Starting phenix.real_space_refine on Thu Jul 2 16:16:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7na7_24267/07_2026/7na7_24267.cif Found real_map, /net/cci-nas-00/data/ceres_data/7na7_24267/07_2026/7na7_24267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7na7_24267/07_2026/7na7_24267.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7na7_24267/07_2026/7na7_24267.cif" model { file = "/net/cci-nas-00/data/ceres_data/7na7_24267/07_2026/7na7_24267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7na7_24267/07_2026/7na7_24267.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7na7_24267/07_2026/7na7_24267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7na7_24267/07_2026/7na7_24267.map" } resolution = 2.7 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= 0.001 sd= 0.023 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 62 5.16 5 C 5786 2.51 5 N 1526 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9036 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1752 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "N" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2339 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 1 Chain: "L" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'1IC:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.91, per 1000 atoms: 0.21 Number of scatterers: 9036 At special positions: 0 Unit cell: (87.75, 120.25, 124.8, 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 62 16.00 O 1662 8.00 N 1526 7.00 C 5786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 159 " - pdb=" SG CYS N 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 198 " 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: 0.91 Conformation dependent library (CDL) restraints added in 329.5 milliseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 1IC L 3 " Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 38.0% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.587A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.359A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.017A 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 242 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.699A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.697A 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 328 through 352 Processing helix chain 'B' and resid 7 through 22 removed outlier: 3.545A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 30 through 44 removed outlier: 4.444A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 40 through 71 removed outlier: 4.142A pdb=" N ALA R 44 " --> pdb=" O ALA R 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 75 Processing helix chain 'R' and resid 76 through 95 Processing helix chain 'R' and resid 95 through 105 Processing helix chain 'R' and resid 112 through 147 removed outlier: 3.713A pdb=" N GLN R 120 " --> pdb=" O CYS R 116 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER R 123 " --> pdb=" O PHE R 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR R 128 " --> pdb=" O GLU R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 155 removed outlier: 3.607A pdb=" N VAL R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 176 removed outlier: 3.570A pdb=" N LEU R 162 " --> pdb=" O GLY R 158 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL R 163 " --> pdb=" O ARG R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 182 Processing helix chain 'R' and resid 191 through 196 removed outlier: 3.771A pdb=" N THR R 195 " --> pdb=" O ASP R 191 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN R 196 " --> pdb=" O PRO R 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 191 through 196' Processing helix chain 'R' and resid 202 through 207 Processing helix chain 'R' and resid 208 through 243 removed outlier: 3.512A pdb=" N SER R 218 " --> pdb=" O VAL R 214 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE R 219 " --> pdb=" O TRP R 215 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE R 220 " --> pdb=" O VAL R 216 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) Proline residue: R 224 - end of helix removed outlier: 3.509A pdb=" N ARG R 243 " --> pdb=" O LEU R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 290 Proline residue: R 278 - end of helix removed outlier: 3.757A pdb=" N PHE R 290 " --> pdb=" O PHE R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 325 removed outlier: 4.074A pdb=" N GLN R 299 " --> pdb=" O LEU R 295 