints weight = 9595.784| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 1.71 r_work: 0.4012 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9443 Z= 0.119 Angle : 0.578 8.761 12805 Z= 0.299 Chirality : 0.042 0.219 1439 Planarity : 0.004 0.061 1630 Dihedral : 4.625 53.525 1298 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.74 % Allowed : 21.74 % Favored : 74.52 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1162 helix: 2.38 (0.25), residues: 413 sheet: 0.86 (0.32), residues: 275 loop : -0.79 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS C 183 PHE 0.035 0.001 PHE A 329 TYR 0.028 0.001 TYR B 285 ARG 0.013 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 449) hydrogen bonds : angle 4.10701 ( 1272) SS BOND : bond 0.00434 ( 3) SS BOND : angle 1.44354 ( 6) covalent geometry : bond 0.00265 ( 9440) covalent geometry : angle 0.57777 (12799) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.7783 (tptt) cc_final: 0.7467 (tptm) REVERT: A 155 MET cc_start: 0.5956 (ttp) cc_final: 0.5685 (ttm) REVERT: A 298 MET cc_start: 0.5110 (mmp) cc_final: 0.4674 (tpt) REVERT: B 38 ARG cc_start: 0.7077 (mtp-110) cc_final: 0.6762 (mtp85) REVERT: B 39 GLU cc_start: 0.6455 (tp30) cc_final: 0.6142 (tp30) REVERT: B 60 ARG cc_start: 0.7093 (ttp80) cc_final: 0.5786 (mmp-170) REVERT: B 147 ARG cc_start: 0.7473 (ttm-80) cc_final: 0.7182 (pmt170) REVERT: B 160 TYR cc_start: 0.5958 (m-10) cc_final: 0.5225 (m-10) REVERT: B 202 ARG cc_start: 0.7021 (mtp85) cc_final: 0.6555 (ptm160) REVERT: B 280 GLU cc_start: 0.7988 (tp30) cc_final: 0.7460 (tm-30) REVERT: B 281 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6258 (mp0) REVERT: B 335 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6592 (tp30) REVERT: C 52 ARG cc_start: 0.7805 (mtt90) cc_final: 0.7539 (mtp85) REVERT: C 101 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7261 (mtp) REVERT: C 175 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7864 (mm-40) REVERT: C 197 ARG cc_start: 0.7672 (ttt90) cc_final: 0.7425 (tpp-160) REVERT: C 234 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.6890 (m-80) REVERT: C 290 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6425 (m-30) REVERT: D 38 MET cc_start: 0.5413 (ttt) cc_final: 0.5139 (tmt) REVERT: D 52 THR cc_start: 0.6225 (t) cc_final: 0.5963 (m) REVERT: H 67 ARG cc_start: 0.5082 (ptt90) cc_final: 0.4703 (ptt90) REVERT: H 192 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7078 (ttp) REVERT: H 235 TYR cc_start: 0.4456 (OUTLIER) cc_final: 0.4071 (t80) REVERT: H 244 LYS cc_start: 0.8368 (ttpp) cc_final: 0.8143 (ttpp) outliers start: 37 outliers final: 26 residues processed: 145 average time/residue: 1.2859 time to fit residues: 198.7742 Evaluate side-chains 149 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 8 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 0.0020 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.209625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.173148 restraints weight = 9692.961| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 1.72 r_work: 0.4006 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9443 Z= 0.122 Angle : 0.602 11.327 12805 Z= 0.305 Chirality : 0.042 0.220 1439 Planarity : 0.004 0.060 1630 Dihedral : 4.617 53.412 1298 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.64 % Allowed : 21.54 % Favored : 74.82 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1162 helix: 2.33 (0.25), residues: 413 sheet: 0.91 (0.32), residues: 273 loop : -0.76 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 332 HIS 0.004 0.001 HIS C 183 PHE 0.014 0.001 PHE A 329 TYR 0.022 0.001 TYR H 