Starting phenix.real_space_refine on Wed Feb 4 05:05:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z8b_39844/02_2026/8z8b_39844.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z8b_39844/02_2026/8z8b_39844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z8b_39844/02_2026/8z8b_39844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z8b_39844/02_2026/8z8b_39844.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z8b_39844/02_2026/8z8b_39844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z8b_39844/02_2026/8z8b_39844.map" } resolution = 2.65 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= 0.007 sd= 0.069 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 70 5.16 5 C 5633 2.51 5 N 1517 2.21 5 O 1655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8875 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2218 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 267} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Time building chain proxies: 2.23, per 1000 atoms: 0.25 Number of scatterers: 8875 At special positions: 0 Unit cell: (107.88, 117.18, 116.25, 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 70 16.00 O 1655 8.00 N 1517 7.00 C 5633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 6 " - pdb=" SG CYS R 157 " distance=1.68 Simple disulfide: pdb=" SG CYS R 7 " - pdb=" SG CYS R 252 " distance=2.12 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 165 " distance=2.02 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 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: 0.71 Conformation dependent library (CDL) restraints added in 387.9 milliseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 38.4% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'R' and resid 11 through 43 removed outlier: 3.600A pdb=" N SER R 15 " --> pdb=" O GLY R 11 " (cutoff:3.500A) Proline residue: R 19 - end of helix Processing helix chain 'R' and resid 48 through 67 Processing helix chain 'R' and resid 68 through 77 Processing helix chain 'R' and resid 85 through 118 removed outlier: 3.914A pdb=" N VAL R 109 " --> pdb=" O PHE R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 126 Processing helix chain 'R' and resid 128 through 148 Processing helix chain 'R' and resid 149 through 153 removed outlier: 4.125A pdb=" N GLU R 153 " --> pdb=" O LEU R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 175 No H-bonds generated for 'chain 'R' and resid 173 through 175' Processing helix chain 'R' and resid 176 through 183 Processing helix chain 'R' and resid 185 through 206 Processing helix chain 'R' and resid 206 through 211 removed outlier: 3.807A pdb=" N ARG R 211 " --> pdb=" O GLN R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 246 removed outlier: 3.601A pdb=" N LYS R 216 " --> pdb=" O GLN R 212 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA R 226 " --> pdb=" O ILE R 222 " (cutoff:3.500A) Proline residue: R 235 - end of helix Processing helix chain 'R' and resid 253 through 264 Processing helix chain 'R' and resid 264 through 279 removed outlier: 4.101A pdb=" N TYR R 268 " --> pdb=" O LEU R 264 " (cutoff:3.500A) Proline residue: R 275 - end of helix Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.657A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.561A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.436A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.120A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.752A 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 352 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.679A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.099A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'R' and resid 156 through 158 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 5.970A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.614A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.752A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.730A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.730A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.522A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.378A 