Starting phenix.real_space_refine on Sun May 11 05:59:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w8w_37359/05_2025/8w8w_37359.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w8w_37359/05_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_37359/05_2025/8w8w_37359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w8w_37359/05_2025/8w8w_37359.map" model { file = "/net/cci-nas-00/data/ceres_data/8w8w_37359/05_2025/8w8w_37359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w8w_37359/05_2025/8w8w_37359.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.060 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'TYR:plan': 1, 'ASP:plan': 7} 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: 5.18, per 1000 atoms: 0.68 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: 1.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.86 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: 2.04 Time building geometry restraints manager: 2.19 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: 1.720 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.020 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:10.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.810 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (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 TRP 0.018 0.002 TRP B 82 HIS 0.007 0.001 HIS R 70 PHE 0.021 0.002 PHE B 151 TYR 0.015 0.002 TYR A 339 ARG 0.003 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.15406 ( 364) hydrogen bonds : angle 5.67754 ( 1041) SS BOND : bond 0.14660 ( 2) SS BOND : angle 32.32813 ( 4) covalent geometry : bond 0.00629 ( 7795) covalent geometry : angle 0.69374 (10565) *********************** 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 : 0.854 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: 1.2090 time to fit residues: 161.1562 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 : 0.656 ------------------------------------------------------------------------------- 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 80 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.172680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.134000 restraints weight = 7872.012| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.91 r_work: 0.3367 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7797 Z= 0.116 Angle : 0.504 6.683 10569 Z= 0.272 Chirality : 0.042 0.147 1216 Planarity : 0.004 0.055 1334 Dihedral : 5.334 58.609 1076 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.42 % Allowed : 22.25 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.27), residues: 957 helix: 1.84 (0.28), residues: 362 sheet: 0.68 (0.36), residues: 202 loop : -1.63 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.010 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.010 0.001 TYR A 339 ARG 0.003 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.04750 ( 364) hydrogen bonds : angle 4.05614 ( 1041) SS BOND : bond 0.00557 ( 2) SS BOND : angle 1.41760 ( 4) covalent geometry : bond 0.00258 ( 7795) covalent geometry : angle 0.50356 (10565) *********************** 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 127 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.799 Fit side-chains REVERT: R 70 HIS cc_start: 0.5826 (OUTLIER) cc_final: 0.5048 (m-70) REVERT: B 59 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.8502 (m-80) REVERT: N 95 TYR cc_start: 0.8808 (m-80) cc_final: 0.8607 (m-80) REVERT: L 11 LYS cc_start: 0.8408 (mttt) cc_final: 0.8021 (mttm) REVERT: A 38 ARG cc_start: 0.7792 (mtm180) cc_final: 0.7170 (mmt-90) REVERT: A 280 ARG cc_start: 0.7921 (ttt90) cc_final: 0.7408 (tpt90) REVERT: A 356 ARG cc_start: 0.7587 (mtm180) cc_final: 0.6854 (ptt-90) REVERT: A 381 ASP cc_start: 0.8425 (m-30) cc_final: 0.8128 (m-30) REVERT: A 386 MET cc_start: 0.8059 (ttp) cc_final: 0.7738 (tmt) outliers start: 28 outliers final: 12 residues processed: 118 average time/residue: 1.1364 time to fit residues: 142.2589 Evaluate side-chains 105 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 0.4980 chunk 26 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 92 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.168422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131459 restraints weight = 7921.142| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.98 r_work: 0.3333 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7797 Z= 0.150 Angle : 0.538 7.193 10569 Z= 0.287 Chirality : 0.043 0.144 1216 Planarity : 0.004 0.055 1334 Dihedral : 4.985 58.879 1063 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.52 % Allowed : 21.