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN R 302 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA R 316 " --> pdb=" O PHE R 312 " (cutoff:3.500A) Proline residue: R 320 - end of helix Processing helix chain 'R' and resid 327 through 338 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.172A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.544A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.518A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.733A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.765A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.659A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.649A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.010A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.802A pdb=" N MET N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 4.223A pdb=" N PHE N 110 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'N' and resid 146 through 148 removed outlier: 6.345A pdb=" N LEU N 174 " --> pdb=" O TYR N 190 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR N 190 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP N 176 " --> pdb=" O LEU N 188 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1230 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: 1.65 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1446 1.30 - 1.43: 2481 1.43 - 1.56: 5218 1.56 - 1.69: 0 1.69 - 1.82: 88 Bond restraints: 9233 Sorted by residual: bond pdb=" CA SER N 106 " pdb=" CB SER N 106 " ideal model delta sigma weight residual 1.531 1.449 0.082 1.22e-02 6.72e+03 4.51e+01 bond pdb=" C PRO N 107 " pdb=" O PRO N 107 " ideal model delta sigma weight residual 1.234 1.169 0.064 1.14e-02 7.69e+03 3.17e+01 bond pdb=" CA SER N 105 " pdb=" CB SER N 105 " ideal model delta sigma weight residual 1.529 1.447 0.082 1.61e-02 3.86e+03 2.62e+01 bond pdb=" C LEU N 174 " pdb=" O LEU N 174 " ideal model delta sigma weight residual 1.236 1.177 0.058 1.14e-02 7.69e+03 2.62e+01 bond pdb=" C TYR N 175 " pdb=" O TYR N 175 " ideal model delta sigma weight residual 1.234 1.185 0.048 1.17e-02 7.31e+03 1.71e+01 ... (remaining 9228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 12259 3.26 - 6.51: 225 6.51 - 9.77: 19 9.77 - 13.03: 2 13.03 - 16.28: 2 Bond angle restraints: 12507 Sorted by residual: angle pdb=" C 1IC L 3 " pdb=" CA 1IC L 3 " pdb=" CB 1IC L 3 " ideal model delta sigma weight residual 110.50 126.38 -15.88 1.50e+00 4.44e-01 1.12e+02 angle pdb=" C GLN R 302 " pdb=" CA GLN R 302 " pdb=" CB GLN R 302 " ideal model delta sigma weight residual 110.63 126.91 -16.28 1.85e+00 2.92e-01 7.75e+01 angle pdb=" N GLU A 8 " pdb=" CA GLU A 8 " pdb=" C GLU A 8 " ideal model delta sigma weight residual 112.92 103.28 9.64 1.23e+00 6.61e-01 6.14e+01 angle pdb=" C ARG N 191 " pdb=" CA ARG N 191 " pdb=" CB ARG N 191 " ideal model delta sigma weight residual 111.80 122.64 -10.84 1.46e+00 4.69e-01 5.51e+01 angle pdb=" N LEU R 103 " pdb=" CA LEU R 103 " pdb=" C LEU R 103 " ideal model delta sigma weight residual 113.01 105.72 7.29 1.20e+00 6.94e-01 3.69e+01 ... (remaining 12502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.26: 5155 22.26 - 44.51: 273 44.51 - 66.77: 23 66.77 - 89.03: 5 89.03 - 111.28: 1 Dihedral angle restraints: 5457 sinusoidal: 2154 harmonic: 3303 Sorted by residual: dihedral pdb=" C GLN R 302 " pdb=" N GLN R 302 " pdb=" CA GLN R 302 " pdb=" CB GLN R 302 " ideal model delta harmonic sigma weight residual -122.60 -141.66 19.06 0 2.50e+00 1.60e-01 5.81e+01 dihedral pdb=" C ARG N 191 " pdb=" N ARG N 191 " pdb=" CA ARG N 191 " pdb=" CB ARG N 191 " ideal model delta harmonic sigma weight residual -122.60 -140.00 17.40 0 2.50e+00 1.60e-01 4.84e+01 dihedral pdb=" C ASN R 305 " pdb=" N ASN R 305 " pdb=" CA ASN R 305 " pdb=" CB ASN R 305 " ideal model delta harmonic sigma weight residual -122.60 -137.94 15.34 0 2.50e+00 1.60e-01 3.76e+01 ... (remaining 5454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.166: 1416 1.166 - 2.333: 0 2.333 - 3.499: 0 3.499 - 4.665: 0 4.665 - 5.831: 2 Chirality restraints: 1418 Sorted by residual: chirality pdb=" C13 CLR R 402 " pdb=" C12 CLR R 402 " pdb=" C14 CLR R 402 " pdb=" C17 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.93 2.90 -5.83 2.00e-01 2.50e+01 8.50e+02 chirality pdb=" C17 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C16 CLR R 402 " pdb=" C20 CLR R 402 " both_signs ideal model delta sigma weight residual False 2.55 -2.63 5.18 2.00e-01 2.50e+01 