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: 3.770A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.107A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.374A 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 11 through 12 removed outlier: 5.959A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.860A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.526A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1236 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: 1.75 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2865 1.34 - 1.46: 2172 1.46 - 1.59: 3928 1.59 - 1.71: 0 1.71 - 1.83: 101 Bond restraints: 9066 Sorted by residual: bond pdb=" N CYS R 7 " pdb=" CA CYS R 7 " ideal model delta sigma weight residual 1.454 1.507 -0.053 1.23e-02 6.61e+03 1.88e+01 bond pdb=" N ILE R 9 " pdb=" CA ILE R 9 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.20e-02 6.94e+03 8.69e+00 bond pdb=" N LYS A 330 " pdb=" CA LYS A 330 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.44e-02 4.82e+03 7.33e+00 bond pdb=" N THR A 329 " pdb=" CA THR A 329 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.26e-02 6.30e+03 7.28e+00 bond pdb=" N ILE R 262 " pdb=" CA ILE R 262 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.21e-02 6.83e+03 7.12e+00 ... (remaining 9061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 11732 1.62 - 3.23: 442 3.23 - 4.85: 79 4.85 - 6.46: 22 6.46 - 8.08: 5 Bond angle restraints: 12280 Sorted by residual: angle pdb=" C CYS R 252 " pdb=" CA CYS R 252 " pdb=" CB CYS R 252 " ideal model delta sigma weight residual 111.80 118.87 -7.07 1.46e+00 4.69e-01 2.34e+01 angle pdb=" N GLU R 184 " pdb=" CA GLU R 184 " pdb=" C GLU R 184 " ideal model delta sigma weight residual 113.38 107.73 5.65 1.23e+00 6.61e-01 2.11e+01 angle pdb=" N PHE R 185 " pdb=" CA PHE R 185 " pdb=" C PHE R 185 " ideal model delta sigma weight residual 114.31 108.55 5.76 1.29e+00 6.01e-01 1.99e+01 angle pdb=" CA CYS R 7 " pdb=" C CYS R 7 " pdb=" O CYS R 7 " ideal model delta sigma weight residual 121.46 116.73 4.73 1.17e+00 7.31e-01 1.64e+01 angle pdb=" N THR R 13 " pdb=" CA THR R 13 " pdb=" C THR R 13 " ideal model delta sigma weight residual 111.33 106.53 4.80 1.21e+00 6.83e-01 1.57e+01 ... (remaining 12275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 4879 17.15 - 34.30: 402 34.30 - 51.44: 83 51.44 - 68.59: 9 68.59 - 85.74: 9 Dihedral angle restraints: 5382 sinusoidal: 2087 harmonic: 3295 Sorted by residual: dihedral pdb=" CA SER R 172 " pdb=" C SER R 172 " pdb=" N ALA R 173 " pdb=" CA ALA R 173 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA PHE R 105 " pdb=" C PHE R 105 " pdb=" N LEU R 106 " pdb=" CA LEU R 106 " ideal model delta harmonic sigma weight residual 180.00 156.53 23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CB CYS R 6 " pdb=" SG CYS R 6 " pdb=" SG CYS R 157 " pdb=" CB CYS R 157 " ideal model delta sinusoidal sigma weight residual 93.00 128.90 -35.90 1 1.00e+01 1.00e-02 1.82e+01 ... (remaining 5379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 999 0.049 - 0.097: 297 0.097 - 0.145: 76 0.145 - 0.194: 8 0.194 - 0.242: 4 Chirality restraints: 1384 Sorted by residual: chirality pdb=" CA CYS R 7 " pdb=" N CYS R 7 " pdb=" C CYS R 7 " pdb=" CB CYS R 7 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ASP R 12 " pdb=" N ASP R 12 " pdb=" C ASP R 12 " pdb=" CB ASP R 12 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA CYS R 252 " pdb=" N CYS R 252 " pdb=" C CYS R 252 " pdb=" CB CYS R 252 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1381 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO S 75 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 6 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C CYS R 6 " 0.051 2.00e-02 2.50e+03 pdb=" O CYS R 6 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS R 7 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO B 236 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.031 5.00e-02 4.00e+02 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1737 2.77 - 3.31: 8238 3.31 - 3.84: 