Starting phenix.real_space_refine on Wed Jan 15 23:06:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xzh_38796/01_2025/8xzh_38796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xzh_38796/01_2025/8xzh_38796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xzh_38796/01_2025/8xzh_38796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xzh_38796/01_2025/8xzh_38796.map" model { file = "/net/cci-nas-00/data/ceres_data/8xzh_38796/01_2025/8xzh_38796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xzh_38796/01_2025/8xzh_38796.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.006 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 72 5.16 5 C 5767 2.51 5 N 1532 2.21 5 O 1677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9048 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2419 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 291} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1743 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2592 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 416 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1773 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 3, 'TRANS': 9} Time building chain proxies: 5.37, per 1000 atoms: 0.59 Number of scatterers: 9048 At special positions: 0 Unit cell: (103, 131.016, 117.008, 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 72 16.00 O 1677 8.00 N 1532 7.00 C 5767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 281 " distance=2.03 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 6 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 995.4 milliseconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 15 sheets defined 40.3% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'R' and resid 26 through 55 Proline residue: R 32 - end of helix Processing helix chain 'R' and resid 64 through 80 Processing helix chain 'R' and resid 81 through 91 removed outlier: 4.163A pdb=" N TRP R 85 " --> pdb=" O THR R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 132 removed outlier: 4.147A pdb=" N PHE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 Processing helix chain 'R' and resid 146 through 161 removed outlier: 3.774A pdb=" N THR R 150 " --> pdb=" O GLY R 146 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA R 161 " --> pdb=" O ALA R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 167 removed outlier: 3.913A pdb=" N MET R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 192 No H-bonds generated for 'chain 'R' and resid 190 through 192' Processing helix chain 'R' and resid 193 through 210 removed outlier: 3.734A pdb=" N TRP R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 232 Processing helix chain 'R' and resid 236 through 274 Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 281 through 299 Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 300 through 310 Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 325 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.710A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.685A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.651A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.251A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.873A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.811A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.618A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.821A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.512A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.797A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 168 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.622A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.484A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.721A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.933A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.771A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.741A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.708A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.705A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.785A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.211A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.201A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.201A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2550 1.33 - 1.45: 1829 1.45 - 1.57: 4764 1.57 - 1.69: 0 1.69 - 1.82: 104 Bond restraints: 9247 Sorted by residual: bond pdb=" N ILE B 37 " pdb=" CA ILE B 37 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.19e-02 7.06e+03 9.85e+00 bond pdb=" N ILE A 253 " pdb=" CA ILE A 253 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.22e+00 bond pdb=" N LEU B 261 " pdb=" CA LEU B 261 