Starting phenix.real_space_refine on Fri Aug 22 20:13:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w8w_37359/08_2025/8w8w_37359.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w8w_37359/08_2025/8w8w_37359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w8w_37359/08_2025/8w8w_37359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w8w_37359/08_2025/8w8w_37359.map" model { file = "/net/cci-nas-00/data/ceres_data/8w8w_37359/08_2025/8w8w_37359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w8w_37359/08_2025/8w8w_37359.cif" } resolution = 2.9 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= -0.002 sd= 0.060 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 63 5.16 5 C 4874 2.51 5 N 1318 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7642 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2054 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "L" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 114 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "A" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1482 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 3, 'TRANS': 181} Chain breaks: 4 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 7, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.93, per 1000 atoms: 0.25 Number of scatterers: 7642 At special positions: 0 Unit cell: (76.5, 97.75, 130.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 63 16.00 O 1386 8.00 N 1318 7.00 C 4874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.19 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=1.90 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: 0.64 Conformation dependent library (CDL) restraints added in 382.4 milliseconds Enol-peptide restraints added in 1.4 microseconds 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1850 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 10 sheets defined 38.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'R' and resid 41 through 65 removed outlier: 4.365A pdb=" N PHE R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU R 46 " --> pdb=" O PRO R 42 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 101 removed outlier: 3.630A pdb=" N PHE R 75 " --> pdb=" O SER R 71 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE R 76 " --> pdb=" O PRO R 72 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU R 77 " --> pdb=" O MET R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 148 removed outlier: 3.575A pdb=" N MET R 123 " --> pdb=" O ILE R 119 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA R 139 " --> pdb=" O LEU R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 182 removed outlier: 3.619A pdb=" N ALA R 167 " --> pdb=" O THR R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 222 removed outlier: 3.547A pdb=" N THR R 194 " --> pdb=" O VAL R 190 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N MET R 195 " --> pdb=" O CYS R 191 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL R 208 " --> pdb=" O GLY R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 268 Proline residue: R 257 - end of helix removed outlier: 3.804A pdb=" N ILE R 266 " --> pdb=" O LEU R 262 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 299 removed outlier: 3.768A pdb=" N ILE R 288 " --> pdb=" O TYR R 284 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET R 289 " --> pdb=" O LEU R 285 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 303 through 310 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.550A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.517A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.584A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.750A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.715A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.830A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.769A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.835A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.505A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.577A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.902A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.560A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.716A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.902A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.741A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.940A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.924A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.544A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.679A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.089A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 