15461 3.84 - 4.37: 18382 4.37 - 4.90: 31740 Nonbonded interactions: 75558 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.243 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.256 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.301 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.310 3.040 nonbonded pdb=" NH2 ARG S 180 " pdb=" OE2 GLU S 222 " model vdw 2.312 3.120 ... (remaining 75553 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: 0.790 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.280 Find NCS groups from input model: 0.040 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:8.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 : 0.007 0.355 9071 Z= 0.338 Angle : 0.892 38.238 12290 Z= 0.501 Chirality : 0.050 0.242 1384 Planarity : 0.005 0.075 1560 Dihedral : 13.192 85.737 3241 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.41 % Allowed : 0.62 % Favored : 98.96 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.25), residues: 1123 helix: 0.40 (0.26), residues: 388 sheet: 0.09 (0.30), residues: 280 loop : -0.48 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 46 TYR 0.025 0.002 TYR S 190 PHE 0.021 0.002 PHE R 105 TRP 0.027 0.002 TRP R 201 HIS 0.006 0.001 HIS R 257 Details of bonding type rmsd covalent geometry : bond 0.00562 ( 9066) covalent geometry : angle 0.73782 (12280) SS BOND : bond 0.16334 ( 5) SS BOND : angle 17.60481 ( 10) hydrogen bonds : bond 0.18291 ( 443) hydrogen bonds : angle 7.23346 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 185 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 256 ARG cc_start: 0.7875 (mpp80) cc_final: 0.7632 (mtm180) REVERT: S 86 LEU cc_start: 0.8894 (mt) cc_final: 0.8687 (mt) outliers start: 4 outliers final: 1 residues processed: 188 average time/residue: 0.7677 time to fit residues: 151.7014 Evaluate side-chains 145 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.121629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.090404 restraints weight = 15713.792| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.41 r_work: 0.3241 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9071 Z= 0.208 Angle : 0.630 8.495 12290 Z= 0.335 Chirality : 0.046 0.224 1384 Planarity : 0.005 0.069 1560 Dihedral : 4.688 33.455 1232 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.18 % Allowed : 11.51 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.25), residues: 1123 helix: 1.44 (0.27), residues: 390 sheet: 0.43 (0.29), residues: 289 loop : -0.50 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 99 TYR 0.034 0.002 TYR S 190 PHE 0.016 0.002 PHE B 234 TRP 0.016 0.002 TRP R 201 HIS 0.008 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 9066) covalent geometry : angle 0.62875 (12280) SS BOND : bond 0.00317 ( 5) SS BOND : angle 1.36105 ( 10) hydrogen bonds : bond 0.04769 ( 443) hydrogen bonds : angle 5.00723 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 62 PHE cc_start: 0.8587 (t80) cc_final: 0.8226 (t80) REVERT: R 184 GLU cc_start: 0.7434 (tt0) cc_final: 0.7179 (tt0) REVERT: B 96 ARG cc_start: 0.8454 (mpt-90) cc_final: 0.8069 (mpt-90) REVERT: B 138 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8263 (mt-10) REVERT: B 197 ARG cc_start: 0.8396 (tpp-160) cc_final: 0.7980 (mmt180) REVERT: G 52 THR cc_start: 0.8531 (m) cc_final: 0.8143 (p) REVERT: S 83 MET cc_start: 0.8608 (mtp) cc_final: 0.8407 (mtm) REVERT: S 158 SER cc_start: 0.9068 (t) cc_final: 0.8846 (p) REVERT: S 202 ARG cc_start: 0.8273 (ptt-90) cc_final: 0.7803 (ptt-90) REVERT: S 218 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7819 (mtm-85) REVERT: S 219 LEU cc_start: 0.8207 (tt) cc_final: 0.7820 (pp) REVERT: S 223 ASP cc_start: 0.8185 (m-30) cc_final: 0.7877 (m-30) outliers start: 21 outliers final: 7 residues processed: 158 average time/residue: 0.7714 time to fit residues: 128.3329 Evaluate side-chains 144 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 176 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.121115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.090036 restraints weight = 