Starting phenix.real_space_refine on Wed Mar 4 00:11:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6omm_20126/03_2026/6omm_20126.cif Found real_map, /net/cci-nas-00/data/ceres_data/6omm_20126/03_2026/6omm_20126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6omm_20126/03_2026/6omm_20126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6omm_20126/03_2026/6omm_20126.map" model { file = "/net/cci-nas-00/data/ceres_data/6omm_20126/03_2026/6omm_20126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6omm_20126/03_2026/6omm_20126.cif" } resolution = 3.17 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5907 2.51 5 N 1510 2.21 5 O 1652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9134 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2341 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 13, 'TRANS': 283} Chain: "L" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 59 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "A" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1754 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 194 Unusual residues: {'CLR': 5, 'PLM': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 2.11, per 1000 atoms: 0.23 Number of scatterers: 9134 At special positions: 0 Unit cell: (122.451, 89.523, 128.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 1652 8.00 N 1510 7.00 C 5907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 358.7 milliseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB QXV L 9 " Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 38.7% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'R' and resid 21 through 50 Proline residue: R 29 - end of helix removed outlier: 3.665A pdb=" N VAL R 35 " --> pdb=" O VAL R 31 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 77 removed outlier: 3.705A pdb=" N SER R 73 " --> pdb=" O LEU R 69 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE R 74 " --> pdb=" O ALA R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 removed outlier: 3.943A pdb=" N LEU R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 removed outlier: 3.702A pdb=" N LYS R 99 " --> pdb=" O TRP R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 Processing helix chain 'R' and resid 138 through 146 Processing helix chain 'R' and resid 146 through 157 removed outlier: 4.231A pdb=" N TRP R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 164 removed outlier: 4.242A pdb=" N LEU R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 185 Processing helix chain 'R' and resid 186 through 210 removed outlier: 4.237A pdb=" N LYS R 192 " --> pdb=" O GLU R 188 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL R 193 " --> pdb=" O GLU R 189 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE R 208 " --> pdb=" O ILE R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 231 removed outlier: 3.712A pdb=" N SER R 215 " --> pdb=" O SER R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 267 removed outlier: 3.707A pdb=" N VAL R 247 " --> pdb=" O LEU R 243 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE R 252 " --> pdb=" O ALA R 248 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP R 254 " --> pdb=" O PHE R 250 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE R 255 " --> pdb=" O PHE R 251 " (cutoff:3.500A) Proline residue: R 256 - end of helix removed outlier: 3.595A pdb=" N VAL R 260 " --> pdb=" O PRO R 256 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 273 Processing helix chain 'R' and resid 278 through 303 removed outlier: 3.646A pdb=" N ILE R 282 " --> pdb=" O LYS R 278 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL R 284 " --> pdb=" O ILE R 280 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix removed outlier: 3.583A pdb=" N ASN R 294 " --> pdb=" O LEU R 290 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 317 Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.741A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 51 removed outlier: 3.705A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 removed outlier: 4.144A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.072A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.521A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.147A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.993A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.647A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'R' and