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.29e-02 6.01e+03 8.38e+00 bond pdb=" N THR R 81 " pdb=" CA THR R 81 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.18e-02 7.18e+03 8.36e+00 bond pdb=" N ILE A 49 " pdb=" CA ILE A 49 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.02e+00 ... (remaining 9242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 11981 2.15 - 4.29: 493 4.29 - 6.44: 50 6.44 - 8.58: 7 8.58 - 10.73: 3 Bond angle restraints: 12534 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.02 103.47 9.55 1.20e+00 6.94e-01 6.33e+01 angle pdb=" C ASP B 38 " pdb=" N PRO B 39 " pdb=" CA PRO B 39 " ideal model delta sigma weight residual 120.31 127.69 -7.38 9.80e-01 1.04e+00 5.67e+01 angle pdb=" C LEU R 30 " pdb=" N ILE R 31 " pdb=" CA ILE R 31 " ideal model delta sigma weight residual 120.24 122.87 -2.63 6.30e-01 2.52e+00 1.75e+01 angle pdb=" N ARG B 197 " pdb=" CA ARG B 197 " pdb=" C ARG B 197 " ideal model delta sigma weight residual 113.38 108.39 4.99 1.23e+00 6.61e-01 1.65e+01 angle pdb=" N LEU A 273 " pdb=" CA LEU A 273 " pdb=" C LEU A 273 " ideal model delta sigma weight residual 111.28 106.87 4.41 1.09e+00 8.42e-01 1.64e+01 ... (remaining 12529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 4953 17.26 - 34.52: 411 34.52 - 51.78: 74 51.78 - 69.05: 20 69.05 - 86.31: 8 Dihedral angle restraints: 5466 sinusoidal: 2104 harmonic: 3362 Sorted by residual: dihedral pdb=" CB CYS L 1 " pdb=" SG CYS L 1 " pdb=" SG CYS L 6 " pdb=" CB CYS L 6 " ideal model delta sinusoidal sigma weight residual 93.00 172.92 -79.92 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual 0.00 30.75 -30.75 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CD ARG S 179 " pdb=" NE ARG S 179 " pdb=" CZ ARG S 179 " pdb=" NH1 ARG S 179 " ideal model delta sinusoidal sigma weight residual 0.00 44.78 -44.78 1 1.00e+01 1.00e-02 2.79e+01 ... (remaining 5463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 955 0.060 - 0.121: 375 0.121 - 0.181: 72 0.181 - 0.241: 15 0.241 - 0.302: 2 Chirality restraints: 1419 Sorted by residual: chirality pdb=" CB VAL G 54 " pdb=" CA VAL G 54 " pdb=" CG1 VAL G 54 " pdb=" CG2 VAL G 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ARG S 179 " pdb=" N ARG S 179 " pdb=" C ARG S 179 " pdb=" CB ARG S 179 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB VAL B 200 " pdb=" CA VAL B 200 " pdb=" CG1 VAL B 200 " pdb=" CG2 VAL B 200 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1416 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG S 179 " -0.767 9.50e-02 1.11e+02 3.44e-01 7.18e+01 pdb=" NE ARG S 179 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG S 179 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG S 179 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG S 179 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 75 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.80e+00 pdb=" C GLN B 75 " -0.054 2.00e-02 2.50e+03 pdb=" O GLN B 75 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP B 76 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 274 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C THR B 274 " -0.040 2.00e-02 2.50e+03 pdb=" O THR B 274 " 0.015 2.00e-02 2.50e+03 pdb=" N SER B 275 " 0.014 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 538 2.72 - 3.26: 8629 3.26 - 3.81: 15032 3.81 - 4.35: 19566 4.35 - 4.90: 33280 Nonbonded interactions: 77045 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.171 3.040 nonbonded pdb=" NH2 ARG S 67 " pdb=" OD2 ASP S 90 " model vdw 2.198 3.120 nonbonded pdb=" O LEU R 108 " pdb=" ND2 ASN R 112 " model vdw 2.225 3.120 nonbonded pdb=" O PHE A 259 " pdb=" NZ LYS A 317 " model vdw 2.243 3.120 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.273 3.120 ... (remaining 77040 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: 0.660 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.970 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.012 0.099 9247 Z= 0.806 Angle : 0.971 10.725 12534 Z= 0.592 Chirality : 0.065 0.302 1419 Planarity : 0.010 0.344 1578 Dihedral : 13.619 86.308 3283 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 0.61 % Allowed : 5.30 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.23), residues: 1139 helix: -0.92 (0.24), residues: 404 sheet: 0.10 (0.28), residues: 297 loop : -1.41 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 99 HIS 0.009 0.002 HIS B 91 PHE 0.025 0.003 PHE R 78 TYR 0.034 0.003 TYR B 105 ARG 0.014 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 186 time to evaluate : 0.972 Fit side-chains REVERT: A 298 GLU cc_start: 0.7437 (tp30) cc_final: 0.7179 (tp30) REVERT: A 306 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7323 (mm-40) REVERT: A 308 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7149 (mt-10) outliers start: 6 outliers final: 3 residues processed: 191 average time/residue: 1.5768 time to fit residues: 317.0087 Evaluate side-chains 168 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 33 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 88 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 46 ASN A 52 GLN A 188 HIS A 204 GLN A 213 HIS A 306 GLN A 322 HIS B 44 GLN B 259 GLN B 340 ASN G 11 GLN G 24 ASN G 59 ASN S 155 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.126799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.103458 restraints weight = 13147.154| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.29 r_work: 0.3235 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9247 Z= 0.202 Angle : 0.570 6.210 12534 Z= 0.309 Chirality : 0.043 0.140 1419 Planarity : 0.005 0.054 1578 Dihedral : 5.571 57.185 1266 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.14 % Allowed : 10.70 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.24), residues: 1139 helix: 0.76 (0.25), residues: 409 sheet: 0.52 (0.29), residues: 282 loop : -0.93 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS L 7 PHE 0.016 0.001 PHE B 199 TYR 0.012 0.001 TYR S 103 ARG 0.008 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: R 55 ARG cc_start: 0.7700 (mpt180) cc_final: 0.6167 (ppt170) REVERT: R 254 VAL cc_start: 0.8486 (t) cc_final: 0.8181 (m) REVERT: R 318 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7455 (mp10) REVERT: R 321 THR cc_start: 0.7969 (m) cc_final: 0.7710 (m) REVERT: A 52 GLN cc_start: 0.5749 (OUTLIER) cc_final: 0.5292 (mt0) REVERT: A 272 ASP cc_start: 0.6564 (m-30) cc_final: 0.6207 (m-30) REVERT: A 276 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.5970 (mp0) REVERT: A 280 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6703 (mmmt) REVERT: A 298 GLU cc_start: 0.7206 (tp30) cc_final: 0.6892 (tp30) REVERT: G 21 MET cc_start: 0.6375 (OUTLIER) cc_final: 0.6065 (ppp) REVERT: G 59 ASN cc_start: 0.7649 (t0) cc_final: 0.7412 (t0) REVERT: G 62 ARG cc_start: 0.7027 (mtm-85) cc_final: 0.6662 (mtm-85) REVERT: S 206 ARG cc_start: 0.7208 (mtm110) cc_final: 0.6623 (ptt-90) outliers start: 21 outliers final: 5 residues processed: 186 average time/residue: 1.5080 time to fit residues: 295.9547 Evaluate side-chains 172 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 90 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.124953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.101453 restraints weight = 13288.728| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.28 r_work: 0.3197 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9247 Z= 0.384 Angle : 0.651 8.884 12534 Z= 0.348 Chirality : 0.047 0.195 1419 Planarity : 0.005 0.059 1578 Dihedral : 5.575 59.005 1264 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.26 % Allowed : 11.62 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1139 helix: 1.10 (0.26), residues: 407 sheet: 0.41 (0.28), residues: 303 loop : -0.83 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.006 0.001 HIS B 91 PHE 0.017 0.002 PHE B 199 TYR 0.018 0.002 TYR S 103 ARG 0.008 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: R 55 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6070 (ppt170) REVERT: R 318 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: R 321 THR cc_start: 0.8058 (m) cc_final: 0.7826 (m) REVERT: A 52 GLN cc_start: 0.5738 (OUTLIER) cc_final: 0.5214 (mt0) REVERT: A 276 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6125 (mt-10) REVERT: A 298 GLU cc_start: 0.7229 (tp30) cc_final: 0.6946 (tp30) REVERT: G 47 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7351 (mp0) REVERT: G 59 ASN cc_start: 0.7830 (t0) cc_final: 0.7467 (t0) REVERT: G 62 ARG cc_start: 0.7058 (mtm-85) cc_final: 0.6670 (mtm-85) REVERT: S 6 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: S 206 ARG cc_start: 0.7284 (mtm110) cc_final: 0.6641 (ptt-90) outliers start: 32 outliers final: 16 residues processed: 182 average time/residue: 1.5292 time to fit residues: 293.7338 Evaluate side-chains 181 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 139 ARG Chi-restraints excluded: chain R residue 180 GLN Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain S residue 6 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 16 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 112 ASN B 340 ASN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.126429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.102985 restraints weight = 13141.385| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.25 r_work: 0.3226 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9247 