15584.544| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.37 r_work: 0.3229 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9071 Z= 0.176 Angle : 0.567 8.170 12290 Z= 0.304 Chirality : 0.043 0.201 1384 Planarity : 0.004 0.066 1560 Dihedral : 4.406 28.128 1230 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.87 % Allowed : 13.69 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.26), residues: 1123 helix: 1.79 (0.27), residues: 384 sheet: 0.53 (0.30), residues: 291 loop : -0.44 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.030 0.002 TYR S 190 PHE 0.013 0.001 PHE B 234 TRP 0.012 0.002 TRP B 169 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9066) covalent geometry : angle 0.56650 (12280) SS BOND : bond 0.00495 ( 5) SS BOND : angle 1.02702 ( 10) hydrogen bonds : bond 0.04366 ( 443) hydrogen bonds : angle 4.78463 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 45 LYS cc_start: 0.8256 (mmpt) cc_final: 0.7992 (mmpt) REVERT: R 215 MET cc_start: 0.7294 (mpp) cc_final: 0.7087 (mmp) REVERT: A 228 SER cc_start: 0.8705 (m) cc_final: 0.8412 (p) REVERT: A 295 THR cc_start: 0.7399 (p) cc_final: 0.7003 (t) REVERT: B 197 ARG cc_start: 0.8451 (tpp-160) cc_final: 0.8012 (mmt180) REVERT: B 254 ASP cc_start: 0.8333 (p0) cc_final: 0.8095 (p0) REVERT: S 158 SER cc_start: 0.9079 (t) cc_final: 0.8863 (p) REVERT: S 202 ARG cc_start: 0.8233 (ptt-90) cc_final: 0.7572 (ptt-90) REVERT: S 218 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7843 (mtm-85) REVERT: S 219 LEU cc_start: 0.8275 (tt) cc_final: 0.7693 (pp) REVERT: S 223 ASP cc_start: 0.8156 (m-30) cc_final: 0.7665 (m-30) outliers start: 18 outliers final: 9 residues processed: 153 average time/residue: 0.7731 time to fit residues: 124.4614 Evaluate side-chains 141 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 154 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.121389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.090849 restraints weight = 15593.136| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.34 r_work: 0.3248 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9071 Z= 0.141 Angle : 0.550 9.685 12290 Z= 0.290 Chirality : 0.042 0.188 1384 Planarity : 0.004 0.063 1560 Dihedral : 4.263 27.942 1230 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.56 % Allowed : 15.46 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.26), residues: 1123 helix: 1.94 (0.27), residues: 383 sheet: 0.42 (0.29), residues: 291 loop : -0.35 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 99 TYR 0.028 0.001 TYR S 190 PHE 0.010 0.001 PHE B 234 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9066) covalent geometry : angle 0.54917 (12280) SS BOND : bond 0.00397 ( 5) SS BOND : angle 1.04704 ( 10) hydrogen bonds : bond 0.03821 ( 443) hydrogen bonds : angle 4.61085 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: R 45 LYS cc_start: 0.8185 (mmpt) cc_final: 0.7949 (mmpt) REVERT: R 62 PHE cc_start: 0.8594 (t80) cc_final: 0.8184 (t80) REVERT: R 184 GLU cc_start: 0.7345 (tt0) cc_final: 0.7123 (tt0) REVERT: A 228 SER cc_start: 0.8801 (m) cc_final: 0.8579 (p) REVERT: A 247 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8180 (mtt) REVERT: B 96 ARG cc_start: 0.8494 (mtt180) cc_final: 0.8186 (mpt-90) REVERT: B 138 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8168 (mt-10) REVERT: B 197 ARG cc_start: 0.8435 (tpp-160) cc_final: 0.8032 (mmt180) REVERT: B 254 ASP cc_start: 0.8364 (p0) cc_final: 0.8097 (p0) REVERT: S 46 GLU cc_start: 0.8399 (tt0) cc_final: 0.7970 (pt0) REVERT: S 158 SER cc_start: 0.9085 (t) cc_final: 0.8831 (p) REVERT: S 202 ARG cc_start: 0.8316 (ptt-90) cc_final: 0.7649 (ptt-90) REVERT: S 218 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7811 (mtm-85) outliers start: 15 outliers final: 9 residues processed: 148 average time/residue: 0.7443 time to fit residues: 116.0215 Evaluate side-chains 144 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 154 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.120844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.090468 restraints weight = 