209 through 214 removed outlier: 7.041A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 1041 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: 1.11 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1225 1.30 - 1.43: 2149 1.43 - 1.56: 4330 1.56 - 1.69: 0 1.69 - 1.82: 91 Bond restraints: 7795 Sorted by residual: bond pdb=" N ARG L 8 " pdb=" CA ARG L 8 " ideal model delta sigma weight residual 1.454 1.395 0.059 1.21e-02 6.83e+03 2.34e+01 bond pdb=" CA LYS L 11 " pdb=" C LYS L 11 " ideal model delta sigma weight residual 1.519 1.467 0.052 1.29e-02 6.01e+03 1.65e+01 bond pdb=" CA TYR R 148 " pdb=" C TYR R 148 " ideal model delta sigma weight residual 1.532 1.477 0.055 1.41e-02 5.03e+03 1.54e+01 bond pdb=" CA GLU A 209 " pdb=" CB GLU A 209 " ideal model delta sigma weight residual 1.534 1.476 0.059 1.60e-02 3.91e+03 1.34e+01 bond pdb=" N LYS A 211 " pdb=" CA LYS A 211 " ideal model delta sigma weight residual 1.459 1.415 0.044 1.27e-02 6.20e+03 1.21e+01 ... (remaining 7790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 10268 1.80 - 3.60: 250 3.60 - 5.41: 32 5.41 - 7.21: 12 7.21 - 9.01: 3 Bond angle restraints: 10565 Sorted by residual: angle pdb=" N TYR R 152 " pdb=" CA TYR R 152 " pdb=" C TYR R 152 " ideal model delta sigma weight residual 110.19 102.23 7.96 1.24e+00 6.50e-01 4.13e+01 angle pdb=" N ALA R 149 " pdb=" CA ALA R 149 " pdb=" C ALA R 149 " ideal model delta sigma weight residual 111.82 118.40 -6.58 1.16e+00 7.43e-01 3.21e+01 angle pdb=" N SER R 154 " pdb=" CA SER R 154 " pdb=" C SER R 154 " ideal model delta sigma weight residual 113.89 106.64 7.25 1.58e+00 4.01e-01 2.10e+01 angle pdb=" C PHE L 7 " pdb=" N ARG L 8 " pdb=" CA ARG L 8 " ideal model delta sigma weight residual 122.07 114.89 7.18 2.01e+00 2.48e-01 1.28e+01 angle pdb=" C GLU A 209 " pdb=" CA GLU A 209 " pdb=" CB GLU A 209 " ideal model delta sigma weight residual 110.24 103.98 6.26 1.88e+00 2.83e-01 1.11e+01 ... (remaining 10560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 3993 17.68 - 35.35: 473 35.35 - 53.03: 121 53.03 - 70.71: 20 70.71 - 88.38: 9 Dihedral angle restraints: 4616 sinusoidal: 1764 harmonic: 2852 Sorted by residual: dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 4613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 955 0.055 - 0.110: 214 0.110 - 0.165: 40 0.165 - 0.220: 4 0.220 - 0.275: 3 Chirality restraints: 1216 Sorted by residual: chirality pdb=" CA TRP L 9 " pdb=" N TRP L 9 " pdb=" C TRP L 9 " pdb=" CB TRP L 9 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB VAL A 224 " pdb=" CA VAL A 224 " pdb=" CG1 VAL A 224 " pdb=" CG2 VAL A 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ARG L 8 " pdb=" N ARG L 8 " pdb=" C ARG L 8 " pdb=" CB ARG L 8 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1213 not shown) Planarity restraints: 1334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 147 " -0.013 2.00e-02 2.50e+03 2.49e-02 6.20e+00 pdb=" C PHE R 147 " 0.043 2.00e-02 2.50e+03 pdb=" O PHE R 147 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR R 148 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO B 236 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET R 203 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" C MET R 203 " -0.031 2.00e-02 2.50e+03 pdb=" O MET R 203 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY R 204 " 0.010 2.00e-02 2.50e+03 ... (remaining 1331 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 138 2.67 - 3.23: 6812 3.23 - 3.79: 11183 3.79 - 4.34: 15832 4.34 - 4.90: 27295 Nonbonded interactions: 61260 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.114 3.040 nonbonded pdb=" OD2 ASP B 254 " pdb=" CB ALA G 33 " model