Z= 0.232 Angle : 0.556 7.653 12534 Z= 0.300 Chirality : 0.043 0.136 1419 Planarity : 0.005 0.056 1578 Dihedral : 5.122 58.283 1260 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.96 % Allowed : 13.25 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1139 helix: 1.62 (0.26), residues: 403 sheet: 0.46 (0.29), residues: 283 loop : -0.72 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE B 199 TYR 0.012 0.001 TYR S 103 ARG 0.008 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 55 ARG cc_start: 0.7702 (mpt180) cc_final: 0.6163 (ppt170) REVERT: A 52 GLN cc_start: 0.5733 (OUTLIER) cc_final: 0.5206 (mt0) REVERT: A 201 VAL cc_start: 0.8612 (p) cc_final: 0.8214 (m) REVERT: A 276 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6122 (mt-10) REVERT: A 298 GLU cc_start: 0.7221 (tp30) cc_final: 0.6877 (tp30) REVERT: B 322 ASP cc_start: 0.8131 (m-30) cc_final: 0.7738 (m-30) REVERT: G 21 MET cc_start: 0.6334 (OUTLIER) cc_final: 0.6027 (ppp) REVERT: G 47 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7298 (mp0) REVERT: G 59 ASN cc_start: 0.7722 (t0) cc_final: 0.7442 (t0) REVERT: G 62 ARG cc_start: 0.7064 (mtm-85) cc_final: 0.6703 (mtm-85) outliers start: 29 outliers final: 17 residues processed: 179 average time/residue: 1.5087 time to fit residues: 285.0412 Evaluate side-chains 179 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 139 ARG Chi-restraints excluded: chain R residue 180 GLN Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 105 optimal weight: 0.4980 chunk 60 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.126553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.103357 restraints weight = 13267.929| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.26 r_work: 0.3229 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9247 Z= 0.226 Angle : 0.548 7.059 12534 Z= 0.294 Chirality : 0.042 0.135 1419 Planarity : 0.005 0.057 1578 Dihedral : 5.033 57.211 1260 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.47 % Allowed : 13.05 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1139 helix: 1.82 (0.26), residues: 401 sheet: 0.53 (0.29), residues: 283 loop : -0.73 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.016 0.002 PHE B 199 TYR 0.012 0.001 TYR S 103 ARG 0.008 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 318 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7460 (mp10) REVERT: A 52 GLN cc_start: 0.5684 (OUTLIER) cc_final: 0.5198 (mt0) REVERT: A 201 VAL cc_start: 0.8516 (p) cc_final: 0.8122 (m) REVERT: A 276 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6059 (mt-10) REVERT: A 298 GLU cc_start: 0.7182 (tp30) cc_final: 0.6856 (tp30) REVERT: B 322 ASP cc_start: 0.8077 (m-30) cc_final: 0.7700 (m-30) REVERT: G 21 MET cc_start: 0.6386 (OUTLIER) cc_final: 0.6086 (ppp) REVERT: G 47 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7269 (mp0) REVERT: G 59 ASN cc_start: 0.7707 (t0) cc_final: 0.7344 (t0) REVERT: G 62 ARG cc_start: 0.7024 (mtm-85) cc_final: 0.6637 (mtm-85) REVERT: S 212 VAL cc_start: 0.8181 (m) cc_final: 0.7875 (t) outliers start: 34 outliers final: 17 residues processed: 181 average time/residue: 1.6139 time to fit residues: 307.9715 Evaluate side-chains 188 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 139 ARG Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 57 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 105 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.125607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.102083 restraints weight = 13130.437| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.29 r_work: 0.3213 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9247 Z= 0.330 Angle : 0.607 6.703 12534 Z= 0.323 Chirality : 0.045 0.143 1419 Planarity : 0.005 0.058 1578 Dihedral : 5.240 58.602 1260 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.57 % Allowed : 14.37 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1139 helix: 1.67 (0.26), residues: 400 sheet: 0.59 (0.28), residues: 304 loop : -0.73 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.006 0.001 HIS B 91 PHE 0.018 0.002 PHE B 199 TYR 0.016 0.002 TYR S 103 ARG 0.009 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: R 55 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.6218 (ppt170) REVERT: R 318 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: A 52 GLN cc_start: 0.5737 (OUTLIER) cc_final: 0.5207 (mt0) REVERT: A 201 VAL cc_start: 0.8618 (p) cc_final: 0.8231 (m) REVERT: A 276 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6109 (mt-10) REVERT: A 298 GLU cc_start: 0.7217 (tp30) cc_final: 0.6898 (tp30) REVERT: A 350 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7697 (t0) REVERT: B 322 ASP cc_start: 0.8124 (m-30) cc_final: 0.7771 (m-30) REVERT: G 47 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7309 (mp0) REVERT: G 62 ARG cc_start: 0.7028 (mtm-85) cc_final: 0.6679 (mtm-85) outliers start: 35 outliers final: 22 residues processed: 186 average time/residue: 1.5538 time to fit residues: 304.1774 Evaluate side-chains 187 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 139 ARG Chi-restraints excluded: chain R residue 180 GLN Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 148 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 43 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 340 ASN G 59 ASN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.126122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.103096 restraints weight = 13307.567| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.25 r_work: 0.3225 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9247 Z= 0.275 Angle : 0.579 6.454 12534 Z= 0.309 Chirality : 0.043 0.139 1419 Planarity : 0.005 0.057 1578 Dihedral : 5.150 57.710 1260 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.36 % Allowed : 14.88 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1139 helix: 1.74 (0.26), residues: 400 sheet: 0.61 (0.28), residues: 304 loop : -0.68 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.018 0.002 PHE B 199 TYR 0.014 0.002 TYR S 103 ARG 0.009 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: R 55 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.6226 (ppt170) REVERT: R 318 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: A 52 GLN cc_start: 0.5724 (OUTLIER) cc_final: 0.5220 (mt0) REVERT: A 201 VAL cc_start: 0.8605 (p) cc_final: 0.8217 (m) REVERT: A 276 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6109 (mt-10) REVERT: A 298 GLU cc_start: 0.7233 (tp30) cc_final: 0.6972 (tp30) REVERT: B 322 ASP cc_start: 0.8103 (m-30) cc_final: 0.7729 (m-30) REVERT: G 47 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7305 (mp0) REVERT: G 59 ASN cc_start: 0.7720 (t0) cc_final: 0.7500 (t0) REVERT: G 62 ARG cc_start: 0.7028 (mtm-85) cc_final: 0.6674 (mtm-85) REVERT: S 6 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7461 (mp0) outliers start: 33 outliers final: 22 residues processed: 184 average time/residue: 1.5271 time to fit residues: 295.8330 Evaluate side-chains 195 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 139 ARG Chi-restraints excluded: chain R residue 180 GLN Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 148 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 106 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN S 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.125449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.101582 restraints weight = 13370.425| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.26 r_work: 0.3198 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9247 Z= 0.321 Angle : 0.608 8.182 12534 Z= 0.323 Chirality : 0.044 0.140 1419 Planarity : 0.005 0.058 1578 Dihedral : 5.285 58.516 1260 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.47 % Allowed : 15.29 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1139 helix: 1.69 (0.26), residues: 400 sheet: 0.60 (0.28), residues: 304 loop : -0.69 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.006 0.001 HIS B 91 PHE 0.019 0.002 PHE B 199 TYR 0.016 0.002 TYR S 103 ARG 0.009 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 318 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7526 (mp10) REVERT: A 52 GLN cc_start: 0.5727 (OUTLIER) cc_final: 0.5207 (mt0) REVERT: A 201 VAL cc_start: 0.8622 (p) cc_final: 0.8233 (m) REVERT: A 276 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6149 (mt-10) REVERT: A 298 GLU cc_start: 0.7276 (tp30) cc_final: 0.7030 (tp30) REVERT: A 350 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7713 (t0) REVERT: B 220 GLN cc_start: 0.8651 (mt0) cc_final: 0.8379 (mt0) REVERT: B 322 ASP cc_start: 0.8152 (m-30) cc_final: 0.7768 (m-30) REVERT: G 47 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7311 (mp0) REVERT: G 62 ARG cc_start: 0.7024 (mtm-85) cc_final: 0.6640 (mtm-85) REVERT: S 6 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7498 (mp0) outliers start: 34 outliers final: 24 residues processed: 186 average time/residue: 1.5568 time to fit residues: 305.1544 Evaluate side-chains 194 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 139 ARG Chi-restraints excluded: chain R residue 180 GLN Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 148 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.127745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.104518 restraints weight = 13265.217| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.08 r_work: 