15555.745| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.32 r_work: 0.3242 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9071 Z= 0.146 Angle : 0.546 8.115 12290 Z= 0.289 Chirality : 0.042 0.191 1384 Planarity : 0.004 0.062 1560 Dihedral : 4.195 27.920 1230 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.59 % Allowed : 15.66 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.26), residues: 1123 helix: 2.06 (0.27), residues: 383 sheet: 0.40 (0.29), residues: 291 loop : -0.29 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 77 TYR 0.029 0.002 TYR S 190 PHE 0.011 0.001 PHE B 151 TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9066) covalent geometry : angle 0.54556 (12280) SS BOND : bond 0.00467 ( 5) SS BOND : angle 0.91891 ( 10) hydrogen bonds : bond 0.03792 ( 443) hydrogen bonds : angle 4.55877 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 45 LYS cc_start: 0.8195 (mmpt) cc_final: 0.7994 (mmpt) REVERT: R 62 PHE cc_start: 0.8602 (t80) cc_final: 0.8173 (t80) REVERT: A 247 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8216 (mtt) REVERT: B 197 ARG cc_start: 0.8433 (tpp-160) cc_final: 0.8007 (mmt180) REVERT: B 217 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8025 (pmm) REVERT: B 254 ASP cc_start: 0.8402 (p0) cc_final: 0.8099 (p0) REVERT: S 46 GLU cc_start: 0.8394 (tt0) cc_final: 0.7979 (pt0) REVERT: S 158 SER cc_start: 0.9083 (t) cc_final: 0.8822 (p) REVERT: S 202 ARG cc_start: 0.8343 (ptt-90) cc_final: 0.8020 (ptt-90) REVERT: S 219 LEU cc_start: 0.8338 (tt) cc_final: 0.7881 (pp) REVERT: S 223 ASP cc_start: 0.8169 (m-30) cc_final: 0.7934 (m-30) outliers start: 25 outliers final: 11 residues processed: 152 average time/residue: 0.7118 time to fit residues: 114.4757 Evaluate side-chains 153 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 186 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN G 59 ASN S 167 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.120186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.089707 restraints weight = 15473.575| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.33 r_work: 0.3227 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9071 Z= 0.163 Angle : 0.567 10.795 12290 Z= 0.297 Chirality : 0.043 0.200 1384 Planarity : 0.004 0.062 1560 Dihedral : 4.256 28.125 1230 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.80 % Allowed : 15.46 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.26), residues: 1123 helix: 2.06 (0.27), residues: 383 sheet: 0.47 (0.29), residues: 287 loop : -0.30 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 62 TYR 0.031 0.001 TYR S 190 PHE 0.011 0.001 PHE S 110 TRP 0.012 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9066) covalent geometry : angle 0.56708 (12280) SS BOND : bond 0.00419 ( 5) SS BOND : angle 0.94504 ( 10) hydrogen bonds : bond 0.03897 ( 443) hydrogen bonds : angle 4.55834 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 45 LYS cc_start: 0.8252 (mmpt) cc_final: 0.7880 (mmpt) REVERT: R 62 PHE cc_start: 0.8605 (t80) cc_final: 0.8167 (t80) REVERT: A 247 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8230 (mtt) REVERT: B 197 ARG cc_start: 0.8431 (tpp-160) cc_final: 0.7877 (mmt180) REVERT: B 254 ASP cc_start: 0.8382 (p0) cc_final: 0.8080 (p0) REVERT: S 46 GLU cc_start: 0.8429 (tt0) cc_final: 0.8033 (pt0) REVERT: S 158 SER cc_start: 0.9102 (t) cc_final: 0.8853 (p) REVERT: S 202 ARG cc_start: 0.8405 (ptt-90) cc_final: 0.8082 (ptt-90) REVERT: S 219 LEU cc_start: 0.8436 (tt) cc_final: 0.7940 (pp) REVERT: S 223 ASP cc_start: 0.8229 (m-30) cc_final: 0.7981 (m-30) outliers start: 27 outliers final: 15 residues processed: 150 average time/residue: 0.7373 time to fit residues: 116.6115 Evaluate side-chains 150 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 195 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 91 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.120112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.089723 restraints weight = 15646.340| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.31 r_work: 0.3227 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9071 