Starting phenix.real_space_refine on Thu Jul 2 15:11:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vat_64904/07_2026/9vat_64904.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vat_64904/07_2026/9vat_64904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vat_64904/07_2026/9vat_64904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vat_64904/07_2026/9vat_64904.map" model { file = "/net/cci-nas-00/data/ceres_data/9vat_64904/07_2026/9vat_64904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vat_64904/07_2026/9vat_64904.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 59 5.16 5 C 5703 2.51 5 N 1529 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8960 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2427 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1739 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1743 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 1.70, per 1000 atoms: 0.19 Number of scatterers: 8960 At special positions: 0 Unit cell: (107.06, 119.78, 118.72, 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 59 16.00 O 1669 8.00 N 1529 7.00 C 5703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.02 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.10 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 354.8 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2162 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 15 sheets defined 40.7% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'R' and resid 51 through 55 Processing helix chain 'R' and resid 59 through 91 Processing helix chain 'R' and resid 95 through 127 removed outlier: 3.976A pdb=" N MET R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) Proline residue: R 121 - end of helix removed outlier: 3.712A pdb=" N LEU R 124 " --> pdb=" O MET R 120 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR R 125 " --> pdb=" O PRO R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 172 removed outlier: 4.017A pdb=" N GLY R 140 " --> pdb=" O PHE R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 180 Processing helix chain 'R' and resid 181 through 206 removed outlier: 3.772A pdb=" N THR R 185 " --> pdb=" O SER R 181 " (cutoff:3.500A) Proline residue: R 202 - end of helix Processing helix chain 'R' and resid 218 through 220 No H-bonds generated for 'chain 'R' and resid 218 through 220' Processing helix chain 'R' and resid 232 through 245 removed outlier: 3.549A pdb=" N VAL R 236 " --> pdb=" O THR R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 272 Processing helix chain 'R' and resid 292 through 329 removed outlier: 3.596A pdb=" N VAL R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 365 removed outlier: 3.569A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 370 through 374 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.594A pdb=" N SER A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 202 through 205 Processing helix chain 'A' and resid 210 through 217 removed outlier: 4.298A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.797A pdb=" N ASP A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 257 Processing helix chain 'A' and resid 258 through 261 removed outlier: 3.875A pdb=" N ILE A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 258 through 261' Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.062A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 56 removed outlier: 4.213A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.669A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 207 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.621A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.621A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.821A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.642A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.790A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.425A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.625A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.535A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.599A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.889A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'D' and resid 143 through 146 Processing sheet with id=AB6, first strand: chain 'D' and resid 182 through 183 removed outlier: 6.674A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1508 1.32 - 1.45: 2669 1.45 - 1.58: 4888 1.58 - 1.71: 0 1.71 - 1.84: 86 Bond restraints: 9151 Sorted by residual: bond pdb=" C VAL B 327 " pdb=" O VAL B 327 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.09e-02 8.42e+03 2.09e+01 bond pdb=" CA ALA B 240 " pdb=" CB ALA B 240 " ideal model delta sigma weight residual 1.532 1.463 0.069 1.68e-02 3.54e+03 1.68e+01 bond pdb=" CG HIS D 35 " pdb=" CD2 HIS D 35 " ideal model delta sigma weight residual 1.354 1.309 0.045 1.10e-02 8.26e+03 1.67e+01 bond pdb=" ND1 HIS B 62 " pdb=" CE1 HIS B 62 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.63e+01 bond pdb=" CA ALA D 49 " pdb=" CB ALA D 49 " ideal model delta sigma weight residual 1.534 1.465 0.070 1.77e-02 3.19e+03 1.55e+01 ... (remaining 9146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 10076 2.07 - 4.13: 2043 4.13 - 6.20: 259 6.20 - 8.27: 