vdw 2.247 3.460 nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.250 3.040 nonbonded pdb=" OD2 ASP R 121 " pdb="CA CA R 501 " model vdw 2.255 2.510 nonbonded pdb=" ND2 ASN B 340 " pdb=" OD1 ASN G 59 " model vdw 2.271 3.120 ... (remaining 61255 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: 2.090 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.440 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 0.158 7797 Z= 0.323 Angle : 0.936 60.885 10569 Z= 0.494 Chirality : 0.049 0.275 1216 Planarity : 0.005 0.059 1334 Dihedral : 16.431 88.383 2760 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.08 % Allowed : 22.25 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.36 (0.27), residues: 957 helix: 0.90 (0.28), residues: 363 sheet: 0.32 (0.35), residues: 216 loop : -1.72 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.015 0.002 TYR A 339 PHE 0.021 0.002 PHE B 151 TRP 0.018 0.002 TRP B 82 HIS 0.007 0.001 HIS R 70 Details of bonding type rmsd covalent geometry : bond 0.00629 ( 7795) covalent geometry : angle 0.69374 (10565) SS BOND : bond 0.14660 ( 2) SS BOND : angle 32.32813 ( 4) hydrogen bonds : bond 0.15406 ( 364) hydrogen bonds : angle 5.67754 ( 1041) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.320 Fit side-chains REVERT: L 11 LYS cc_start: 0.8430 (mttt) cc_final: 0.8135 (mttm) REVERT: A 20 ARG cc_start: 0.5593 (mmm160) cc_final: 0.5371 (mmt180) REVERT: A 38 ARG cc_start: 0.7466 (mtm180) cc_final: 0.6821 (mmt-90) REVERT: A 274 LYS cc_start: 0.7462 (ttmt) cc_final: 0.7069 (tttm) REVERT: A 280 ARG cc_start: 0.7467 (ttt90) cc_final: 0.6835 (tpt90) REVERT: A 356 ARG cc_start: 0.6918 (mtm180) cc_final: 0.6640 (mmm-85) REVERT: A 381 ASP cc_start: 0.7718 (m-30) cc_final: 0.7443 (m-30) REVERT: A 386 MET cc_start: 0.7319 (ttp) cc_final: 0.7052 (tmt) outliers start: 17 outliers final: 11 residues processed: 126 average time/residue: 0.6325 time to fit residues: 84.0090 Evaluate side-chains 107 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain N residue 71 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 123 GLN L 6 HIS A 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.171462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.132642 restraints weight = 7902.845| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.90 r_work: 0.3351 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7797 Z= 0.130 Angle : 0.524 6.998 10569 Z= 0.282 Chirality : 0.043 0.145 1216 Planarity : 0.004 0.056 1334 Dihedral : 5.419 58.495 1076 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.79 % Allowed : 22.13 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.29 (0.27), residues: 957 helix: 1.76 (0.28), residues: 362 sheet: 0.62 (0.36), residues: 204 loop : -1.62 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 72 TYR 0.012 0.001 TYR A 339 PHE 0.015 0.001 PHE A 212 TRP 0.013 0.002 TRP B 82 HIS 0.010 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7795) covalent geometry : angle 0.52315 (10565) SS BOND : bond 0.00460 ( 2) SS BOND : angle 1.50075 ( 4) hydrogen bonds : bond 0.04991 ( 364) hydrogen bonds : angle 4.11435 ( 1041) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.302 Fit side-chains REVERT: R 70 HIS cc_start: 0.5883 (OUTLIER) cc_final: 0.5288 (m-70) REVERT: R 304 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6624 (mm) REVERT: B 59 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8379 (m-80) REVERT: N 95 TYR cc_start: 0.8832 (m-80) cc_final: 0.8620 (m-80) REVERT: L 11 LYS cc_start: 0.8439 (mttt) cc_final: 0.8057 (mttm) REVERT: A 38 ARG cc_start: 0.7866 (mtm180) cc_final: 0.7284 (mmt-90) REVERT: A 208 PHE cc_start: 0.5103 (m-80) cc_final: 0.4571 (t80) REVERT: A 280 ARG cc_start: 0.7911 (ttt90) cc_final: 0.7446 (tpt90) REVERT: A 356 ARG cc_start: 0.7635 (mtm180) cc_final: 0.6901 (ptt-90) REVERT: A 381 ASP cc_start: 0.8405 (m-30) cc_final: 0.8100 (m-30) REVERT: A 386 MET cc_start: 0.8151 (ttp) cc_final: 0.7836 (tmt) outliers start: 31 outliers final: 12 residues processed: 124 average time/residue: 0.5810 time to fit residues: 76.4361 Evaluate side-chains 110 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN G 59 