Z= 0.159 Angle : 0.562 9.763 12290 Z= 0.295 Chirality : 0.043 0.197 1384 Planarity : 0.004 0.062 1560 Dihedral : 4.230 28.041 1230 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.39 % Allowed : 16.80 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.26), residues: 1123 helix: 2.16 (0.27), residues: 382 sheet: 0.48 (0.29), residues: 287 loop : -0.28 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 77 TYR 0.031 0.002 TYR S 190 PHE 0.012 0.001 PHE B 151 TRP 0.011 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9066) covalent geometry : angle 0.56159 (12280) SS BOND : bond 0.00379 ( 5) SS BOND : angle 0.98271 ( 10) hydrogen bonds : bond 0.03836 ( 443) hydrogen bonds : angle 4.55687 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 62 PHE cc_start: 0.8615 (t80) cc_final: 0.8221 (t80) REVERT: B 197 ARG cc_start: 0.8406 (tpp-160) cc_final: 0.8011 (mmt180) REVERT: B 254 ASP cc_start: 0.8388 (p0) cc_final: 0.8085 (p0) REVERT: G 42 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7998 (mm-30) REVERT: S 46 GLU cc_start: 0.8436 (tt0) cc_final: 0.8024 (pt0) REVERT: S 158 SER cc_start: 0.9093 (t) cc_final: 0.8836 (p) REVERT: S 202 ARG cc_start: 0.8443 (ptt-90) cc_final: 0.7920 (ptt-90) REVERT: S 219 LEU cc_start: 0.8476 (tt) cc_final: 0.7925 (pp) REVERT: S 223 ASP cc_start: 0.8271 (m-30) cc_final: 0.7902 (m-30) outliers start: 23 outliers final: 17 residues processed: 143 average time/residue: 0.7290 time to fit residues: 109.9524 Evaluate side-chains 151 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 195 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 100 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.120817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.090607 restraints weight = 15533.102| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.33 r_work: 0.3245 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9071 Z= 0.124 Angle : 0.547 11.117 12290 Z= 0.284 Chirality : 0.042 0.182 1384 Planarity : 0.004 0.061 1560 Dihedral : 4.121 27.679 1230 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.76 % Allowed : 17.74 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.26), residues: 1123 helix: 2.24 (0.27), residues: 384 sheet: 0.47 (0.29), residues: 287 loop : -0.24 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 62 TYR 0.028 0.001 TYR S 190 PHE 0.011 0.001 PHE B 151 TRP 0.010 0.001 TRP B 297 HIS 0.003 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9066) covalent geometry : angle 0.54642 (12280) SS BOND : bond 0.00325 ( 5) SS BOND : angle 0.95764 ( 10) hydrogen bonds : bond 0.03541 ( 443) hydrogen bonds : angle 4.47617 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 62 PHE cc_start: 0.8546 (t80) cc_final: 0.8121 (t80) REVERT: R 78 ARG cc_start: 0.8298 (mpp-170) cc_final: 0.7910 (mtm-85) REVERT: B 197 ARG cc_start: 0.8418 (tpp-160) cc_final: 0.8013 (mmt180) REVERT: B 254 ASP cc_start: 0.8348 (p0) cc_final: 0.8058 (p0) REVERT: G 42 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7986 (mm-30) REVERT: S 46 GLU cc_start: 0.8470 (tt0) cc_final: 0.8009 (pt0) REVERT: S 158 SER cc_start: 0.9089 (t) cc_final: 0.8824 (p) REVERT: S 202 ARG cc_start: 0.8358 (ptt-90) cc_final: 0.7827 (ptt-90) REVERT: S 219 LEU cc_start: 0.8382 (tt) cc_final: 0.7806 (pp) REVERT: S 223 ASP cc_start: 0.8211 (m-30) cc_final: 0.7809 (m-30) outliers start: 17 outliers final: 12 residues processed: 150 average time/residue: 0.7017 time to fit residues: 111.2642 Evaluate side-chains 148 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.120962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.090846 restraints weight = 15569.615| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.33 r_work: 0.3251 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9071 Z= 0.118 Angle : 0.538 10.098 12290 Z= 0.280 Chirality : 0.042 0.179 1384 Planarity : 0.004 0.061 1560 Dihedral : 4.069 27.508 1230 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.14 % Allowed : 18.46 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.26), residues: 1123 helix: 2.36 (0.27), residues: 379 