34 8.27 - 10.34: 5 Bond angle restraints: 12417 Sorted by residual: angle pdb=" N LEU B 190 " pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " ideal model delta sigma weight residual 111.39 101.05 10.34 1.75e+00 3.27e-01 3.49e+01 angle pdb=" C PRO C 49 " pdb=" CA PRO C 49 " pdb=" CB PRO C 49 " ideal model delta sigma weight residual 111.44 103.08 8.36 1.51e+00 4.39e-01 3.07e+01 angle pdb=" CA GLY D 195 " pdb=" C GLY D 195 " pdb=" O GLY D 195 " ideal model delta sigma weight residual 122.37 118.54 3.83 7.30e-01 1.88e+00 2.76e+01 angle pdb=" N PRO C 49 " pdb=" CA PRO C 49 " pdb=" C PRO C 49 " ideal model delta sigma weight residual 114.03 120.36 -6.33 1.23e+00 6.61e-01 2.65e+01 angle pdb=" N LEU B 79 " pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " ideal model delta sigma weight residual 111.23 103.53 7.70 1.53e+00 4.27e-01 2.53e+01 ... (remaining 12412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 4945 17.08 - 34.16: 384 34.16 - 51.24: 56 51.24 - 68.32: 16 68.32 - 85.40: 2 Dihedral angle restraints: 5403 sinusoidal: 2049 harmonic: 3354 Sorted by residual: dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual -86.00 -171.40 85.40 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CA ALA R 135 " pdb=" C ALA R 135 " pdb=" N PHE R 136 " pdb=" CA PHE R 136 " ideal model delta harmonic sigma weight residual -180.00 -154.84 -25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CB CYS D 147 " pdb=" SG CYS D 147 " pdb=" SG CYS D 217 " pdb=" CB CYS D 217 " ideal model delta sinusoidal sigma weight residual 93.00 54.10 38.90 1 1.00e+01 1.00e-02 2.13e+01 ... (remaining 5400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 706 0.068 - 0.135: 498 0.135 - 0.203: 175 0.203 - 0.271: 38 0.271 - 0.339: 6 Chirality restraints: 1423 Sorted by residual: chirality pdb=" CB ILE R 170 " pdb=" CA ILE R 170 " pdb=" CG1 ILE R 170 " pdb=" CG2 ILE R 170 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA ASN R 256 " pdb=" N ASN R 256 " pdb=" C ASN R 256 " pdb=" CB ASN R 256 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA HIS D 35 " pdb=" N HIS D 35 " pdb=" C HIS D 35 " pdb=" CB HIS D 35 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1420 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 161 " 0.100 2.00e-02 2.50e+03 5.14e-02 5.28e+01 pdb=" CG TYR D 161 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR D 161 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR D 161 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR D 161 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 161 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 161 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR D 161 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS R 104 " -0.070 2.00e-02 2.50e+03 5.71e-02 4.89e+01 pdb=" CG HIS R 104 " 0.116 2.00e-02 2.50e+03 pdb=" ND1 HIS R 104 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS R 104 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS R 104 " -0.029 2.00e-02 2.50e+03 pdb=" NE2 HIS R 104 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 111 " 0.037 2.00e-02 2.50e+03 3.58e-02 3.20e+01 pdb=" CG TRP D 111 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP D 111 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP D 111 " -0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP D 111 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP D 111 " -0.038 2.00e-02 2.50e+03 pdb=" CE3 TRP D 111 " -0.031 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 111 " 0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 111 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP D 111 " 0.039 2.00e-02 2.50e+03 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 222 2.69 - 3.24: 9186 3.24 - 3.80: 14876 3.80 - 4.35: 20112 4.35 - 4.90: 32017 Nonbonded interactions: 76413 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR D 163 " model vdw 2.140 3.040 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.173 3.040 nonbonded pdb=" ND2 ASN D 157 " pdb=" OH TYR D 161 " model vdw 2.363 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.397 3.040 nonbonded pdb=" OE2 GLU A 187 " pdb=" NE ARG A 198 " model vdw 2.416 3.120 ... (remaining 76408 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.190 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 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 0.070 9153 Z= 0.679 Angle : 1.675 10.337 12421 Z= 1.131 Chirality : 0.096 0.339 1423 Planarity : 0.012 0.129 1570 Dihedral : 12.527 74.735 3235 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.90 % Allowed : 6.00 % Favored : 91.11 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.22), residues: 1136 helix: -0.63 (0.23), residues: 416 sheet: -1.27 (0.32), residues: 246 loop : -1.86 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.005 ARG B 251 TYR 0.100 0.014 TYR D 161 PHE 0.059 0.009 PHE A 260 TRP 0.072 0.017 TRP D 111 HIS 0.038 0.006 HIS R 104 Details of bonding type rmsd/Z covalent geometry : bond 0.01055 / 0.68 ( 9151) covalent geometry : angle 1.67509 / 1.13 (12417) SS BOND : bond 0.04763 / 3.40 ( 2) SS BOND : angle 2.48334 / 2.11 ( 4) hydrogen bonds : bond 0.18886 / 13.25 ( 469) hydrogen bonds : angle 7.63355 / 5.73 ( 