235 ARG 0.012 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 449) hydrogen bonds : angle 4.13020 ( 1272) SS BOND : bond 0.00435 ( 3) SS BOND : angle 1.44997 ( 6) covalent geometry : bond 0.00275 ( 9440) covalent geometry : angle 0.60114 (12799) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 116 ILE cc_start: 0.5412 (OUTLIER) cc_final: 0.5036 (tt) REVERT: A 140 LYS cc_start: 0.7780 (tptt) cc_final: 0.7460 (tptm) REVERT: A 155 MET cc_start: 0.5832 (ttp) cc_final: 0.5558 (ttm) REVERT: A 287 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.5926 (mtp180) REVERT: A 298 MET cc_start: 0.5108 (mmp) cc_final: 0.4680 (tpt) REVERT: B 38 ARG cc_start: 0.7128 (mtp-110) cc_final: 0.6799 (mtp85) REVERT: B 39 GLU cc_start: 0.6403 (tp30) cc_final: 0.6144 (tp30) REVERT: B 60 ARG cc_start: 0.7137 (ttp80) cc_final: 0.5806 (mmp-170) REVERT: B 147 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.7023 (pmt170) REVERT: B 160 TYR cc_start: 0.5810 (m-10) cc_final: 0.5123 (m-10) REVERT: B 202 ARG cc_start: 0.7113 (mtp85) cc_final: 0.6585 (ptm160) REVERT: B 280 GLU cc_start: 0.8014 (tp30) cc_final: 0.7536 (tm-30) REVERT: B 281 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6274 (mp0) REVERT: B 335 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6582 (tp30) REVERT: C 52 ARG cc_start: 0.7779 (mtt90) cc_final: 0.7544 (mtp85) REVERT: C 101 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7312 (mtp) REVERT: C 175 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7904 (mm-40) REVERT: C 188 MET cc_start: 0.7143 (mmm) cc_final: 0.6875 (mmp) REVERT: C 197 ARG cc_start: 0.7677 (ttt90) cc_final: 0.7425 (tpp-160) REVERT: C 234 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.6878 (m-80) REVERT: C 290 ASP cc_start: 0.6746 (OUTLIER) cc_final: 0.6404 (m-30) REVERT: D 38 MET cc_start: 0.5456 (ttt) cc_final: 0.5221 (tmt) REVERT: D 52 THR cc_start: 0.6159 (t) cc_final: 0.5907 (m) REVERT: H 67 ARG cc_start: 0.5116 (ptt90) cc_final: 0.4721 (ptt90) REVERT: H 192 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7121 (ttp) REVERT: H 235 TYR cc_start: 0.4434 (OUTLIER) cc_final: 0.4055 (t80) REVERT: H 244 LYS cc_start: 0.8341 (ttpp) cc_final: 0.7855 (ttpp) outliers start: 36 outliers final: 23 residues processed: 141 average time/residue: 1.5507 time to fit residues: 231.4619 Evaluate side-chains 148 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 22 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN B 336 ASN C 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.208210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.166271 restraints weight = 9535.930| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.01 r_work: 0.3927 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9443 Z= 0.142 Angle : 0.614 9.059 12805 Z= 0.316 Chirality : 0.043 0.233 1439 Planarity : 0.005 0.059 1630 Dihedral : 4.760 53.650 1298 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.84 % Allowed : 21.74 % Favored : 74.42 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1162 helix: 2.27 (0.25), residues: 412 sheet: 0.74 (0.32), residues: 278 loop : -0.74 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 332 HIS 0.004 0.001 HIS C 183 PHE 0.023 0.002 PHE A 329 TYR 0.024 0.002 TYR B 285 ARG 0.011 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 449) hydrogen bonds : angle 4.23703 ( 1272) SS BOND : bond 0.00456 ( 3) SS BOND : angle 1.55434 ( 6) covalent geometry : bond 0.00325 ( 9440) covalent geometry : angle 0.61340 (12799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12983.14 seconds wall clock time: 224 minutes 32.38 seconds (13472.38 seconds total)