resid 167 through 168 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 7.108A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.526A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.528A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.157A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.979A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.897A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.907A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.536A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.563A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.048A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2798 1.34 - 1.46: 2015 1.46 - 1.58: 4429 1.58 - 1.70: 1 1.70 - 1.82: 96 Bond restraints: 9339 Sorted by residual: bond pdb=" C QXV L 9 " pdb=" NXT QXV L 9 " ideal model delta sigma weight residual 1.339 1.444 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" CG LEU B 336 " pdb=" CD2 LEU B 336 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.00e+01 bond pdb=" CG LEU B 70 " pdb=" CD2 LEU B 70 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.68e+00 bond pdb=" CG LEU B 336 " pdb=" CD1 LEU B 336 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.19e+00 bond pdb=" C LEU R 162 " pdb=" N PHE R 163 " ideal model delta sigma weight residual 1.334 1.369 -0.034 1.43e-02 4.89e+03 5.77e+00 ... (remaining 9334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 11967 1.84 - 3.68: 566 3.68 - 5.52: 91 5.52 - 7.37: 30 7.37 - 9.21: 8 Bond angle restraints: 12662 Sorted by residual: angle pdb=" N VAL R 160 " pdb=" CA VAL R 160 " pdb=" C VAL R 160 " ideal model delta sigma weight residual 110.72 116.43 -5.71 1.01e+00 9.80e-01 3.20e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.32e+01 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 129.67 -8.13 1.91e+00 2.74e-01 1.81e+01 angle pdb=" C ALA B 257 " pdb=" N ASP B 258 " pdb=" CA ASP B 258 " ideal model delta sigma weight residual 122.35 127.61 -5.26 1.46e+00 4.69e-01 1.30e+01 angle pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " pdb=" CG ASN B 119 " ideal model delta sigma weight residual 112.60 116.08 -3.48 1.00e+00 1.00e+00 1.21e+01 ... (remaining 12657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 5426 15.10 - 30.20: 247 30.20 - 45.30: 80 45.30 - 60.40: 1 60.40 - 75.50: 4 Dihedral angle restraints: 5758 sinusoidal: 2468 harmonic: 3290 Sorted by residual: dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual -86.00 -121.33 35.33 1 1.00e+01 1.00e-02 1.77e+01 dihedral pdb=" CA HIS E 35 " pdb=" C HIS E 35 " pdb=" N TRP E 36 " pdb=" CA TRP E 36 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1298 0.096 - 0.192: 135 0.192 - 0.288: 7 0.288 - 0.384: 6 0.384 - 0.480: 4 Chirality restraints: 1450 Sorted by residual: chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" C14 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C15 CLR R 404 " pdb=" C8 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 1447 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 158 " 0.016 2.00e-02 2.50e+03 3.03e-02 9.16e+00 pdb=" C LEU R 158 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU R 158 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO R 159 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 111 " 0.018 2.00e-02 2.50e+03 1.69e-02 7.11e+00 pdb=" CG TRP E 111 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP E 111 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP E 111 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 111 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 111 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 111 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 111 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 111 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 27 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C ILE R 27 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE R 27 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU R 28 " 0.013 2.00e-02 2.50e+03 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 911 2.76 - 3.29: 8556 3.29 - 3.83: 15205 3.83 - 4.36: 17772 4.36 - 4.90: 31044 Nonbonded interactions: 73488 Sorted by model distance: nonbonded pdb=" O ALA R 153 " pdb=" OG1 THR R 157 " model vdw 2.222 3.040 