1329) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 50 PRO cc_start: 0.6446 (OUTLIER) cc_final: 0.5918 (Cg_endo) REVERT: R 98 GLN cc_start: 0.9539 (tp-100) cc_final: 0.9335 (tp-100) REVERT: R 112 ASP cc_start: 0.9401 (OUTLIER) cc_final: 0.9043 (p0) REVERT: R 125 TYR cc_start: 0.8663 (p90) cc_final: 0.8004 (m-80) REVERT: R 144 TYR cc_start: 0.8714 (t80) cc_final: 0.8344 (t80) REVERT: R 203 MET cc_start: 0.8890 (tpp) cc_final: 0.8679 (tpp) REVERT: R 207 MET cc_start: 0.8947 (mmt) cc_final: 0.8689 (mmt) REVERT: R 249 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8937 (tmm) REVERT: R 329 ILE cc_start: 0.9075 (mt) cc_final: 0.8850 (mm) REVERT: A 243 ARG cc_start: 0.9539 (ttm-80) cc_final: 0.9177 (ttm-80) REVERT: A 307 GLN cc_start: 0.9436 (mm-40) cc_final: 0.9077 (mm110) REVERT: B 15 LYS cc_start: 0.9651 (mmtp) cc_final: 0.9402 (mtmt) REVERT: C 28 ILE cc_start: 0.9130 (tp) cc_final: 0.8798 (tp) REVERT: D 83 MET cc_start: 0.8998 (mtm) cc_final: 0.8677 (mtm) REVERT: D 211 ASP cc_start: 0.9014 (OUTLIER) cc_final: 0.8781 (m-30) outliers start: 28 outliers final: 7 residues processed: 281 average time/residue: 0.1053 time to fit residues: 38.2769 Evaluate side-chains 174 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 PRO Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 249 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 211 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 81 ASN R 131 HIS R 365 ASN R 373 HIS B 88 ASN B 183 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.066600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.050456 restraints weight = 29355.047| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 3.56 r_work: 0.2658 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9153 Z= 0.172 Angle : 0.655 11.248 12421 Z= 0.352 Chirality : 0.044 0.178 1423 Planarity : 0.004 0.039 1570 Dihedral : 5.355 58.472 1271 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.90 % Allowed : 13.65 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.24), residues: 1136 helix: 1.48 (0.24), residues: 408 sheet: -0.63 (0.32), residues: 264 loop : -1.16 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 313 TYR 0.016 0.002 TYR R 319 PHE 0.031 0.002 PHE R 375 TRP 0.022 0.002 TRP B 169 HIS 0.006 0.001 HIS R 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 9151) covalent geometry : angle 0.65509 / 0.35 (12417) SS BOND : bond 0.00481 / 0.32 ( 2) SS BOND : angle 1.33689 / 0.88 ( 4) hydrogen bonds : bond 0.05612 / 3.80 ( 469) hydrogen bonds : angle 5.12327 / 3.78 ( 1329) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 88 LEU cc_start: 0.8527 (mm) cc_final: 0.8248 (mm) REVERT: R 98 GLN cc_start: 0.9171 (tp-100) cc_final: 0.8658 (tp-100) REVERT: R 171 CYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8734 (t) REVERT: R 249 MET cc_start: 0.9008 (tmm) cc_final: 0.8768 (tmm) REVERT: R 334 TRP cc_start: 0.7239 (m100) cc_final: 0.6646 (m100) REVERT: R 371 PHE cc_start: 0.8699 (m-80) cc_final: 0.7846 (m-80) REVERT: A 198 ARG cc_start: 0.8917 (mtp85) cc_final: 0.8673 (mtp85) REVERT: A 209 ARG cc_start: 0.8805 (mtt-85) cc_final: 0.8411 (tpt90) REVERT: A 307 GLN cc_start: 0.9435 (mm-40) cc_final: 0.9214 (mm-40) REVERT: B 172 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8808 (tm-30) REVERT: B 215 GLU cc_start: 0.8779 (mp0) cc_final: 0.8552 (mp0) REVERT: C 21 MET cc_start: 0.9473 (tpp) cc_final: 0.9182 (ttp) REVERT: C 28 ILE cc_start: 0.9080 (tp) cc_final: 0.8835 (tp) REVERT: C 47 GLU cc_start: 0.8665 (pt0) cc_final: 0.8373 (pm20) REVERT: C 58 GLU cc_start: 0.9343 (mp0) cc_final: 0.8842 (mp0) REVERT: D 83 MET cc_start: 0.9253 (mtm) cc_final: 0.8922 (mtp) REVERT: D 211 ASP cc_start: 0.8634 (m-30) cc_final: 0.8117 (m-30) outliers start: 28 outliers final: 15 residues processed: 188 average time/residue: 0.0871 time to fit residues: 22.4218 Evaluate side-chains 164 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 362 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 225 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 85 optimal weight: 0.0170 chunk 8 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 240 ASN R 365 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.066150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.050276 restraints weight = 29365.803| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.52 r_work: 0.2666 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9153 Z= 0.137 Angle : 0.589 9.323 12421 Z= 0.314 Chirality : 0.042 0.181 1423 Planarity : 0.004 0.045 1570 Dihedral : 4.845 59.594 1253 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.00 % Allowed : 14.06 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.24), residues: 1136 helix: 1.93 (0.24), residues: 415 sheet: -0.31 (0.31), residues: 261 loop : -0.82 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 243 TYR 0.018 0.001 TYR R 145 PHE 0.033 0.001 PHE R 345 TRP 0.018 0.002 TRP B 169 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 9151) covalent geometry : angle 0.58855 / 0.31 (12417) SS BOND : bond 0.00337 / 0.23 ( 2) SS BOND : angle 0.83664 / 0.64 ( 4) hydrogen bonds : bond 0.04715 / 3.16 ( 469) hydrogen bonds : angle 4.65312 / 3.41 ( 1329) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 