ASN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.173748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.136103 restraints weight = 7961.792| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.86 r_work: 0.3366 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7797 Z= 0.116 Angle : 0.494 6.604 10569 Z= 0.266 Chirality : 0.042 0.139 1216 Planarity : 0.004 0.053 1334 Dihedral : 4.828 58.853 1063 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.28 % Allowed : 21.76 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.48 (0.27), residues: 957 helix: 2.02 (0.28), residues: 362 sheet: 0.54 (0.36), residues: 207 loop : -1.53 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 342 TYR 0.009 0.001 TYR A 339 PHE 0.012 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.010 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7795) covalent geometry : angle 0.49362 (10565) SS BOND : bond 0.00193 ( 2) SS BOND : angle 1.33338 ( 4) hydrogen bonds : bond 0.04565 ( 364) hydrogen bonds : angle 3.85638 ( 1041) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.270 Fit side-chains REVERT: R 70 HIS cc_start: 0.5721 (OUTLIER) cc_final: 0.5003 (m-70) REVERT: R 252 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7057 (mp) REVERT: R 304 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6622 (mm) REVERT: B 17 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7177 (tm-30) REVERT: B 59 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.8428 (m-80) REVERT: B 61 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8552 (ppp) REVERT: B 245 SER cc_start: 0.8897 (p) cc_final: 0.8680 (t) REVERT: N 38 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7949 (ptt180) REVERT: L 11 LYS cc_start: 0.8444 (mttt) cc_final: 0.8027 (mttm) REVERT: A 38 ARG cc_start: 0.7888 (mtm180) cc_final: 0.7338 (mmt-90) REVERT: A 208 PHE cc_start: 0.5250 (m-80) cc_final: 0.4586 (t80) REVERT: A 280 ARG cc_start: 0.7897 (ttt90) cc_final: 0.7456 (tpt90) REVERT: A 314 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: A 356 ARG cc_start: 0.7640 (mtm180) cc_final: 0.6964 (ptt-90) REVERT: A 381 ASP cc_start: 0.8415 (m-30) cc_final: 0.8147 (m-30) outliers start: 35 outliers final: 15 residues processed: 120 average time/residue: 0.5687 time to fit residues: 72.3475 Evaluate side-chains 117 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 314 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.168328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.131500 restraints weight = 7968.212| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.80 r_work: 0.3342 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7797 Z= 0.149 Angle : 0.526 7.083 10569 Z= 0.281 Chirality : 0.043 0.145 1216 Planarity : 0.004 0.056 1334 Dihedral : 4.888 58.233 1063 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.52 % Allowed : 21.76 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.47 (0.27), residues: 957 helix: 2.02 (0.27), residues: 361 sheet: 0.64 (0.36), residues: 204 loop : -1.59 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 374 TYR 0.013 0.001 TYR A 339 PHE 0.014 0.001 PHE B 151 TRP 0.014 0.002 TRP B 82 HIS 0.012 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7795) covalent geometry : angle 0.52546 (10565) SS BOND : bond 0.00498 ( 2) SS BOND : angle 0.96021 ( 4) hydrogen bonds : bond 0.05059 ( 364) hydrogen bonds : angle 3.93289 ( 1041) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.299 Fit side-chains REVERT: R 70 HIS cc_start: 0.5603 (OUTLIER) cc_final: 0.4959 (m-70) REVERT: R 252 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7111 (mp) REVERT: R 304 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6628 (mm) REVERT: B 59 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.8316 (m-80) REVERT: B 61 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8531 (ppp) REVERT: B 245 SER cc_start: 0.8917 (p) cc_final: 0.8695 (t) REVERT: N 38 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7987 (ptt180) REVERT: L 11 LYS cc_start: 0.8451 (mttt) cc_final: 0.8045 (mttm) REVERT: A 24 LYS cc_start: 0.6888 (mmtt) cc_final: 0.6477 (mmpt) REVERT: A 25 LYS cc_start: 0.7175 (mptp) cc_final: 