6.72e+02 chirality pdb=" CA 1IC L 3 " pdb=" N 1IC L 3 " pdb=" C 1IC L 3 " pdb=" CB 1IC L 3 " both_signs ideal model delta sigma weight residual False -2.48 -1.84 -0.65 2.00e-01 2.50e+01 1.04e+01 ... (remaining 1415 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU N 174 " 0.026 2.00e-02 2.50e+03 5.27e-02 2.78e+01 pdb=" C LEU N 174 " -0.091 2.00e-02 2.50e+03 pdb=" O LEU N 174 " 0.035 2.00e-02 2.50e+03 pdb=" N TYR N 175 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 6 " -0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C SER A 6 " 0.075 2.00e-02 2.50e+03 pdb=" O SER A 6 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA A 7 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL N 147 " -0.047 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO N 148 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO N 148 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO N 148 " -0.039 5.00e-02 4.00e+02 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 566 2.72 - 3.27: 8743 3.27 - 3.81: 14984 3.81 - 4.36: 19413 4.36 - 4.90: 33264 Nonbonded interactions: 76970 Sorted by model distance: nonbonded pdb=" OG1 THR R 76 " pdb=" OD1 ASN R 79 " model vdw 2.178 3.040 nonbonded pdb=" O GLY R 57 " pdb=" ND2 ASN R 61 " model vdw 2.250 3.120 nonbonded pdb=" O MET G 38 " pdb=" OE1 GLU G 42 " model vdw 2.277 3.040 nonbonded pdb=" O PRO R 192 " pdb=" OD1 ASN R 196 " model vdw 2.284 3.040 nonbonded pdb=" O PHE N 32 " pdb=" NH2 ARG N 72 " model vdw 2.322 3.120 ... (remaining 76965 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: 4.290 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: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.600 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.006 0.082 9236 Z= 0.382 Angle : 1.043 16.282 12513 Z= 0.655 Chirality : 0.218 5.831 1418 Planarity : 0.006 0.071 1566 Dihedral : 12.925 111.283 3316 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.61 % Allowed : 3.98 % Favored : 95.41 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 3.03 % 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: 0.32 (0.23), residues: 1119 helix: 0.86 (0.26), residues: 388 sheet: 0.67 (0.28), residues: 298 loop : -0.62 (0.26), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 214 TYR 0.034 0.003 TYR N 102 PHE 0.019 0.002 PHE R 179 TRP 0.017 0.002 TRP N 176 HIS 0.008 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.38 ( 9233) covalent geometry : angle 1.04259 / 0.65 (12507) SS BOND : bond 0.00460 / 0.23 ( 3) SS BOND : angle 1.09701 / 0.42 ( 6) hydrogen bonds : bond 0.17976 / 12.03 ( 437) hydrogen bonds : angle 6.76181 / 4.76 ( 1230) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 237 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7165 (m-30) cc_final: 0.6770 (m-30) REVERT: A 186 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6501 (mt-10) REVERT: A 245 GLU cc_start: 0.6504 (tp30) cc_final: 0.6069 (tp30) REVERT: A 316 THR cc_start: 0.8443 (m) cc_final: 0.8046 (p) REVERT: B 137 ARG cc_start: 0.7770 (tpp-160) cc_final: 0.7519 (tpt90) REVERT: N 150 THR cc_start: 0.8011 (t) cc_final: 0.7784 (p) REVERT: R 237 ARG cc_start: 0.7084 (ttp80) cc_final: 0.6751 (ttp80) REVERT: R 283 ARG cc_start: 0.6910 (mtp85) cc_final: 0.6671 (mtt-85) REVERT: R 327 SER cc_start: 0.7871 (t) cc_final: 0.7481 (p) REVERT: L 10 GLN cc_start: 0.5134 (mt0) cc_final: 0.4931 (pm20) outliers start: 6 outliers final: 0 residues processed: 241 average time/residue: 0.4931 time to fit residues: 127.7841 Evaluate side-chains 205 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 230 ASN B 295 ASN N 82 GLN N 142 GLN N 179 GLN N 183 GLN R 120 GLN R 302 GLN R 319 ASN L 9 HIS L 10 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.123655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.111290 restraints weight = 12817.178| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.49 r_work: 0.3369 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9236 Z= 0.164 Angle : 0.781 31.245 12513 Z= 0.364 Chirality : 0.065 1.786 1418 Planarity : 0.005 0.051 1566 Dihedral : 5.042 25.293 1263 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.55 % Allowed : 13.35 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.65 (0.24), residues: 1119 helix: 1.22 (0.26), residues: 397 sheet: 0.76 (0.28), residues: 295 loop : -0.48 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 202 TYR 0.023 0.002 TYR N 190 PHE 0.022 0.002 PHE A 189 TRP 0.019 0.002 TRP B 