55 ASP cc_start: 0.9111 (t0) cc_final: 0.8901 (t0) REVERT: R 88 LEU cc_start: 0.8525 (mm) cc_final: 0.8246 (mm) REVERT: R 98 GLN cc_start: 0.9123 (tp-100) cc_final: 0.8659 (tp-100) REVERT: R 171 CYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8842 (t) REVERT: R 175 LYS cc_start: 0.8944 (mtmt) cc_final: 0.8740 (mtpt) REVERT: R 207 MET cc_start: 0.7702 (tpp) cc_final: 0.6911 (tpp) REVERT: R 249 MET cc_start: 0.9064 (tmm) cc_final: 0.8818 (tmm) REVERT: R 266 MET cc_start: 0.9339 (mtp) cc_final: 0.9118 (ttm) REVERT: R 269 GLN cc_start: 0.9281 (pt0) cc_final: 0.8953 (pp30) REVERT: R 334 TRP cc_start: 0.7375 (m100) cc_final: 0.6821 (m100) REVERT: R 339 TYR cc_start: 0.7725 (t80) cc_final: 0.7446 (t80) REVERT: R 365 ASN cc_start: 0.9283 (OUTLIER) cc_final: 0.8477 (m110) REVERT: R 371 PHE cc_start: 0.8928 (m-80) cc_final: 0.8681 (m-80) REVERT: A 249 MET cc_start: 0.9188 (mpp) cc_final: 0.8887 (mpp) REVERT: A 307 GLN cc_start: 0.9512 (mm-40) cc_final: 0.9287 (mm110) REVERT: B 42 ARG cc_start: 0.7836 (tmm-80) cc_final: 0.7595 (tmm-80) REVERT: B 172 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8839 (tm-30) REVERT: B 215 GLU cc_start: 0.8891 (mp0) cc_final: 0.8582 (mp0) REVERT: C 17 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8708 (mm-30) REVERT: C 21 MET cc_start: 0.9440 (tpp) cc_final: 0.9216 (ttm) REVERT: C 22 GLU cc_start: 0.8745 (tp30) cc_final: 0.8227 (tp30) REVERT: C 28 ILE cc_start: 0.9261 (tp) cc_final: 0.9013 (tp) REVERT: C 47 GLU cc_start: 0.8781 (pt0) cc_final: 0.8420 (pm20) REVERT: C 58 GLU cc_start: 0.9371 (mp0) cc_final: 0.8842 (mp0) REVERT: D 73 ASP cc_start: 0.8268 (t0) cc_final: 0.7925 (t0) REVERT: D 113 GLN cc_start: 0.8928 (tp40) cc_final: 0.8276 (tm-30) REVERT: D 211 ASP cc_start: 0.8656 (m-30) cc_final: 0.8274 (m-30) outliers start: 29 outliers final: 17 residues processed: 173 average time/residue: 0.0809 time to fit residues: 19.7397 Evaluate side-chains 162 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 205 PHE Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 362 ILE Chi-restraints excluded: chain R residue 363 LEU Chi-restraints excluded: chain R residue 365 ASN Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 129 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.061750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.046359 restraints weight = 31076.792| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.50 r_work: 0.2555 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 9153 Z= 0.352 Angle : 0.681 8.091 12421 Z= 0.368 Chirality : 0.046 0.181 1423 Planarity : 0.004 0.042 1570 Dihedral : 4.920 65.305 1251 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.34 % Allowed : 15.10 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1136 helix: 2.03 (0.24), residues: 408 sheet: -0.18 (0.31), residues: 280 loop : -0.65 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 322 TYR 0.020 0.002 TYR R 145 PHE 0.024 0.002 PHE R 345 TRP 0.015 0.002 TRP B 82 HIS 0.007 0.002 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00782 / 0.35 ( 9151) covalent geometry : angle 0.68115 / 0.37 (12417) SS BOND : bond 0.00668 / 0.45 ( 2) SS BOND : angle 1.03293 / 0.75 ( 4) hydrogen bonds : bond 0.05253 / 3.55 ( 469) hydrogen bonds : angle 4.89876 / 3.60 ( 1329) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 98 GLN cc_start: 0.9195 (tp-100) cc_final: 0.8608 (tp-100) REVERT: R 145 TYR cc_start: 0.8654 (m-80) cc_final: 0.8436 (m-80) REVERT: R 149 ASP cc_start: 0.9308 (t0) cc_final: 0.8993 (t70) REVERT: R 171 CYS cc_start: 0.9100 (t) cc_final: 0.8697 (t) REVERT: R 175 LYS cc_start: 0.8977 (mtmt) cc_final: 0.8618 (mtpt) REVERT: R 207 MET cc_start: 0.7552 (tpp) cc_final: 0.7089 (tpp) REVERT: R 249 MET cc_start: 0.9143 (tmm) cc_final: 0.8805 (tmm) REVERT: R 266 MET cc_start: 0.9483 (mtp) cc_final: 0.9242 (ttm) REVERT: R 269 GLN cc_start: 0.9317 (pt0) cc_final: 0.8946 (pp30) REVERT: R 365 ASN cc_start: 0.9373 (OUTLIER) cc_final: 0.9066 (t0) REVERT: A 209 ARG cc_start: 0.9005 (mtt-85) cc_final: 0.8520 (tpt90) REVERT: A 244 MET cc_start: 0.9541 (tpp) cc_final: 0.9337 (ttp) REVERT: A 307 GLN cc_start: 0.9584 (mm-40) cc_final: 0.9182 (mm-40) REVERT: B 42 ARG cc_start: 0.7989 (tmm-80) cc_final: 0.7727 (tmm-80) REVERT: B 49 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8276 (tpp80) REVERT: B 124 TYR cc_start: 0.9456 (m-80) cc_final: 0.9200 (m-80) REVERT: B 172 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8880 (tm-30) REVERT: C 17 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8789 (mm-30) REVERT: C 21 MET cc_start: 0.9448 (tpp) cc_final: 0.9246 (ttm) REVERT: C 22 GLU cc_start: 0.8831 (tp30) cc_final: 0.8174 (tp30) REVERT: C 28 ILE cc_start: 0.9248 (tp) cc_final: 0.9040 (tp) REVERT: C 47 GLU cc_start: 0.8775 (pt0) cc_final: 0.8393 (pm20) REVERT: C 58 GLU cc_start: 0.9364 (mp0) cc_final: 0.8836 (mp0) REVERT: D 73 ASP cc_start: 0.8442 (t0) cc_final: 0.8086 (t0) REVERT: D 89 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8439 (pt0) REVERT: D 113 GLN cc_start: 0.9120 (tp40) cc_final: 0.8477 (tm-30) REVERT: D 211 ASP cc_start: 0.8799 (m-30) cc_final: 0.8465 (m-30) REVERT: D 222 GLU cc_start: 0.8587 (tp30) cc_final: 0.8218 (tp30) outliers start: 42 outliers final: 34 residues processed: 161 average time/residue: 0.0838 time to fit residues: 19.0804 Evaluate side-chains 167 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 205 PHE Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 315 CYS Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 363 LEU Chi-restraints excluded: chain R residue 365 ASN Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 225 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.064794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.049298 restraints weight = 29722.845| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.54 r_work: 0.2641 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9153 Z= 0.116 Angle : 0.548 7.302 12421 Z= 0.294 Chirality : 0.042 0.191 1423 Planarity : 0.004 0.045 1570 Dihedral : 4.561 60.818 1251 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.90 % Allowed : 17.58 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.25), residues: 1136 helix: 2.31 (0.25), residues: 409 sheet: 0.17 (0.32), residues: 271 loop : -0.64 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 322 TYR 0.016 0.001 TYR R 145 PHE 0.019 0.001 PHE R 345 TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 9151) covalent geometry : angle 0.54784 / 0.29 (12417) SS BOND : bond 0.00368 / 0.25 ( 2) SS BOND : angle 0.70535 / 0.50 ( 4) hydrogen bonds : bond 0.04326 / 2.90 ( 469) hydrogen bonds : angle 4.38763 / 3.22 ( 1329) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 98 GLN cc_start: 0.9152 (tp-100) cc_final: 0.8645 (tp-100) REVERT: R 149 ASP cc_start: 0.9282 (t0) cc_final: 0.8683 (t0) REVERT: R 171 CYS cc_start: 0.9042 (t) cc_final: 0.8707 (t) REVERT: R 207 MET cc_start: 0.7598 (tpp) cc_final: 0.6823 (tpt) REVERT: R 249 MET cc_start: 0.9098 (tmm) cc_final: 0.8753 (tmm) REVERT: R 269 GLN cc_start: 0.9345 (pt0) cc_final: 0.8948 (pp30) REVERT: R 346 TYR cc_start: 0.7889 (t80) cc_final: 0.7634 (t80) REVERT: R 365 ASN cc_start: 0.9334 (m-40) cc_final: 0.8966 (t0) REVERT: A 25 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8758 (tm-30) REVERT: A 209 ARG cc_start: 0.8909 (mtt-85) cc_final: 0.8478 (tpt90) REVERT: A 244 MET cc_start: 0.9487 (tpp) cc_final: 0.9266 (tpp) REVERT: A 249 MET cc_start: 0.9261 (mpp) cc_final: 0.9046 (mpp) REVERT: A 307 GLN cc_start: 0.9568 (mm-40) cc_final: 0.9289 (mm110) REVERT: B 42 ARG cc_start: 0.7996 (tmm-80) cc_final: 0.7687 (tmm-80) REVERT: B 172 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8902 (tm-30) REVERT: B 260 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8426 (tt0) REVERT: C 14 LYS cc_start: 0.9717 (mtpp) cc_final: 0.9511 (mmtm) REVERT: C 17 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8855 (mm-30) REVERT: C 21 MET cc_start: 0.9432 (tpp) cc_final: 0.9219 (ttm) REVERT: C 22 GLU cc_start: 0.8710 (tp30) cc_final: 0.8225 (tp30) REVERT: C 28 ILE cc_start: 0.9348 (tp) cc_final: 0.8739 (tp) REVERT: C 47 GLU cc_start: 0.8764 (pt0) cc_final: 0.8330 (pm20) REVERT: C 48 ASP cc_start: 0.9060 (t70) cc_final: 0.7888 (t0) REVERT: C 58 GLU cc_start: 0.9358 (mp0) cc_final: 0.8806 (mp0) REVERT: D 73 ASP cc_start: 0.8525 (t0) cc_final: 0.8160 (t0) REVERT: D 89 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8488 (pt0) REVERT: D 93 MET cc_start: 0.8936 (ttm) cc_final: 0.8431 (ttm) REVERT: D 113 GLN cc_start: 0.9010 (tp40) cc_final: 0.8336 (tm-30) REVERT: D 211 ASP cc_start: 0.8801 (m-30) cc_final: 0.8508 (m-30) REVERT: D 219 GLN cc_start: 0.9343 (pp30) cc_final: 0.8898 (pp30) REVERT: D 222 GLU cc_start: 0.8555 (tp30) cc_final: 0.8322 (tp30) outliers start: 28 outliers final: 17 residues processed: 171 average time/residue: 0.0845 time to fit residues: 20.2934 Evaluate side-chains 157 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 205 PHE Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 363 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 225 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.061223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.046048 restraints weight = 30740.375| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.48 r_work: 0.2548 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 9153 Z= 0.351 Angle : 0.677 7.078 12421 Z= 0.365 Chirality : 0.045 0.184 1423 Planarity : 0.004 0.042 1570 Dihedral : 5.115 78.144 1251 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.34 % Allowed : 16.96 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.25), residues: 1136 helix: 2.09 (0.24), residues: 408 sheet: -0.00 (0.32), residues: 286 loop : -0.53 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 322 TYR 0.021 0.002 TYR R 145 PHE 0.019 0.002 PHE R 345 TRP 0.016 0.002 TRP R 129 HIS 0.006 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00782 / 0.35 ( 9151) covalent geometry : angle 0.67663 / 0.36 (12417) SS BOND : bond 0.00656 / 0.44 ( 2) SS BOND : angle 0.88325 / 0.62 ( 4) hydrogen bonds : bond 0.05043 / 3.41 ( 469) hydrogen bonds : angle 4.82641 / 3.56 ( 1329) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 98 GLN cc_start: 0.9185 (tp-100) cc_final: 0.8581 (tp-100) REVERT: R 149 ASP cc_start: 0.9324 (t0) cc_final: 0.8747 (t70) REVERT: R 171 CYS cc_start: 0.9078 (t) cc_final: 0.8758 (t) REVERT: R 207 MET cc_start: 0.7484 (tpp) cc_final: 0.6700 (tpp) REVERT: R 249 MET cc_start: 0.9097 (tmm) cc_final: 0.8756 (tmm) REVERT: R 269 GLN cc_start: 0.9374 (pt0) cc_final: 0.8995 (pp30) REVERT: R 365 ASN cc_start: 0.9364 (m-40) cc_final: 0.9015 (t0) REVERT: A 209 ARG cc_start: 0.8955 (mtt-85) cc_final: 0.8530 (tpt90) REVERT: A 244 MET cc_start: 0.9653 (tpp) cc_final: 0.9264 (tpp) REVERT: A 307 GLN cc_start: 0.9596 (mm-40) cc_final: 0.9171 (mm110) REVERT: B 42 ARG cc_start: 0.7967 (tmm-80) cc_final: 0.7709 (tmm-80) REVERT: B 124 TYR cc_start: 0.9473 (m-80) cc_final: 0.9201 (m-80) REVERT: B 172 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8928 (tm-30) REVERT: B 260 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8481 (tt0) REVERT: B 273 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.8991 (mp) REVERT: C 17 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8905 (mm-30) REVERT: C 22 GLU cc_start: 0.8835 (tp30) cc_final: 0.8312 (tp30) REVERT: C 47 GLU cc_start: 0.8816 (pt0) cc_final: 0.8398 (pm20) REVERT: C 48 ASP cc_start: 0.9115 (t70) cc_final: 0.7717 (t70) REVERT: C 58 GLU cc_start: 0.9360 (mp0) cc_final: 0.8795 (mp0) REVERT: D 73 ASP cc_start: 0.8624 (t0) cc_final: 0.8224 (t0) REVERT: D 89 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8573 (pt0) REVERT: D 93 MET cc_start: 0.9026 (ttm) cc_final: 0.8723 (ttm) REVERT: D 113 GLN cc_start: 0.9198 (tp40) cc_final: 0.8572 (tm-30) REVERT: D 211 ASP cc_start: 0.8940 (m-30) cc_final: 0.8635 (m-30) outliers start: 42 outliers final: 34 residues processed: 161 average time/residue: 0.0946 time to fit residues: 21.3018 Evaluate side-chains 169 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 205 PHE Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 315 CYS Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 363 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 225 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.062244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.047347 restraints weight = 30256.483| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.47 r_work: 0.2589 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 9153 Z= 0.208 Angle : 0.613 8.056 12421 Z= 0.327 Chirality : 0.044 0.207 1423 Planarity : 0.004 0.043 1570 Dihedral : 4.913 72.946 1251 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.10 % Allowed : 17.79 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.25), residues: 1136 helix: 2.17 (0.25), residues: 407 sheet: 0.16 (0.32), residues: 283 loop : -0.49 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 322 TYR 0.020 0.001 TYR R 145 PHE 0.016 0.002 PHE R 345 TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 ( 9151) covalent geometry : angle 0.61264 / 0.33 (12417) SS BOND : bond 0.00515 / 0.34 ( 2) SS BOND : angle 0.69174 / 0.43 ( 4) hydrogen bonds : bond 0.04585 / 3.09 ( 469) hydrogen bonds : angle 4.67924 / 3.43 ( 1329) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 98 GLN cc_start: 0.9210 (tp-100) cc_final: 0.8679 (tp-100) REVERT: R 149 ASP cc_start: 0.9292 (t0) cc_final: 0.8707 (t70) REVERT: R 171 CYS cc_start: 0.9108 (t) cc_final: 0.8766 (t) REVERT: R 207 MET cc_start: 0.7537 (tpp) cc_final: 0.7027 (tpp) REVERT: R 249 MET cc_start: 0.9081 (tmm) cc_final: 0.8738 (tmm) REVERT: R 269 GLN cc_start: 0.9387 (pt0) cc_final: 0.8991 (pp30) REVERT: R 346 TYR cc_start: 0.8185 (t80) cc_final: 0.7917 (t80) REVERT: R 365 ASN cc_start: 0.9319 (m-40) cc_final: 0.9000 (t0) REVERT: A 209 ARG cc_start: 0.8928 (mtt-85) cc_final: 0.8511 (tpt90) REVERT: A 244 MET cc_start: 0.9600 (tpp) cc_final: 0.9196 (tpp) REVERT: A 307 GLN cc_start: 0.9589 (mm-40) cc_final: 0.9184 (mm110) REVERT: B 42 ARG cc_start: 0.7975 (tmm-80) cc_final: 0.7738 (tmm-80) REVERT: B 172 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8905 (tm-30) REVERT: B 273 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8934 (mp) REVERT: C 14 LYS cc_start: 0.9735 (mtpp) cc_final: 0.9462 (mmtm) REVERT: C 17 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8927 (mm-30) REVERT: C 22 GLU cc_start: 0.8813 (tp30) cc_final: 0.8281 (tp30) REVERT: C 47 GLU cc_start: 0.8845 (pt0) cc_final: 0.8367 (pm20) REVERT: C 48 ASP cc_start: 0.9085 (t70) cc_final: 0.7823 (t70) REVERT: C 58 GLU cc_start: 0.9373 (mp0) cc_final: 0.8802 (mp0) REVERT: D 73 ASP cc_start: 0.8669 (t0) cc_final: 0.8278 (t0) REVERT: D 89 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8538 (pt0) REVERT: D 93 MET cc_start: 0.9020 (ttm) cc_final: 0.8563 (ttm) REVERT: D 206 ARG cc_start: 0.8929 (mtm180) cc_final: 0.8703 (mpp80) REVERT: D 211 ASP cc_start: 0.8925 (m-30) cc_final: 0.8617 (m-30) REVERT: D 222 GLU cc_start: 0.8932 (tp30) cc_final: 0.8708 (tp30) outliers start: 30 outliers final: 24 residues processed: 154 average time/residue: 0.0916 time to fit residues: 19.7632 Evaluate side-chains 157 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 205 PHE Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 315 CYS Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 225 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.061554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.046749 restraints weight = 30249.512| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.44 