0.6788 (mtmt) REVERT: A 38 ARG cc_start: 0.7963 (mtm180) cc_final: 0.7406 (mmt-90) REVERT: A 208 PHE cc_start: 0.5560 (m-80) cc_final: 0.4799 (t80) REVERT: A 265 ARG cc_start: 0.7897 (mmt-90) cc_final: 0.7087 (mtm110) REVERT: A 280 ARG cc_start: 0.7936 (ttt90) cc_final: 0.7489 (tpt90) REVERT: A 314 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6337 (mp0) REVERT: A 356 ARG cc_start: 0.7625 (mtm180) cc_final: 0.7004 (ptt-90) REVERT: A 381 ASP cc_start: 0.8456 (m-30) cc_final: 0.8190 (m-30) outliers start: 37 outliers final: 17 residues processed: 125 average time/residue: 0.6136 time to fit residues: 80.8678 Evaluate side-chains 120 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 314 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.0070 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 21 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.169217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132278 restraints weight = 7841.282| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.80 r_work: 0.3353 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7797 Z= 0.127 Angle : 0.498 6.655 10569 Z= 0.267 Chirality : 0.042 0.151 1216 Planarity : 0.004 0.057 1334 Dihedral : 4.761 58.393 1063 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.65 % Allowed : 21.76 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.56 (0.27), residues: 957 helix: 2.13 (0.27), residues: 360 sheet: 0.63 (0.36), residues: 204 loop : -1.52 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 374 TYR 0.010 0.001 TYR A 339 PHE 0.013 0.001 PHE B 151 TRP 0.014 0.002 TRP B 82 HIS 0.010 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7795) covalent geometry : angle 0.49528 (10565) SS BOND : bond 0.00515 ( 2) SS BOND : angle 2.49551 ( 4) hydrogen bonds : bond 0.04630 ( 364) hydrogen bonds : angle 3.82434 ( 1041) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.280 Fit side-chains REVERT: R 70 HIS cc_start: 0.5685 (OUTLIER) cc_final: 0.5023 (m-70) REVERT: R 252 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7082 (mp) REVERT: B 17 GLN cc_start: 0.7506 (tm-30) cc_final: 0.7071 (tm-30) REVERT: B 59 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8398 (m-80) REVERT: B 61 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8560 (ppp) REVERT: B 118 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7903 (p0) REVERT: B 245 SER cc_start: 0.8915 (p) cc_final: 0.8702 (t) REVERT: N 34 MET cc_start: 0.8845 (mmm) cc_final: 0.8566 (mmm) REVERT: N 38 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7949 (ptt180) REVERT: L 11 LYS cc_start: 0.8442 (mttt) cc_final: 0.8031 (mttm) REVERT: A 25 LYS cc_start: 0.7170 (mptp) cc_final: 0.6779 (mtmm) REVERT: A 38 ARG cc_start: 0.7921 (mtm180) cc_final: 0.7364 (mmt-90) REVERT: A 208 PHE cc_start: 0.5619 (m-80) cc_final: 0.4744 (t80) REVERT: A 265 ARG cc_start: 0.7883 (mmt-90) cc_final: 0.7031 (ptt-90) REVERT: A 280 ARG cc_start: 0.7906 (ttt90) cc_final: 0.7446 (tpt90) REVERT: A 314 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6305 (mp0) REVERT: A 356 ARG cc_start: 0.7620 (mtm180) cc_final: 0.7002 (ptt-90) REVERT: A 381 ASP cc_start: 0.8431 (m-30) cc_final: 0.8167 (m-30) REVERT: A 392 GLU cc_start: 0.8467 (tt0) cc_final: 0.8199 (mt-10) outliers start: 38 outliers final: 19 residues processed: 122 average time/residue: 0.5740 time to fit residues: 73.7261 Evaluate side-chains 122 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 314 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 82 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.169532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132281 restraints weight = 7865.229| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.96 r_work: 0.3341 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7797 Z= 0.122 Angle : 0.488 6.597 10569 Z= 0.261 Chirality : 0.042 0.163 1216 Planarity : 0.004 0.056 1334 Dihedral : 4.676 58.267 1063 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.16 % Allowed : 22.25 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.61 (0.27), residues: 957 helix: 2.21 (0.27), residues: 361 sheet: 0.62 (0.36), residues: 205 loop : -1.53 