169 HIS 0.008 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 9233) covalent geometry : angle 0.78142 / 0.36 (12507) SS BOND : bond 0.00327 / 0.17 ( 3) SS BOND : angle 0.72129 / 0.34 ( 6) hydrogen bonds : bond 0.04703 / 3.18 ( 437) hydrogen bonds : angle 4.90894 / 3.48 ( 1230) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7912 (m-30) cc_final: 0.7594 (m-30) REVERT: A 29 LYS cc_start: 0.8252 (tttm) cc_final: 0.8026 (tttm) REVERT: A 245 GLU cc_start: 0.7396 (tp30) cc_final: 0.7049 (tp30) REVERT: A 316 THR cc_start: 0.8558 (m) cc_final: 0.8233 (p) REVERT: A 324 THR cc_start: 0.7519 (m) cc_final: 0.6826 (p) REVERT: A 341 ASP cc_start: 0.8110 (t0) cc_final: 0.7906 (t0) REVERT: A 345 LYS cc_start: 0.8541 (mttt) cc_final: 0.8276 (mttt) REVERT: R 142 TYR cc_start: 0.8563 (t80) cc_final: 0.8325 (t80) REVERT: R 150 ARG cc_start: 0.8187 (ttm110) cc_final: 0.7974 (ttm170) REVERT: R 237 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7597 (ttp80) REVERT: L 10 GLN cc_start: 0.6110 (mt0) cc_final: 0.5546 (pm20) outliers start: 25 outliers final: 11 residues processed: 228 average time/residue: 0.5429 time to fit residues: 132.4111 Evaluate side-chains 213 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 158 SER Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain R residue 73 GLU Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 328 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 101 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 155 ASN B 295 ASN G 17 GLN N 179 GLN L 9 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.108652 restraints weight = 12697.462| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.47 r_work: 0.3330 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9236 Z= 0.194 Angle : 0.772 30.373 12513 Z= 0.358 Chirality : 0.066 1.850 1418 Planarity : 0.004 0.053 1566 Dihedral : 5.016 32.294 1263 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.08 % Allowed : 14.58 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.58 (0.24), residues: 1119 helix: 1.21 (0.26), residues: 390 sheet: 0.68 (0.29), residues: 296 loop : -0.52 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 283 TYR 0.015 0.002 TYR A 302 PHE 0.019 0.002 PHE A 189 TRP 0.019 0.002 TRP B 169 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 ( 9233) covalent geometry : angle 0.77190 / 0.36 (12507) SS BOND : bond 0.00322 / 0.15 ( 3) SS BOND : angle 1.07834 / 0.55 ( 6) hydrogen bonds : bond 0.04915 / 3.32 ( 437) hydrogen bonds : angle 4.76564 / 3.37 ( 1230) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7913 (m-30) cc_final: 0.7610 (m-30) REVERT: A 245 GLU cc_start: 0.7365 (tp30) cc_final: 0.7074 (tp30) REVERT: A 341 ASP cc_start: 0.7952 (t0) cc_final: 0.7683 (t0) REVERT: B 258 ASP cc_start: 0.7748 (t0) cc_final: 0.7517 (t0) REVERT: N 202 ARG cc_start: 0.8199 (ttp-110) cc_final: 0.7679 (ttp-170) REVERT: R 142 TYR cc_start: 0.8546 (t80) cc_final: 0.8297 (t80) REVERT: R 150 ARG cc_start: 0.8156 (ttm110) cc_final: 0.7923 (ttm170) REVERT: R 237 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7613 (ttp80) REVERT: R 283 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7368 (mtt180) REVERT: R 332 VAL cc_start: 0.8572 (p) cc_final: 0.8270 (m) outliers start: 40 outliers final: 20 residues processed: 239 average time/residue: 0.5171 time to fit residues: 132.5946 Evaluate side-chains 221 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 283 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 328 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 GLN B 239 ASN B 295 ASN N 82 GLN N 179 GLN R 186 HIS R 302 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.121525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109397 restraints weight = 12942.617| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.49 r_work: 0.3346 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9236 Z= 0.163 Angle : 0.747 31.302 12513 Z= 0.339 Chirality : 0.064 1.784 1418 Planarity : 0.004 0.054 1566 Dihedral : 5.167 40.238 1263 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.75 % Allowed : 16.82 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.57 (0.24), residues: 1119 helix: 1.33 (0.26), residues: 387 sheet: 0.54 (0.28), residues: 299 loop : -0.52 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.014 0.001 TYR N 190 PHE 0.016 0.001 PHE A 189 TRP 0.018 0.002 TRP B 169 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 9233) covalent geometry : angle 0.74674 / 0.34 (12507) SS BOND : bond 0.00270 / 0.13 ( 3) SS BOND : angle 1.42035 / 0.79 ( 6) hydrogen bonds : bond 0.04398 / 2.96 ( 437) hydrogen bonds : angle 4.67378 / 3.32 ( 1230) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7966 (m-30) cc_final: 0.7665 (m-30) REVERT: A 243 MET cc_start: 0.8491 (tpp) cc_final: 0.8250 (tpp) REVERT: A 245 GLU cc_start: 0.7357 (tp30) cc_final: 0.7074 (tp30) REVERT: B 150 ARG cc_start: 0.8852 (mmt-90) cc_final: 0.8624 (mpt180) REVERT: N 150 THR cc_start: 0.8172 (t) cc_final: 0.7960 (p) REVERT: R 124 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7267 (mm-30) REVERT: R 142 TYR cc_start: 0.8546 (t80) cc_final: 0.8324 (t80) REVERT: R 150 ARG cc_start: 0.8159 (ttm110) cc_final: 0.7916 (ttm170) REVERT: R 237 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7621 (ttp80) REVERT: R 283 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7101 (mtt180) REVERT: R 332 VAL cc_start: 0.8555 (p) cc_final: 0.8256 (m) outliers start: 27 outliers final: 19 residues processed: 217 average time/residue: 0.5502 time to fit residues: 127.4727 Evaluate side-chains 224 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 283 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 328 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 0.0170 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 156 GLN B 220 GLN B 239 ASN B 295 ASN N 82 GLN N 179 GLN R 186 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.123332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110807 restraints weight = 12317.582| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.50 r_work: 0.3351 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9236 Z= 0.181 Angle : 0.753 30.604 12513 Z= 0.343 Chirality : 0.066 1.844 1418 Planarity : 0.004 0.056 1566 Dihedral : 5.074 34.889 1263 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.67 % Allowed : 17.13 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.53 (0.24), residues: 1119 helix: 1.27 (0.26), residues: 391 sheet: 0.45 (0.28), residues: 299 loop : -0.49 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.013 0.001 TYR R 313 PHE 0.017 0.002 PHE A 189 TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 9233) covalent geometry : angle 0.75210 / 0.34 (12507) SS BOND : bond 0.00327 / 0.16 ( 3) SS BOND : angle 1.68190 / 0.94 ( 6) hydrogen bonds : bond 0.04419 / 2.97 ( 437) hydrogen bonds : angle 4.67700 / 3.31 ( 1230) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8017 (m-30) cc_final: 0.7698 (m-30) REVERT: A 243 MET cc_start: 0.8475 (tpp) cc_final: 0.8220 (tpp) REVERT: A 245 GLU cc_start: 0.7342 (tp30) cc_final: 0.7055 (tp30) REVERT: B 219 ARG cc_start: 0.8142 (mtp85) cc_final: 0.7899 (mtt-85) REVERT: B 258 ASP cc_start: 0.7790 (t0) cc_final: 0.7453 (t0) REVERT: N 202 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.8052 (ttp-170) REVERT: R 82 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8028 (mm) REVERT: R 124 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7331 (mm-30) REVERT: R 142 TYR cc_start: 0.8552 (t80) cc_final: 0.8313 (t80) REVERT: R 150 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7877 (ttm170) REVERT: R 237 ARG cc_start: 0.7964 (ttp80) cc_final: 0.7640 (ttp80) REVERT: R 270 PHE cc_start: 0.7605 (m-10) cc_final: 0.7357 (m-80) REVERT: R 283 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7134 (mtt180) REVERT: R 332 VAL cc_start: 0.8546 (p) cc_final: 0.8251 (m) outliers start: 36 outliers final: 24 residues processed: 224 average time/residue: 0.4541 time to fit residues: 108.9786 Evaluate side-chains 229 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain N residue 202 ARG Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 283 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 328 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN B 44 GLN B 156 GLN B 239 ASN B 295 ASN N 82 GLN N 179 GLN R 186 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.123012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.110434 restraints weight = 12257.612| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.50 r_work: 0.3350 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9236 Z= 0.187 Angle : 0.761 30.613 12513 Z= 0.346 Chirality : 0.066 1.857 1418 Planarity : 0.004 0.059 1566 Dihedral : 5.049 30.801 1263 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.59 % Allowed : 17.02 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.48 (0.24), residues: 