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.27), residues: 957 helix: 1.89 (0.27), residues: 361 sheet: 0.60 (0.36), residues: 204 loop : -1.62 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.014 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.014 0.001 TYR A 339 ARG 0.002 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.05197 ( 364) hydrogen bonds : angle 4.01086 ( 1041) SS BOND : bond 0.00425 ( 2) SS BOND : angle 1.36841 ( 4) covalent geometry : bond 0.00357 ( 7795) covalent geometry : angle 0.53784 (10565) *********************** 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 139 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 0.910 Fit side-chains REVERT: R 70 HIS cc_start: 0.5773 (OUTLIER) cc_final: 0.5089 (m-70) REVERT: R 252 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7176 (mp) REVERT: R 302 ARG cc_start: 0.8459 (mmp-170) cc_final: 0.8199 (mmm160) REVERT: B 59 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8386 (m-80) REVERT: B 61 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8348 (ppp) REVERT: B 245 SER cc_start: 0.8900 (p) cc_final: 0.8672 (t) REVERT: N 38 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7999 (ptt180) REVERT: L 11 LYS cc_start: 0.8479 (mttt) cc_final: 0.8058 (mttm) REVERT: A 24 LYS cc_start: 0.6813 (mmtt) cc_final: 0.6350 (mmpt) REVERT: A 25 LYS cc_start: 0.7126 (mptp) cc_final: 0.6784 (mtmt) REVERT: A 38 ARG cc_start: 0.7939 (mtm180) cc_final: 0.7399 (mmt-90) REVERT: A 208 PHE cc_start: 0.5368 (m-80) cc_final: 0.4657 (t80) REVERT: A 280 ARG cc_start: 0.7941 (ttt90) cc_final: 0.7501 (tpt90) REVERT: A 314 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: A 356 ARG cc_start: 0.7687 (mtm180) cc_final: 0.7008 (ptt-90) REVERT: A 381 ASP cc_start: 0.8449 (m-30) cc_final: 0.8197 (m-30) REVERT: A 392 GLU cc_start: 0.8532 (tt0) cc_final: 0.8326 (mt-10) outliers start: 37 outliers final: 15 residues processed: 127 average time/residue: 1.2154 time to fit residues: 163.8611 Evaluate side-chains 119 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 0.0570 chunk 7 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.174178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136354 restraints weight = 7937.231| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.84 r_work: 0.3377 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7797 Z= 0.111 Angle : 0.475 6.380 10569 Z= 0.256 Chirality : 0.042 0.140 1216 Planarity : 0.004 0.056 1334 Dihedral : 4.701 58.656 1063 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.52 % Allowed : 21.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.27), residues: 957 helix: 2.12 (0.27), residues: 362 sheet: 0.60 (0.36), residues: 204 loop : -1.55 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.009 0.001 HIS A 357 PHE 0.012 0.001 PHE B 151 TYR 0.008 0.001 TYR A 339 ARG 0.003 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 364) hydrogen bonds : angle 3.77728 ( 1041) SS BOND : bond 0.00343 ( 2) SS BOND : angle 0.82159 ( 4) covalent geometry : bond 0.00251 ( 7795) covalent geometry : angle 0.47512 (10565) *********************** 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 135 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.786 Fit side-chains REVERT: R 70 HIS cc_start: 0.5703 (OUTLIER) cc_final: 0.4960 (m-70) REVERT: R 252 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7049 (mp) REVERT: R 302 ARG cc_start: 0.8469 (mmp-170) cc_final: 0.8107 (mmm160) REVERT: B 59 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8454 (m-80) REVERT: B 61 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8380 (ppp) REVERT: B 245 SER cc_start: 0.8906 (p) cc_final: 0.8693 (t) REVERT: N 38 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7915 (ptt180) REVERT: N 85 SER cc_start: 0.8342 (m) cc_final: 0.7854 (p) REVERT: L 11 LYS cc_start: 0.8445 (mttt) cc_final: 0.8043 (mttm) REVERT: A 25 LYS cc_start: 0.7082 (mptp) cc_final: 0.6708 (mtmt) REVERT: A 38 ARG cc_start: 0.7867 (mtm180) cc_final: 0.7319 (mmt-90) REVERT: A 208 PHE cc_start: 0.5380 (m-80) cc_final: 0.4673 (t80) REVERT: A 280 ARG cc_start: 0.7879 (ttt90) cc_final: 0.7440 (tpt90) REVERT: A 314 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6426 (mp0) REVERT: A 356 ARG cc_start: 0.7582 (mtm180) cc_final: 0.6961 (ptt-90) REVERT: A 381 ASP cc_start: 0.8404 (m-30) cc_final: 0.8134 (m-30) REVERT: A 392 GLU cc_start: 0.8434 (tt0) cc_final: 0.8171 (mt-10) outliers start: 37 outliers final: 17 residues processed: 121 average time/residue: 1.1745 time to fit residues: 150.9935 Evaluate side-chains 118 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 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 38 ARG Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 386 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 26 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.172564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134474 restraints weight = 7831.411| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.83 r_work: 0.3359 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7797 Z= 0.131 Angle : 0.501 6.695 10569 Z= 0.268 Chirality : 0.042 0.144 1216 Planarity : 0.004 0.057 1334 Dihedral : 4.735 58.113 1063 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.52 % Allowed : 21.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.27), residues: 957 helix: 2.16 (0.27), residues: 361 sheet: 0.57 (0.36), residues: 206 loop : -1.53 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.010 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.012 0.001 TYR A 339 ARG 0.002 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04710 ( 364) hydrogen bonds : angle 3.81461 ( 1041) SS BOND : bond 0.00502 ( 2) SS BOND : angle 2.46041 ( 4) covalent geometry : bond 0.00309 ( 7795) covalent geometry : angle 0.49863 (10565) *********************** 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 138 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.791 Fit side-chains REVERT: R 70 HIS cc_start: 0.5648 (OUTLIER) cc_final: 0.5041 (m-70) REVERT: R 252 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7031 (mp) REVERT: R 302 ARG cc_start: 0.8484 (mmp-170) cc_final: 0.8118 (mmm160) REVERT: B 59 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8394 (m-80) REVERT: B 118 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7871 (p0) REVERT: B 245 SER cc_start: 0.8928 (p) cc_final: 0.8711 (t) REVERT: N 38 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7935 (ptt180) REVERT: N 85 SER cc_start: 0.8333 (m) cc_final: 0.7858 (p) REVERT: L 11 LYS cc_start: 0.8423 (mttt) cc_final: 0.8008 (mttm) REVERT: A 25 LYS cc_start: 0.7120 (mptp) cc_final: 0.6728 (mtmt) REVERT: A 38 ARG cc_start: 0.7895 (mtm180) cc_final: 0.7323 (mmt-90) REVERT: A 208 PHE cc_start: 0.5558 (m-80) cc_final: 0.4694 (t80) REVERT: A 265 ARG cc_start: 0.7747 (mmt-90) cc_final: 0.6960 (ptt-90) REVERT: A 280 ARG cc_start: 0.7899 (ttt90) cc_final: 0.7414 (tpt90) REVERT: A 314 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6303 (mp0) REVERT: A 356 ARG cc_start: 0.7609 (mtm180) cc_final: 0.6991 (ptt-90) REVERT: A 381 ASP cc_start: 0.8408 (m-30) cc_final: 0.8129 (m-30) outliers start: 37 outliers final: 19 residues processed: 124 average time/residue: 1.1600 time to fit residues: 152.3742 Evaluate side-chains 121 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.169839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.131095 restraints weight = 7843.842| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.88 r_work: 0.3354 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1780 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= 0.123 Angle : 0.489 6.573 10569 Z= 0.262 Chirality : 0.042 0.153 1216 Planarity : 0.004 0.056 1334 Dihedral : 4.674 58.146 1063 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.16 % Allowed : 22.62 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.27), residues: 957 helix: 2.22 (0.27), residues: 361 sheet: 0.59 (0.36), residues: 206 loop : -1.50 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.010 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.010 0.001 TYR A 339 ARG 0.002 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.04559 ( 364) hydrogen bonds : angle 3.77436 ( 1041) SS BOND : bond 0.00405 ( 2) SS BOND : angle 1.23569 ( 4) covalent geometry : bond 0.00289 ( 7795) covalent geometry : angle 0.48827 (10565) *********************** 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 134 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.791 Fit side-chains REVERT: R 70 HIS cc_start: 0.5645 (OUTLIER) cc_final: 0.5051 (m-70) REVERT: R 252 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.6992 (mp) REVERT: R 302 ARG cc_start: 0.8484 (mmp-170) cc_final: 0.8103 (mmm160) REVERT: B 59 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.8393 (m-80) REVERT: B 70 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8608 (pt) REVERT: B 118 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7858 (p0) REVERT: B 245 SER cc_start: 0.8928 (p) cc_final: 0.8713 (t) REVERT: N 38 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7925 (ptt180) REVERT: N 85 SER cc_start: 0.8315 (m) cc_final: 0.7837 (p) REVERT: L 11 LYS cc_start: 0.8417 (mttt) cc_final: 0.7997 (mttm) REVERT: A 25 LYS cc_start: 0.7092 (mptp) cc_final: 0.6697 (mtmm) REVERT: A 38 ARG cc_start: 0.7866 (mtm180) cc_final: 0.7274 (mmt-90) REVERT: A 208 PHE cc_start: 0.5652 (m-80) cc_final: 0.4701 (t80) REVERT: A 265 ARG cc_start: 0.7701 (mmt-90) cc_final: 0.6908 (ptt-90) REVERT: A 280 ARG cc_start: 0.7870 (ttt90) cc_final: 0.7399 (tpt90) REVERT: A 314 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6278 (mp0) REVERT: A 356 ARG cc_start: 0.7593 (mtm180) cc_final: 0.6958 (ptt-90) REVERT: A 381 ASP cc_start: 0.8362 (m-30) cc_final: 0.8088 (m-30) outliers start: 34 outliers final: 20 residues processed: 121 average time/residue: 1.2587 time to fit residues: 161.0520 Evaluate side-chains 123 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 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 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 314 GLU Chi-restraints excluded: chain A residue 320 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 63 optimal weight: 0.0770 chunk 68 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.174961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.137464 restraints weight = 7873.488| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.82 r_work: 0.3395 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1931 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= 0.103 Angle : 0.459 6.132 10569 Z= 0.247 Chirality : 0.041 0.169 1216 Planarity : 0.003 0.055 1334 Dihedral : 4.509 58.573 1063 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.91 % Allowed : 22.86 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.27), residues: 957 helix: 2.38 (0.27), residues: 363 sheet: 0.64 (0.36), residues: 205 loop : -1.41 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.011 0.001 PHE B 151 TYR 0.008 0.001 TYR A 339 ARG 0.002 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 364) hydrogen bonds : angle 3.65927 ( 1041) SS BOND : bond 0.00329 ( 2) SS BOND : angle 0.78714 ( 4) covalent geometry : bond 0.00231 ( 7795) covalent geometry : angle 0.45851 (10565) *********************** 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 133 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.782 Fit side-chains REVERT: R 70 HIS cc_start: 0.5378 (OUTLIER) cc_final: 0.4953 (m-70) REVERT: B 59 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8455 (m-80) REVERT: B 70 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8543 (pt) REVERT: B 118 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7832 (p0) REVERT: N 38 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7856 (ptt180) REVERT: N 85 SER cc_start: 0.8331 (m) cc_final: 0.7871 (p) REVERT: L 11 LYS cc_start: 0.8401 (mttt) cc_final: 0.8006 (mttm) REVERT: A 25 LYS cc_start: 0.7115 (mptp) cc_final: 0.6724 (mtmm) REVERT: A 38 ARG cc_start: 0.7811 (mtm180) cc_final: 0.7194 (mmt-90) REVERT: A 208 PHE cc_start: 0.5714 (m-80) cc_final: 0.4666 (t80) REVERT: A 265 ARG cc_start: 0.7741 (mmt-90) cc_final: 0.6967 (ptt-90) REVERT: A 280 ARG cc_start: 0.7817 (ttt90) cc_final: 0.7403 (tpt90) REVERT: A 314 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6318 (mp0) REVERT: A 356 ARG cc_start: 0.7601 (mtm180) cc_final: 0.6987 (ptt-90) REVERT: A 381 ASP cc_start: 0.8383 (m-30) cc_final: 0.8109 (m-30) outliers start: 32 outliers final: 20 residues processed: 122 average time/residue: 1.2789 time to fit residues: 164.7545 Evaluate side-chains 119 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain B residue 44 GLN 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 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 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 314 GLU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 386 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 3 optimal weight: 0.0170 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- 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 = 0.169400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131585 restraints weight = 7863.619| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.00 r_work: 0.3335 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1849 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= 0.129 Angle : 0.497 6.654 10569 Z= 0.266 Chirality : 0.042 0.168 1216 Planarity : 0.004 0.055 1334 Dihedral : 4.641 58.166 1063 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.16 % Allowed : 23.23 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.27), residues: 957 helix: 2.31 (0.27), residues: 361 sheet: 0.61 (0.36), residues: 206 loop : -1.44 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.008 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.011 0.001 TYR A 339 ARG 0.002 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04586 ( 364) hydrogen bonds : angle 3.77316 ( 1041) SS BOND : bond 0.00365 ( 2) SS BOND : angle 0.74707 ( 4) covalent geometry : bond 0.00304 ( 7795) covalent geometry : angle 0.49708 (10565) *********************** 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: 34 poor density : 94 time to evaluate : 0.776 Fit side-chains REVERT: R 70 HIS cc_start: 0.5419 (OUTLIER) cc_final: 0.5068 (m-70) REVERT: B 59 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8318 (m-80) REVERT: B 70 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8586 (pt) REVERT: N 38 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7919 (ptt180) REVERT: N 85 SER cc_start: 0.8333 (m) cc_final: 0.7872 (p) REVERT: L 4 MET cc_start: 0.7577 (ttp) cc_final: 0.7369 (ttm) REVERT: A 25 LYS cc_start: 0.7210 (mptp) cc_final: 0.6805 (mtmm) REVERT: A 38 ARG cc_start: 0.7979 (mtm180) cc_final: 0.7371 (mmt-90) REVERT: A 208 PHE cc_start: 0.5866 (m-80) cc_final: 0.4807 (t80) REVERT: A 265 ARG cc_start: 0.7765 (mmt-90) cc_final: 0.6973 (ptt-90) REVERT: A 280 ARG cc_start: 0.7928 (ttt90) cc_final: 0.7480 (tpt90) REVERT: A 314 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: A 356 ARG cc_start: 0.7652 (mtm180) cc_final: 0.7011 (ptt-90) REVERT: A 381 ASP cc_start: 0.8482 (m-30) cc_final: 0.8213 (m-30) outliers start: 34 outliers final: 19 residues processed: 115 average time/residue: 1.2889 time to fit residues: 156.5279 Evaluate side-chains 119 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain B residue 44 GLN 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 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 Chi-restraints excluded: chain A residue 320 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 83 optimal weight: 0.4980 chunk 72 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.171005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.133814 restraints weight = 7904.924| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.99 r_work: 0.3366 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1968 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= 0.106 Angle : 0.469 6.178 10569 Z= 0.253 Chirality : 0.042 0.179 1216 Planarity : 0.003 0.055 1334 Dihedral : 4.523 58.486 1063 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.55 % Allowed : 23.96 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 957 helix: 2.41 (0.27), residues: 363 sheet: 0.61 (0.36), residues: 209 loop : -1.33 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.011 0.001 PHE B 151 TYR 0.009 0.001 TYR A 339 ARG 0.002 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 364) hydrogen bonds : angle 3.68521 ( 1041) SS BOND : bond 0.00300 ( 2) SS BOND : angle 0.54288 ( 4) covalent geometry : bond 0.00239 ( 7795) covalent geometry : angle 0.46922 (10565) *********************** 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 126 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.831 Fit side-chains REVERT: R 70 HIS cc_start: 0.5348 (OUTLIER) cc_final: 0.4993 (m-70) REVERT: B 59 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.8472 (m-80) REVERT: B 70 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8572 (pt) REVERT: N 38 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7865 (ptt180) REVERT: N 85 SER cc_start: 0.8340 (m) cc_final: 0.7871 (p) REVERT: L 4 MET cc_start: 0.7568 (ttp) cc_final: 0.7363 (ttm) REVERT: A 25 LYS cc_start: 0.7152 (mptp) cc_final: 0.6781 (mtmm) REVERT: A 38 ARG cc_start: 0.7873 (mtm180) cc_final: 0.7215 (mmt-90) REVERT: A 208 PHE cc_start: 0.5832 (m-80) cc_final: 0.4733 (t80) REVERT: A 265 ARG cc_start: 0.7756 (mmt-90) cc_final: 0.6990 (ptt-90) REVERT: A 280 ARG cc_start: 0.7863 (ttt90) cc_final: 0.7425 (tpt90) REVERT: A 314 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6318 (mp0) REVERT: A 356 ARG cc_start: 0.7534 (mtm180) cc_final: 0.6941 (ptt-90) REVERT: A 381 ASP cc_start: 0.8411 (m-30) cc_final: 0.8144 (m-30) outliers start: 29 outliers final: 19 residues processed: 118 average time/residue: 1.2445 time to fit residues: 156.5563 Evaluate side-chains 118 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain B residue 44 GLN 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 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 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 24 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.167097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.129213 restraints weight = 7862.501| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.95 r_work: 0.3319 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7797 Z= 0.193 Angle : 0.590 8.767 10569 Z= 0.312 Chirality : 0.045 0.178 1216 Planarity : 0.004 0.055 1334 Dihedral : 4.943 57.244 1063 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.93 % Allowed : 24.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.27), residues: 957 helix: 2.02 (0.27), residues: 363 sheet: 0.55 (0.36), residues: 211 loop : -1.44 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.010 0.002 HIS A 357 PHE 0.016 0.002 PHE B 151 TYR 0.015 0.002 TYR A 339 ARG 0.003 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.05496 ( 364) hydrogen bonds : angle 4.01884 ( 1041) SS BOND : bond 0.00903 ( 2) SS BOND : angle 4.85589 ( 4) covalent geometry : bond 0.00479 ( 7795) covalent geometry : angle 0.58231 (10565) ********************** 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 119 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.902 Fit side-chains REVERT: R 70 HIS cc_start: 0.5653 (OUTLIER) cc_final: 0.5233 (m-70) REVERT: B 59 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.8258 (m-80) REVERT: N 38 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7982 (ptt180) REVERT: L 4 MET cc_start: 0.7617 (ttp) cc_final: 0.7378 (ttm) REVERT: A 24 LYS cc_start: 0.7019 (mmtt) cc_final: 0.6629 (mmpt) REVERT: A 25 LYS cc_start: 0.7273 (mptp) cc_final: 0.6897 (mtmm) REVERT: A 27 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7672 (mm-30) REVERT: A 38 ARG cc_start: 0.8017 (mtm180) cc_final: 0.7410 (mmt-90) REVERT: A 208 PHE cc_start: 0.5951 (m-80) cc_final: 0.4836 (t80) REVERT: A 265 ARG cc_start: 0.7759 (mmt-90) cc_final: 0.6996 (ptt-90) REVERT: A 280 ARG cc_start: 0.7942 (ttt90) cc_final: 0.7478 (tpt90) REVERT: A 314 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6320 (mp0) REVERT: A 356 ARG cc_start: 0.7572 (mtm180) cc_final: 0.6951 (ptt-90) REVERT: A 381 ASP cc_start: 0.8463 (m-30) cc_final: 0.8219 (m-30) outliers start: 24 outliers final: 19 residues processed: 112 average time/residue: 1.3297 time to fit residues: 157.0392 Evaluate side-chains 117 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain B residue 44 GLN 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 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 A residue 248 VAL 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 32 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.169742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130418 restraints weight = 7742.367| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.90 r_work: 0.3360 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1896 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= 0.121 Angle : 0.523 11.190 10569 Z= 0.278 Chirality : 0.043 0.175 1216 Planarity : 0.004 0.055 1334 Dihedral : 4.896 57.831 1063 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.67 % Allowed : 23.72 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 957 helix: 2.30 (0.27), residues: 360 sheet: 0.66 (0.36), residues: 210 loop : -1.41 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.001 PHE R 120 TYR 0.010 0.001 TYR A 339 ARG 0.005 0.000 ARG R 302 Details of bonding type rmsd hydrogen bonds : bond 0.04550 ( 364) hydrogen bonds : angle 3.83597 ( 1041) SS BOND : bond 0.00112 ( 2) SS BOND : angle 4.46072 ( 4) covalent geometry : bond 0.00281 ( 7795) covalent geometry : angle 0.51562 (10565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5606.37 seconds wall clock time: 97 minutes 6.03 seconds (5826.03 seconds total)