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.010 0.001 TYR A 339 PHE 0.013 0.001 PHE B 151 TRP 0.014 0.002 TRP B 82 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7795) covalent geometry : angle 0.48726 (10565) SS BOND : bond 0.00501 ( 2) SS BOND : angle 1.41272 ( 4) hydrogen bonds : bond 0.04524 ( 364) hydrogen bonds : angle 3.76998 ( 1041) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.268 Fit side-chains REVERT: R 70 HIS cc_start: 0.5686 (OUTLIER) cc_final: 0.5090 (m-70) REVERT: R 252 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7078 (mp) REVERT: B 17 GLN cc_start: 0.7614 (tm-30) cc_final: 0.7164 (tm-30) REVERT: B 59 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: B 61 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8521 (ppp) REVERT: B 118 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7945 (p0) REVERT: N 38 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7949 (ptt180) REVERT: L 11 LYS cc_start: 0.8449 (mttt) cc_final: 0.8042 (mttm) REVERT: A 25 LYS cc_start: 0.7187 (mptp) cc_final: 0.6795 (mtmm) REVERT: A 38 ARG cc_start: 0.7955 (mtm180) cc_final: 0.7369 (mmt-90) REVERT: A 208 PHE cc_start: 0.5806 (m-80) cc_final: 0.4778 (t80) REVERT: A 265 ARG cc_start: 0.7842 (mmt-90) cc_final: 0.7008 (ptt-90) REVERT: A 280 ARG cc_start: 0.7918 (ttt90) cc_final: 0.7465 (tpt90) REVERT: A 314 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6293 (mp0) REVERT: A 356 ARG cc_start: 0.7657 (mtm180) cc_final: 0.7030 (ptt-90) REVERT: A 381 ASP cc_start: 0.8433 (m-30) cc_final: 0.8169 (m-30) REVERT: A 392 GLU cc_start: 0.8452 (tt0) cc_final: 0.8199 (mt-10) outliers start: 34 outliers final: 20 residues processed: 120 average time/residue: 0.6065 time to fit residues: 76.6303 Evaluate side-chains 121 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 373 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 88 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 92 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.174353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136503 restraints weight = 7884.422| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.83 r_work: 0.3376 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7797 Z= 0.105 Angle : 0.466 6.219 10569 Z= 0.251 Chirality : 0.042 0.171 1216 Planarity : 0.003 0.055 1334 Dihedral : 4.553 58.674 1063 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.40 % Allowed : 22.62 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.75 (0.27), residues: 957 helix: 2.32 (0.27), residues: 363 sheet: 0.67 (0.36), residues: 204 loop : -1.44 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.008 0.001 TYR A 339 PHE 0.012 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 7795) covalent geometry : angle 0.46612 (10565) SS BOND : bond 0.00308 ( 2) SS BOND : angle 0.88940 ( 4) hydrogen bonds : bond 0.04173 ( 364) hydrogen bonds : angle 3.68701 ( 1041) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.296 Fit side-chains REVERT: R 70 HIS cc_start: 0.5436 (OUTLIER) cc_final: 0.4983 (m-70) REVERT: R 252 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7042 (mp) REVERT: B 17 GLN cc_start: 0.7600 (tm-30) cc_final: 0.7149 (tm-30) REVERT: B 59 TYR cc_start: 0.8907 (OUTLIER) cc_final: 0.8458 (m-80) REVERT: B 61 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8585 (ppp) REVERT: N 38 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7876 (ptt180) REVERT: N 85 SER cc_start: 0.8336 (m) cc_final: 0.7874 (p) REVERT: L 11 LYS cc_start: 0.8416 (mttt) cc_final: 0.8018 (mttm) REVERT: A 25 LYS cc_start: 0.7139 (mptp) cc_final: 0.6742 (mtmm) REVERT: A 38 ARG cc_start: 0.7884 (mtm180) cc_final: 0.7260 (mmt-90) REVERT: A 208 PHE cc_start: 0.5706 (m-80) cc_final: 0.4707 (t80) REVERT: A 265 ARG cc_start: 0.7782 (mmt-90) cc_final: 0.6991 (ptt-90) REVERT: A 280 ARG cc_start: 0.7810 (ttt90) cc_final: 0.7405 (tpt90) REVERT: A 314 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6294 (mp0) REVERT: A 356 ARG cc_start: 0.7601 (mtm180) cc_final: 0.6986 (ptt-90) REVERT: A 381 ASP cc_start: 0.8387 (m-30) cc_final: 0.8113 (m-30) outliers start: 36 outliers final: 24 residues processed: 123 average time/residue: 0.5887 