1119 helix: 1.21 (0.26), residues: 391 sheet: 0.42 (0.28), residues: 299 loop : -0.48 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 42 TYR 0.014 0.001 TYR R 313 PHE 0.018 0.002 PHE A 189 TRP 0.020 0.002 TRP B 169 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 ( 9233) covalent geometry : angle 0.76030 / 0.35 (12507) SS BOND : bond 0.00287 / 0.14 ( 3) SS BOND : angle 1.59179 / 0.88 ( 6) hydrogen bonds : bond 0.04415 / 2.95 ( 437) hydrogen bonds : angle 4.68730 / 3.32 ( 1230) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8003 (m-30) cc_final: 0.7669 (m-30) REVERT: A 243 MET cc_start: 0.8467 (tpp) cc_final: 0.8209 (tpp) REVERT: A 245 GLU cc_start: 0.7325 (tp30) cc_final: 0.7051 (tp30) REVERT: A 260 THR cc_start: 0.8641 (m) cc_final: 0.8391 (p) REVERT: B 42 ARG cc_start: 0.7446 (mmm-85) cc_final: 0.7155 (mmm-85) REVERT: B 215 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6066 (pp20) REVERT: B 219 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7750 (mtt-85) REVERT: N 202 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8069 (ttp-170) REVERT: R 124 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7353 (mm-30) REVERT: R 142 TYR cc_start: 0.8536 (t80) cc_final: 0.8315 (t80) REVERT: R 150 ARG cc_start: 0.8164 (ttm110) cc_final: 0.7911 (ttm170) REVERT: R 237 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7639 (ttp80) REVERT: R 283 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7187 (mtt180) outliers start: 45 outliers final: 26 residues processed: 223 average time/residue: 0.4102 time to fit residues: 97.9884 Evaluate side-chains 227 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain N residue 202 ARG Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 283 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 12 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN B 17 GLN B 156 GLN B 239 ASN N 82 GLN N 179 GLN R 186 HIS L 9 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.122678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110211 restraints weight = 12435.558| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.51 r_work: 0.3356 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9236 Z= 0.165 Angle : 0.749 30.523 12513 Z= 0.340 Chirality : 0.066 1.868 1418 Planarity : 0.004 0.059 1566 Dihedral : 4.970 33.118 1263 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.98 % Allowed : 17.53 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.53 (0.25), residues: 1119 helix: 1.25 (0.26), residues: 391 sheet: 0.38 (0.28), residues: 291 loop : -0.39 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 42 TYR 0.013 0.001 TYR R 313 PHE 0.017 0.002 PHE A 189 TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 9233) covalent geometry : angle 0.74888 / 0.34 (12507) SS BOND : bond 0.00280 / 0.13 ( 3) SS BOND : angle 1.46764 / 0.81 ( 6) hydrogen bonds : bond 0.04292 / 2.86 ( 437) hydrogen bonds : angle 4.65031 / 3.29 ( 1230) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7993 (m-30) cc_final: 0.7641 (m-30) REVERT: A 243 MET cc_start: 0.8454 (tpp) cc_final: 0.8195 (tpp) REVERT: A 245 GLU cc_start: 0.7276 (tp30) cc_final: 0.6994 (tp30) REVERT: A 260 THR cc_start: 0.8648 (m) cc_final: 0.8387 (p) REVERT: A 324 THR cc_start: 0.7600 (m) cc_final: 0.6990 (p) REVERT: B 219 ARG cc_start: 0.8144 (mtp85) cc_final: 0.7895 (mtt-85) REVERT: N 202 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8068 (ttp-170) REVERT: R 142 TYR cc_start: 0.8529 (t80) cc_final: 0.8319 (t80) REVERT: R 150 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7884 (ttm170) REVERT: R 237 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7650 (ttp80) REVERT: R 283 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7319 (mtt180) outliers start: 39 outliers final: 26 residues processed: 214 average time/residue: 0.4510 time to fit residues: 103.5903 Evaluate side-chains 229 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain N residue 202 ARG Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 283 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 328 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 1.9990 chunk 46 optimal weight: 0.0070 chunk 59 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 104 optimal weight: 0.0980 chunk 88 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 70 optimal weight: 0.8980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN B 156 GLN B 239 ASN B 293 ASN N 179 GLN R 186 