r_work: 0.2576 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9153 Z= 0.245 Angle : 0.636 12.584 12421 Z= 0.338 Chirality : 0.044 0.200 1423 Planarity : 0.004 0.041 1570 Dihedral : 4.870 72.205 1251 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.31 % Allowed : 18.20 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.25), residues: 1136 helix: 2.22 (0.25), residues: 403 sheet: 0.25 (0.32), residues: 276 loop : -0.53 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 322 TYR 0.019 0.002 TYR R 145 PHE 0.016 0.002 PHE R 345 TRP 0.012 0.002 TRP B 82 HIS 0.004 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.25 ( 9151) covalent geometry : angle 0.63576 / 0.34 (12417) SS BOND : bond 0.00553 / 0.37 ( 2) SS BOND : angle 0.70874 / 0.41 ( 4) hydrogen bonds : bond 0.04659 / 3.14 ( 469) hydrogen bonds : angle 4.73115 / 3.47 ( 1329) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 98 GLN cc_start: 0.9211 (tp-100) cc_final: 0.8676 (tp-100) REVERT: R 149 ASP cc_start: 0.9297 (t0) cc_final: 0.8709 (t70) REVERT: R 171 CYS cc_start: 0.9099 (t) cc_final: 0.8747 (t) REVERT: R 207 MET cc_start: 0.7616 (tpp) cc_final: 0.6831 (tpp) REVERT: R 249 MET cc_start: 0.9101 (tmm) cc_final: 0.8748 (tmm) REVERT: R 269 GLN cc_start: 0.9391 (pt0) cc_final: 0.8997 (pp30) REVERT: R 365 ASN cc_start: 0.9364 (m-40) cc_final: 0.9044 (t0) REVERT: A 209 ARG cc_start: 0.8941 (mtt-85) cc_final: 0.8518 (tpt90) REVERT: A 244 MET cc_start: 0.9617 (tpp) cc_final: 0.9209 (tpp) REVERT: A 307 GLN cc_start: 0.9593 (mm-40) cc_final: 0.9167 (mm110) REVERT: B 172 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8921 (tm-30) REVERT: B 273 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.8944 (mp) REVERT: C 17 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8899 (mm-30) REVERT: C 22 GLU cc_start: 0.8820 (tp30) cc_final: 0.8278 (tp30) REVERT: C 47 GLU cc_start: 0.8821 (pt0) cc_final: 0.8347 (pm20) REVERT: C 48 ASP cc_start: 0.9122 (t70) cc_final: 0.7987 (t0) REVERT: C 58 GLU cc_start: 0.9370 (mp0) cc_final: 0.8786 (mp0) REVERT: D 73 ASP cc_start: 0.8679 (t0) cc_final: 0.8261 (t0) REVERT: D 89 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8558 (pt0) REVERT: D 93 MET cc_start: 0.9035 (ttm) cc_final: 0.8632 (ttm) REVERT: D 211 ASP cc_start: 0.9000 (m-30) cc_final: 0.8286 (m-30) outliers start: 32 outliers final: 26 residues processed: 154 average time/residue: 0.1016 time to fit residues: 21.7476 Evaluate side-chains 155 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 205 PHE Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 315 CYS Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 225 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 89 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 104 optimal weight: 0.0070 chunk 63 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 103 optimal weight: 0.2980 chunk 85 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 overall best weight: 3.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.062625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.047516 restraints weight = 30205.244| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.54 r_work: 0.2595 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9153 Z= 0.176 Angle : 0.614 10.683 12421 Z= 0.328 Chirality : 0.043 0.226 1423 Planarity : 0.003 0.042 1570 Dihedral : 4.539 70.759 1250 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.00 % Allowed : 18.20 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.25), residues: 1136 helix: 2.28 (0.25), residues: 403 sheet: 0.39 (0.33), residues: 271 loop : -0.52 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 322 TYR 0.018 0.001 TYR R 145 PHE 0.015 0.001 PHE R 345 TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 ( 9151) covalent geometry : angle 0.61433 / 0.33 (12417) SS BOND : bond 0.00471 / 0.32 ( 2) SS BOND : angle 0.61477 / 0.37 ( 4) hydrogen bonds : bond 0.04408 / 2.98 ( 469) hydrogen bonds : angle 4.62932 / 3.39 ( 1329) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 98 GLN cc_start: 0.9178 (tp-100) cc_final: 0.8645 (tp-100) REVERT: R 149 ASP cc_start: 0.9315 (t0) cc_final: 0.8707 (t70) REVERT: R 171 CYS cc_start: 0.9129 (t) cc_final: 0.8776 (t) REVERT: R 175 LYS cc_start: 0.9383 (mtmm) cc_final: 0.9106 (mtmm) REVERT: R 207 MET cc_start: 0.7673 (tpp) cc_final: 0.7197 (tpp) REVERT: R 249 MET cc_start: 0.9088 (tmm) cc_final: 0.8731 (tmm) REVERT: R 269 GLN cc_start: 0.9398 (pt0) cc_final: 0.8993 (pp30) REVERT: R 346 TYR cc_start: 0.8041 (t80) cc_final: 0.7797 (t80) REVERT: R 365 ASN cc_start: 0.9336 (m-40) cc_final: 0.9027 (t0) REVERT: A 209 ARG cc_start: 0.8931 (mtt-85) cc_final: 0.8507 (tpt90) REVERT: A 244 MET cc_start: 0.9605 (tpp) cc_final: 0.9178 (tpp) REVERT: A 307 GLN cc_start: 0.9599 (mm-40) cc_final: 0.9280 (mm110) REVERT: A 333 GLN cc_start: 0.9258 (tp40) cc_final: 0.9033 (tp-100) REVERT: B 172 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8905 (tm-30) REVERT: B 262 MET cc_start: 0.8838 (mtt) cc_final: 0.8588 (mmm) REVERT: C 17 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8884 (mm-30) REVERT: C 22 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8272 (tp30) REVERT: C 47 GLU cc_start: 0.8826 (pt0) cc_final: 