sheet: 0.45 (0.29), residues: 286 loop : -0.26 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 62 TYR 0.028 0.001 TYR S 190 PHE 0.010 0.001 PHE B 151 TRP 0.011 0.001 TRP B 63 HIS 0.003 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9066) covalent geometry : angle 0.53787 (12280) SS BOND : bond 0.00270 ( 5) SS BOND : angle 1.01035 ( 10) hydrogen bonds : bond 0.03455 ( 443) hydrogen bonds : angle 4.46559 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 62 PHE cc_start: 0.8586 (t80) cc_final: 0.8206 (t80) REVERT: B 197 ARG cc_start: 0.8402 (tpp-160) cc_final: 0.7995 (mmt180) REVERT: B 254 ASP cc_start: 0.8350 (p0) cc_final: 0.8060 (p0) REVERT: G 42 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7951 (mm-30) REVERT: S 46 GLU cc_start: 0.8465 (tt0) cc_final: 0.8007 (pt0) REVERT: S 158 SER cc_start: 0.9124 (t) cc_final: 0.8832 (p) REVERT: S 202 ARG cc_start: 0.8392 (ptt-90) cc_final: 0.7860 (ptt-90) REVERT: S 219 LEU cc_start: 0.8417 (tt) cc_final: 0.7852 (pp) REVERT: S 223 ASP cc_start: 0.8235 (m-30) cc_final: 0.7826 (m-30) outliers start: 11 outliers final: 9 residues processed: 146 average time/residue: 0.6552 time to fit residues: 101.1392 Evaluate side-chains 145 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 87 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.120606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.090664 restraints weight = 15768.360| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.36 r_work: 0.3253 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9071 Z= 0.115 Angle : 0.546 9.337 12290 Z= 0.284 Chirality : 0.042 0.177 1384 Planarity : 0.004 0.057 1560 Dihedral : 4.054 27.238 1230 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.14 % Allowed : 18.78 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.26), residues: 1123 helix: 2.33 (0.27), residues: 382 sheet: 0.47 (0.29), residues: 285 loop : -0.24 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 62 TYR 0.027 0.001 TYR S 190 PHE 0.010 0.001 PHE B 151 TRP 0.011 0.001 TRP R 245 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9066) covalent geometry : angle 0.54516 (12280) SS BOND : bond 0.00285 ( 5) SS BOND : angle 1.08747 ( 10) hydrogen bonds : bond 0.03371 ( 443) hydrogen bonds : angle 4.42574 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: R 62 PHE cc_start: 0.8576 (t80) cc_final: 0.8184 (t80) REVERT: R 78 ARG cc_start: 0.8330 (mpp-170) cc_final: 0.7933 (mtm-85) REVERT: B 197 ARG cc_start: 0.8385 (tpp-160) cc_final: 0.7936 (mmt180) REVERT: B 254 ASP cc_start: 0.8383 (p0) cc_final: 0.8092 (p0) REVERT: G 42 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7963 (mm-30) REVERT: S 46 GLU cc_start: 0.8537 (tt0) cc_final: 0.8070 (pt0) REVERT: S 158 SER cc_start: 0.9114 (t) cc_final: 0.8828 (p) REVERT: S 219 LEU cc_start: 0.8463 (tt) cc_final: 0.7929 (pp) outliers start: 11 outliers final: 9 residues processed: 141 average time/residue: 0.6723 time to fit residues: 100.0028 Evaluate side-chains 142 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.120991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.090595 restraints weight = 15473.047| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.35 r_work: 0.3243 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9071 Z= 0.132 Angle : 0.559 11.364 12290 Z= 0.290 Chirality : 0.042 0.184 1384 Planarity : 0.004 0.058 1560 Dihedral : 4.095 27.341 1230 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.35 % Allowed : 18.57 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.26), residues: 1123 helix: 2.27 (0.27), residues: 387 sheet: 0.47 (0.29), residues: 286 loop : -0.23 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 77 TYR 0.032 0.001 TYR S 190 PHE 0.010 0.001 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9066) covalent geometry : angle 0.55863 (12280) SS BOND : bond 0.00297 ( 5) SS BOND : angle 1.17401 ( 10) hydrogen bonds : bond 0.03500 ( 443) hydrogen bonds : angle 4.41865 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4740.00 seconds wall clock time: 81 minutes 29.44 seconds (4889.44 seconds total)