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.111199 restraints weight = 12328.190| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.51 r_work: 0.3371 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9236 Z= 0.130 Angle : 0.731 30.422 12513 Z= 0.328 Chirality : 0.065 1.879 1418 Planarity : 0.004 0.058 1566 Dihedral : 4.798 33.380 1263 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.96 % Allowed : 19.47 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.61 (0.25), residues: 1119 helix: 1.50 (0.27), residues: 378 sheet: 0.32 (0.28), residues: 290 loop : -0.38 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 42 TYR 0.012 0.001 TYR N 190 PHE 0.016 0.001 PHE R 309 TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9233) covalent geometry : angle 0.73020 / 0.33 (12507) SS BOND : bond 0.00231 / 0.11 ( 3) SS BOND : angle 1.35151 / 0.75 ( 6) hydrogen bonds : bond 0.04034 / 2.70 ( 437) hydrogen bonds : angle 4.54660 / 3.21 ( 1230) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7998 (m-30) cc_final: 0.7647 (m-30) REVERT: A 197 LYS cc_start: 0.8130 (mttm) cc_final: 0.7899 (mtpp) REVERT: A 243 MET cc_start: 0.8445 (tpp) cc_final: 0.8189 (tpp) REVERT: A 245 GLU cc_start: 0.7285 (tp30) cc_final: 0.6979 (tp30) REVERT: A 260 THR cc_start: 0.8648 (m) cc_final: 0.8379 (p) REVERT: A 324 THR cc_start: 0.7512 (m) cc_final: 0.6914 (p) REVERT: B 22 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7643 (ptm160) REVERT: B 215 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6575 (pp20) REVERT: B 217 MET cc_start: 0.7870 (pmm) cc_final: 0.7361 (pmm) REVERT: B 219 ARG cc_start: 0.8146 (mtp85) cc_final: 0.7920 (mtt-85) REVERT: N 202 ARG cc_start: 0.8317 (ttm170) cc_final: 0.8038 (ttp-170) REVERT: R 119 PHE cc_start: 0.6410 (OUTLIER) cc_final: 0.5888 (p90) REVERT: R 142 TYR cc_start: 0.8523 (t80) cc_final: 0.8314 (t80) REVERT: R 150 ARG cc_start: 0.8109 (ttm110) cc_final: 0.7856 (ttm170) REVERT: R 237 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7666 (ttp80) REVERT: R 283 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7306 (mtt180) outliers start: 29 outliers final: 18 residues processed: 214 average time/residue: 0.5221 time to fit residues: 119.5566 Evaluate side-chains 222 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 283 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 328 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 0.0170 chunk 78 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN B 156 GLN B 239 ASN B 293 ASN N 179 GLN R 186 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111187 restraints weight = 12239.250| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.50 r_work: 0.3358 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9236 Z= 0.163 Angle : 0.752 30.400 12513 Z= 0.339 Chirality : 0.066 1.882 1418 Planarity : 0.004 0.061 1566 Dihedral : 4.880 32.145 1263 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.06 % Allowed : 19.67 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.55 (0.25), residues: 1119 helix: 1.42 (0.27), residues: 379 sheet: 0.29 (0.28), residues: 290 loop : -0.40 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 42 TYR 0.013 0.001 TYR R 313 PHE 0.016 0.001 PHE A 189 TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS N 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 9233) covalent geometry : angle 0.75113 / 0.34 (12507) SS BOND : bond 0.00264 / 0.13 ( 3) SS BOND : angle 1.40466 / 0.77 ( 6) hydrogen bonds : bond 0.04205 / 2.81 ( 437) hydrogen bonds : angle 4.60080 / 3.25 ( 1230) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8018 (m-30) cc_final: 0.7667 (m-30) REVERT: A 243 MET cc_start: 0.8469 (tpp) cc_final: 0.8222 (tpp) REVERT: A 245 GLU cc_start: 0.7286 (tp30) cc_final: 0.7023 (tp30) REVERT: A 260 THR cc_start: 0.8662 (m) cc_final: 0.8376 (p) REVERT: A 324 THR cc_start: 0.7602 (m) cc_final: 0.6984 (p) REVERT: B 42 ARG cc_start: 0.7509 (mmm-85) cc_final: 0.7277 (mmm-85) REVERT: B 215 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6650 (pp20) REVERT: B 219 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7951 (mtt-85) REVERT: N 202 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7938 (ttp-170) REVERT: R 119 PHE cc_start: 0.6433 (OUTLIER) cc_final: 0.5918 (p90) REVERT: R 142 TYR cc_start: 0.8528 (t80) cc_final: 0.8321 (t80) REVERT: R 150 ARG cc_start: 0.8125 (ttm110) cc_final: 0.7870 (ttm170) REVERT: R 237 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7684 (ttp80) REVERT: R 283 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7350 (mtt180) outliers start: 30 outliers final: 22 residues processed: 213 average time/residue: 0.5268 time to fit residues: 120.0691 Evaluate side-chains 222 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 202 ARG Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 283 ARG Chi-restraints excluded: chain R residue 328 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 0.0050 chunk 93 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 102 optimal weight: 0.9980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN B 156 GLN B 239 ASN B 293 ASN N 179 GLN R 186 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.123819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.111327 restraints weight = 12263.293| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.50 r_work: 0.3374 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9236 Z= 0.133 Angle : 0.737 30.319 12513 Z= 0.330 Chirality : 0.065 1.891 1418 Planarity : 0.004 0.060 1566 Dihedral : 4.778 32.561 1263 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.34 % Allowed : 20.59 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.59 (0.25), residues: 1119 helix: 1.52 (0.27), residues: 379 sheet: 0.22 (0.28), residues: 290 loop : -0.37 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 32 TYR 0.011 0.001 TYR N 190 PHE 0.016 0.001 PHE R 309 TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 9233) covalent geometry : angle 0.73626 / 0.33 (12507) SS BOND : bond 0.00239 / 0.11 ( 3) SS BOND : angle 1.23272 / 0.68 ( 6) hydrogen bonds : bond 0.03994 / 2.68 ( 437) hydrogen bonds : angle 4.53731 / 3.20 ( 1230) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8016 (m-30) cc_final: 0.7664 (m-30) REVERT: A 197 LYS cc_start: 0.8119 (mttm) cc_final: 0.7905 (mtpp) REVERT: A 243 MET cc_start: 0.8456 (tpp) cc_final: 0.8151 (tpp) REVERT: A 245 GLU cc_start: 0.7272 (tp30) cc_final: 0.7018 (tp30) REVERT: A 324 THR cc_start: 0.7534 (m) cc_final: 0.6926 (p) REVERT: B 22 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7587 (ptm160) REVERT: B 42 ARG cc_start: 0.7499 (mmm-85) cc_final: 0.7268 (mmm-85) REVERT: B 215 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6544 (pp20) REVERT: B 217 MET cc_start: 0.7830 (pmm) cc_final: 0.7016 (pmm) REVERT: B 219 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7936 (mtt-85) REVERT: N 202 ARG cc_start: 0.8311 (ttm170) cc_final: 0.7921 (ttp-170) REVERT: R 119 PHE cc_start: 0.6421 (OUTLIER) cc_final: 0.5900 (p90) REVERT: R 142 TYR cc_start: 0.8517 (t80) cc_final: 0.8314 (t80) REVERT: R 150 ARG cc_start: 0.8090 (ttm110) cc_final: 0.7834 (ttm170) REVERT: R 237 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7667 (ttp80) outliers start: 23 outliers final: 17 residues processed: 210 average time/residue: 0.5284 time to fit residues: 118.8976 Evaluate side-chains 219 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 328 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 chunk 75 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 0.0270 chunk 15 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 105 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 156 GLN B 239 ASN B 293 ASN N 179 GLN R 186 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.125007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112480 restraints weight = 12198.083| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.50 r_work: 0.3388 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9236 Z= 0.114 Angle : 0.720 30.254 12513 Z= 0.321 Chirality : 0.065 1.897 1418 Planarity : 0.004 0.060 1566 Dihedral : 4.627 31.079 1263 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.45 % Allowed : 20.49 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.69 (0.25), residues: 1119 helix: 1.71 (0.27), residues: 373 sheet: 0.23 (0.29), residues: 288 loop : -0.36 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 32 TYR 0.012 0.001 TYR N 190 PHE 0.016 0.001 PHE R 309 TRP 0.016 0.001 TRP B 169 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 9233) covalent geometry : angle 0.72018 / 0.32 (12507) SS BOND : bond 0.00198 / 0.09 ( 3) SS BOND : angle 1.04289 / 0.57 ( 6) hydrogen bonds : bond 0.03781 / 2.55 ( 437) hydrogen bonds : angle 4.42482 / 3.12 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3534.42 seconds wall clock time: 61 minutes 6.63 seconds (3666.63 seconds total)