0.8346 (pm20) REVERT: C 48 ASP cc_start: 0.9132 (t70) cc_final: 0.8079 (t0) REVERT: C 58 GLU cc_start: 0.9370 (mp0) cc_final: 0.8781 (mp0) REVERT: D 73 ASP cc_start: 0.8660 (t0) cc_final: 0.8228 (t0) REVERT: D 89 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8558 (pt0) REVERT: D 93 MET cc_start: 0.9031 (ttm) cc_final: 0.8512 (ttm) REVERT: D 211 ASP cc_start: 0.8912 (m-30) cc_final: 0.8628 (m-30) outliers start: 29 outliers final: 25 residues processed: 153 average time/residue: 0.0823 time to fit residues: 17.9880 Evaluate side-chains 158 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 205 PHE Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 225 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.063155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.048095 restraints weight = 30284.427| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.54 r_work: 0.2617 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9153 Z= 0.152 Angle : 0.604 10.476 12421 Z= 0.321 Chirality : 0.043 0.233 1423 Planarity : 0.003 0.043 1570 Dihedral : 4.364 68.134 1249 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.38 % Allowed : 18.72 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.26), residues: 1136 helix: 2.34 (0.25), residues: 403 sheet: 0.49 (0.33), residues: 272 loop : -0.45 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 322 TYR 0.016 0.001 TYR R 145 PHE 0.014 0.001 PHE R 345 TRP 0.017 0.002 TRP R 134 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 9151) covalent geometry : angle 0.60388 / 0.32 (12417) SS BOND : bond 0.00416 / 0.28 ( 2) SS BOND : angle 0.55873 / 0.36 ( 4) hydrogen bonds : bond 0.04167 / 2.82 ( 469) hydrogen bonds : angle 4.50335 / 3.30 ( 1329) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 53 GLU cc_start: 0.8718 (tp30) cc_final: 0.8401 (tp30) REVERT: R 98 GLN cc_start: 0.9142 (tp-100) cc_final: 0.8605 (tp-100) REVERT: R 145 TYR cc_start: 0.8625 (m-80) cc_final: 0.8379 (m-80) REVERT: R 149 ASP cc_start: 0.9273 (t0) cc_final: 0.8623 (t0) REVERT: R 171 CYS cc_start: 0.9071 (t) cc_final: 0.8789 (t) REVERT: R 175 LYS cc_start: 0.9404 (mtmm) cc_final: 0.9165 (mtmm) REVERT: R 207 MET cc_start: 0.7630 (tpp) cc_final: 0.7185 (tpp) REVERT: R 249 MET cc_start: 0.9103 (tmm) cc_final: 0.8728 (tmm) REVERT: R 269 GLN cc_start: 0.9385 (pt0) cc_final: 0.8986 (pp30) REVERT: R 345 PHE cc_start: 0.9282 (t80) cc_final: 0.8975 (t80) REVERT: R 346 TYR cc_start: 0.8008 (t80) cc_final: 0.7743 (t80) REVERT: R 365 ASN cc_start: 0.9302 (m-40) cc_final: 0.8949 (t0) REVERT: A 25 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8712 (tm-30) REVERT: A 209 ARG cc_start: 0.8914 (mtt-85) cc_final: 0.8513 (tpt90) REVERT: A 244 MET cc_start: 0.9608 (tpp) cc_final: 0.9190 (tpp) REVERT: A 307 GLN cc_start: 0.9587 (mm-40) cc_final: 0.9273 (mm110) REVERT: A 333 GLN cc_start: 0.9218 (tp40) cc_final: 0.8930 (mp10) REVERT: B 172 GLU cc_start: 0.9174 (tm-30) cc_final: 0.8898 (tm-30) REVERT: B 262 MET cc_start: 0.8821 (mtt) cc_final: 0.8609 (mmm) REVERT: C 17 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8875 (mm-30) REVERT: C 22 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8224 (tp30) REVERT: C 32 LYS cc_start: 0.9243 (tttp) cc_final: 0.9017 (tptt) REVERT: C 47 GLU cc_start: 0.8753 (pt0) cc_final: 0.8252 (pm20) REVERT: C 48 ASP cc_start: 0.9130 (t70) cc_final: 0.8103 (t0) REVERT: C 58 GLU cc_start: 0.9398 (mp0) cc_final: 0.8829 (mp0) REVERT: D 73 ASP cc_start: 0.8660 (t0) cc_final: 0.8237 (t0) REVERT: D 89 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8528 (pt0) REVERT: D 93 MET cc_start: 0.9055 (ttm) cc_final: 0.8457 (ttm) REVERT: D 211 ASP cc_start: 0.8966 (m-30) cc_final: 0.8688 (m-30) REVERT: D 219 GLN cc_start: 0.9314 (pp30) cc_final: 0.8931 (pp30) outliers start: 23 outliers final: 20 residues processed: 152 average time/residue: 0.0770 time to fit residues: 16.5859 Evaluate side-chains 157 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 205 PHE Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 225 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.063178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.048053 restraints weight = 29945.903| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.54 r_work: 0.2615 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9153 Z= 0.161 Angle : 0.608 11.392 12421 Z= 0.322 Chirality : 0.042 0.224 1423 Planarity : 0.003 0.043 1570 Dihedral : 4.333 67.620 1249 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.48 % Allowed : 18.30 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.26), residues: 1136 helix: 2.41 (0.25), residues: 403 sheet: 0.57 (0.33), residues: 266 loop : -0.44 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 322 TYR 0.016 0.001 TYR R 145 PHE 0.014 0.001 PHE R 345 TRP 0.017 0.002 TRP R 316 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 9151) covalent geometry : angle 0.60782 / 0.32 (12417) SS BOND : bond 0.00465 / 0.32 ( 2) SS BOND : angle 0.61923 / 0.46 ( 4) hydrogen bonds : bond 0.04160 / 2.81 ( 469) hydrogen bonds : angle 4.50327 / 3.30 ( 1329) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1641.79 seconds wall clock time: 29 minutes 8.54 seconds (1748.54 seconds total)