0.3272 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9247 Z= 0.160 Angle : 0.520 6.980 12534 Z= 0.278 Chirality : 0.041 0.127 1419 Planarity : 0.004 0.056 1578 Dihedral : 4.830 52.596 1260 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.75 % Allowed : 16.62 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1139 helix: 1.96 (0.26), residues: 403 sheet: 0.60 (0.29), residues: 284 loop : -0.60 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE B 199 TYR 0.009 0.001 TYR S 178 ARG 0.010 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 272 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6626 (mtm) REVERT: R 318 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7448 (mp10) REVERT: A 201 VAL cc_start: 0.8443 (p) cc_final: 0.8080 (m) REVERT: A 276 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6042 (mt-10) REVERT: A 298 GLU cc_start: 0.7114 (tp30) cc_final: 0.6843 (tp30) REVERT: A 350 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7642 (t0) REVERT: B 40 VAL cc_start: 0.7798 (m) cc_final: 0.7556 (t) REVERT: B 46 ARG cc_start: 0.5939 (mpp-170) cc_final: 0.5620 (mpp-170) REVERT: B 220 GLN cc_start: 0.8654 (mt0) cc_final: 0.8382 (mt0) REVERT: B 322 ASP cc_start: 0.8044 (m-30) cc_final: 0.7674 (m-30) REVERT: G 47 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7317 (mp0) REVERT: G 62 ARG cc_start: 0.7024 (mtm-85) cc_final: 0.6665 (mtm-85) REVERT: S 212 VAL cc_start: 0.8167 (m) cc_final: 0.7864 (t) outliers start: 27 outliers final: 14 residues processed: 187 average time/residue: 1.5166 time to fit residues: 300.8528 Evaluate side-chains 186 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 139 ARG Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain S residue 147 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 30 optimal weight: 0.0870 chunk 77 optimal weight: 7.9990 chunk 50 optimal weight: 0.5980 chunk 110 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 0.0170 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 340 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.128861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.105700 restraints weight = 13470.525| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.11 r_work: 0.3297 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9247 Z= 0.135 Angle : 0.494 6.944 12534 Z= 0.264 Chirality : 0.040 0.123 1419 Planarity : 0.004 0.057 1578 Dihedral : 4.202 27.068 1257 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.14 % Allowed : 17.33 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1139 helix: 2.02 (0.27), residues: 409 sheet: 0.66 (0.30), residues: 282 loop : -0.51 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS L 7 PHE 0.011 0.001 PHE B 199 TYR 0.009 0.001 TYR S 178 ARG 0.009 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 272 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6638 (mtm) REVERT: A 201 VAL cc_start: 0.8432 (p) cc_final: 0.8101 (m) REVERT: A 276 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6198 (mt-10) REVERT: A 298 GLU cc_start: 0.7119 (tp30) cc_final: 0.6820 (tp30) REVERT: A 350 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7619 (t0) REVERT: B 46 ARG cc_start: 0.5929 (mpp-170) cc_final: 0.5614 (mpp-170) REVERT: B 322 ASP cc_start: 0.8071 (m-30) cc_final: 0.7704 (m-30) REVERT: G 47 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7341 (mp0) REVERT: G 59 ASN cc_start: 0.7686 (t0) cc_final: 0.7451 (t0) REVERT: G 62 ARG cc_start: 0.7132 (mtm-85) cc_final: 0.6813 (mtm-85) REVERT: S 212 VAL cc_start: 0.8101 (m) cc_final: 0.7829 (t) outliers start: 21 outliers final: 11 residues processed: 175 average time/residue: 1.5513 time to fit residues: 285.7667 Evaluate side-chains 182 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 139 ARG Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain S residue 147 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.126935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.103674 restraints weight = 13354.096| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.33 r_work: 0.3240 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9247 Z= 0.232 Angle : 0.560 7.088 12534 Z= 0.297 Chirality : 0.042 0.134 1419 Planarity : 0.005 0.057 1578 Dihedral : 4.485 22.214 1257 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.55 % Allowed : 17.13 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1139 helix: 1.99 (0.26), residues: 403 sheet: 0.69 (0.29), residues: 288 loop : -0.48 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.002 PHE A 196 TYR 0.012 0.001 TYR S 103 ARG 0.010 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9685.68 seconds wall clock time: 171 minutes 14.69 seconds (10274.69 seconds total)