time to fit residues: 76.4397 Evaluate side-chains 124 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 373 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.172590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.133743 restraints weight = 7770.832| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.87 r_work: 0.3369 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7797 Z= 0.112 Angle : 0.476 6.364 10569 Z= 0.256 Chirality : 0.042 0.169 1216 Planarity : 0.004 0.055 1334 Dihedral : 4.557 58.673 1063 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.03 % Allowed : 22.98 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.77 (0.27), residues: 957 helix: 2.38 (0.27), residues: 361 sheet: 0.72 (0.36), residues: 203 loop : -1.49 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.009 0.001 TYR A 339 PHE 0.012 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7795) covalent geometry : angle 0.47619 (10565) SS BOND : bond 0.00358 ( 2) SS BOND : angle 0.78446 ( 4) hydrogen bonds : bond 0.04281 ( 364) hydrogen bonds : angle 3.67857 ( 1041) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.247 Fit side-chains REVERT: R 70 HIS cc_start: 0.5369 (OUTLIER) cc_final: 0.4984 (m-70) REVERT: B 17 GLN cc_start: 0.7505 (tm-30) cc_final: 0.7012 (tm-30) REVERT: B 59 TYR cc_start: 0.8906 (OUTLIER) cc_final: 0.8369 (m-80) REVERT: B 61 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8555 (ppp) REVERT: N 38 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7876 (ptt180) REVERT: N 85 SER cc_start: 0.8317 (m) cc_final: 0.7833 (p) REVERT: A 25 LYS cc_start: 0.7076 (mptp) cc_final: 0.6687 (mtmm) REVERT: A 38 ARG cc_start: 0.7863 (mtm180) cc_final: 0.7206 (mmt-90) REVERT: A 208 PHE cc_start: 0.5771 (m-80) cc_final: 0.4679 (t80) REVERT: A 265 ARG cc_start: 0.7752 (mmt-90) cc_final: 0.6932 (ptt-90) REVERT: A 280 ARG cc_start: 0.7821 (ttt90) cc_final: 0.7368 (tpt90) REVERT: A 314 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6283 (mp0) REVERT: A 356 ARG cc_start: 0.7582 (mtm180) cc_final: 0.6945 (ptt-90) REVERT: A 381 ASP cc_start: 0.8344 (m-30) cc_final: 0.8060 (m-30) outliers start: 33 outliers final: 23 residues processed: 116 average time/residue: 0.6593 time to fit residues: 80.3967 Evaluate side-chains 121 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 373 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 39 optimal weight: 0.0020 chunk 6 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 31 optimal weight: 0.0870 chunk 86 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.176979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139621 restraints weight = 7898.129| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.83 r_work: 0.3411 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7797 Z= 0.088 Angle : 0.439 5.833 10569 Z= 0.237 Chirality : 0.041 0.169 1216 Planarity : 0.003 0.054 1334 Dihedral : 4.361 59.336 1063 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.30 % Allowed : 23.59 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.00 (0.27), residues: 957 helix: 2.53 (0.27), residues: 366 sheet: 0.77 (0.36), residues: 204 loop : -1.32 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.006 0.001 TYR A 339 PHE 0.010 0.001 PHE B 151 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 7795) covalent geometry : angle 0.43854 (10565) SS BOND : bond 0.00279 ( 2) SS BOND : angle 0.35171 ( 4) hydrogen bonds : bond 0.03632 ( 364) hydrogen bonds : angle 3.53009 ( 1041) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.310 Fit side-chains REVERT: R 70 HIS cc_start: 0.5225 (OUTLIER) cc_final: 0.4928 (m-70) REVERT: B 17 GLN cc_start: 0.7620 (tm-30) cc_final: 0.7163 (tm-30) REVERT: B 59 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8501 (m-80) REVERT: N 38 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7802 (ptt180) REVERT: N 85 SER cc_start: 0.8341 (m) cc_final: 0.7878 (p) REVERT: N 95 TYR cc_start: 0.8836 (m-80) cc_final: 0.8534 (m-80) REVERT: L 4 MET cc_start: 0.7588 (ttp) cc_final: 0.7357 (ttm) REVERT: A 38 ARG cc_start: 0.7851 (mtm180) cc_final: 0.7167 (mmt-90) REVERT: A 208 PHE cc_start: 0.5707 (m-80) cc_final: 0.4480 (t80) REVERT: A 265 ARG cc_start: 0.7785 (mmt-90) cc_final: 0.6985 (ptt-90) REVERT: A 280 ARG cc_start: 0.7758 (ttt90) cc_final: 0.7523 (ttt180) REVERT: A 314 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6282 (mp0) REVERT: A 356 ARG cc_start: 0.7512 (mtm180) cc_final: 0.6977 (ptt-90) REVERT: A 381 ASP cc_start: 0.8373 (m-30) cc_final: 0.8086 (m-30) outliers start: 27 outliers final: 15 residues processed: 116 average time/residue: 0.6140 time to fit residues: 75.2003 Evaluate side-chains 112 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 320 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 89 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 84 optimal weight: 0.0980 chunk 94 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 0.0670 chunk 63 optimal weight: 0.7980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 220 GLN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.173290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.135157 restraints weight = 7846.789| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.86 r_work: 0.3398 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7797 Z= 0.093 Angle : 0.446 6.034 10569 Z= 0.240 Chirality : 0.041 0.173 1216 Planarity : 0.003 0.054 1334 Dihedral : 4.360 59.230 1063 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.69 % Allowed : 24.57 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.07 (0.27), residues: 957 helix: 2.60 (0.27), residues: 366 sheet: 0.71 (0.36), residues: 209 loop : -1.25 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 302 TYR 0.007 0.001 TYR A 339 PHE 0.010 0.001 PHE B 241 TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 7795) covalent geometry : angle 0.44576 (10565) SS BOND : bond 0.00267 ( 2) SS BOND : angle 0.52899 ( 4) hydrogen bonds : bond 0.03744 ( 364) hydrogen bonds : angle 3.52151 ( 1041) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.302 Fit side-chains REVERT: R 302 ARG cc_start: 0.8455 (mmp-170) cc_final: 0.8115 (mmm160) REVERT: B 17 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7069 (tm-30) REVERT: B 59 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: N 38 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7824 (ptt180) REVERT: N 85 SER cc_start: 0.8321 (m) cc_final: 0.7845 (p) REVERT: N 95 TYR cc_start: 0.8832 (m-80) cc_final: 0.8515 (m-80) REVERT: A 38 ARG cc_start: 0.7819 (mtm180) cc_final: 0.7124 (mmt-90) REVERT: A 208 PHE cc_start: 0.5714 (m-80) cc_final: 0.4484 (t80) REVERT: A 265 ARG cc_start: 0.7726 (mmt-90) cc_final: 0.6917 (ptt-90) REVERT: A 314 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6325 (mp0) REVERT: A 356 ARG cc_start: 0.7491 (mtm180) cc_final: 0.6891 (ptt-90) REVERT: A 381 ASP cc_start: 0.8349 (m-30) cc_final: 0.8064 (m-30) outliers start: 22 outliers final: 14 residues processed: 108 average time/residue: 0.6801 time to fit residues: 77.2550 Evaluate side-chains 109 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 373 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 68 optimal weight: 0.0000 chunk 25 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.173355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135280 restraints weight = 7904.600| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.87 r_work: 0.3401 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7797 Z= 0.094 Angle : 0.455 7.324 10569 Z= 0.244 Chirality : 0.041 0.186 1216 Planarity : 0.003 0.054 1334 Dihedral : 4.389 59.289 1063 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.57 % Allowed : 24.69 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.12 (0.27), residues: 957 helix: 2.65 (0.27), residues: 365 sheet: 0.72 (0.36), residues: 209 loop : -1.22 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.007 0.001 TYR A 339 PHE 0.010 0.001 PHE B 151 TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 7795) covalent geometry : angle 0.44770 (10565) SS BOND : bond 0.00557 ( 2) SS BOND : angle 4.13898 ( 4) hydrogen bonds : bond 0.03704 ( 364) hydrogen bonds : angle 3.50128 ( 1041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2973.92 seconds wall clock time: 51 minutes 25.11 seconds (3085.11 seconds total)