nonbonded pdb=" OG SER B 281 " pdb=" O HIS C 44 " model vdw 2.279 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.352 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.357 3.040 ... (remaining 73483 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: 1.140 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.570 Find NCS groups from input model: 0.050 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.005 0.105 9342 Z= 0.242 Angle : 0.929 9.207 12668 Z= 0.483 Chirality : 0.064 0.480 1450 Planarity : 0.006 0.048 1555 Dihedral : 9.848 75.504 3629 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.21), residues: 1123 helix: -1.84 (0.20), residues: 410 sheet: -1.61 (0.29), residues: 273 loop : -2.06 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 68 TYR 0.021 0.002 TYR E 59 PHE 0.033 0.003 PHE R 161 TRP 0.046 0.004 TRP E 111 HIS 0.008 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 9339) covalent geometry : angle 0.92817 (12662) SS BOND : bond 0.00268 ( 3) SS BOND : angle 1.85640 ( 6) hydrogen bonds : bond 0.11264 ( 438) hydrogen bonds : angle 6.81575 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 39 LEU cc_start: 0.8789 (tt) cc_final: 0.8500 (tt) REVERT: R 90 LYS cc_start: 0.7884 (mttt) cc_final: 0.6884 (mmmt) REVERT: R 174 THR cc_start: 0.6256 (p) cc_final: 0.5610 (p) REVERT: R 179 ASN cc_start: 0.7691 (t0) cc_final: 0.7161 (m110) REVERT: R 191 LEU cc_start: 0.6671 (tp) cc_final: 0.6432 (pp) REVERT: R 300 MET cc_start: 0.8486 (mtt) cc_final: 0.8215 (mtm) REVERT: A 48 THR cc_start: 0.8560 (m) cc_final: 0.8288 (p) REVERT: A 327 THR cc_start: 0.8168 (p) cc_final: 0.7403 (m) REVERT: A 346 ASN cc_start: 0.8778 (m-40) cc_final: 0.8511 (m110) REVERT: B 267 ASP cc_start: 0.8710 (m-30) cc_final: 0.8263 (t0) REVERT: B 273 ILE cc_start: 0.8378 (mp) cc_final: 0.8163 (mt) REVERT: B 291 ASP cc_start: 0.7792 (t70) cc_final: 0.7490 (t70) REVERT: B 297 TRP cc_start: 0.8763 (m100) cc_final: 0.8362 (m100) REVERT: E 217 SER cc_start: 0.8145 (t) cc_final: 0.6768 (p) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1223 time to fit residues: 52.1147 Evaluate side-chains 204 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 307 GLN A 204 GLN B 32 GLN B 62 HIS B 91 HIS C 58 GLN E 13 GLN E 142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.143942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111490 restraints weight = 13593.992| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.68 r_work: 0.3178 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 9342 Z= 0.138 Angle : 0.607 8.266 12668 Z= 0.312 Chirality : 0.042 0.147 1450 Planarity : 0.004 0.035 1555 Dihedral : 6.011 56.012 1596 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.36 % Allowed : 12.30 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.23), residues: 1123 helix: 0.16 (0.25), residues: 417 sheet: -1.13 (0.30), residues: 265 loop : -1.60 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 129 TYR 0.014 0.001 TYR E 190 PHE 0.018 0.001 PHE R 96 TRP 0.018 0.002 TRP B 169 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9339) covalent geometry : angle 0.60563 (12662) SS BOND : bond 0.00886 ( 3) SS BOND : angle 2.14711 ( 6) hydrogen bonds : bond 0.03390 ( 438) hydrogen bonds : angle 5.29318 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 71 ASP cc_start: 0.7681 (t70) cc_final: 0.7345 (t70) REVERT: R 90 LYS cc_start: 0.8186 (mttt) cc_final: 0.7932 (mmmm) REVERT: R 191 LEU cc_start: 0.6961 (tp) cc_final: 0.6559 (pp) REVERT: R 300 MET cc_start: 0.8457 (mtt) cc_final: 0.8112 (mtm) REVERT: L 7 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6687 (mtp) REVERT: A 48 THR cc_start: 0.8325 (m) cc_final: 0.8074 (p) REVERT: A 52 GLN cc_start: 0.6927 (OUTLIER) cc_final: 0.6362 (tt0) REVERT: A 315 ASP cc_start: 0.7194 (p0) cc_final: 0.6938 (p0) REVERT: A 327 THR cc_start: 0.7971 (p) cc_final: 0.7628 (m) REVERT: A 346 ASN cc_start: 0.8880 (m-40) cc_final: 0.8578 (m110) REVERT: B 101 MET cc_start: 0.8711 (mmm) cc_final: 0.8408 (mmm) REVERT: B 267 ASP cc_start: 0.8124 (m-30) cc_final: 0.7912 (t0) REVERT: B 291 ASP cc_start: 0.7644 (t70) cc_final: 0.7218 (t70) REVERT: B 297 TRP cc_start: 0.8975 (m100) cc_final: 0.8440 (m100) REVERT: C 13 ARG cc_start: 0.7800 (ptp-110) cc_final: 0.7580 (ttm-80) REVERT: E 6 GLU cc_start: 0.8048 (mp0) cc_final: 0.7623 (mp0) REVERT: E 220 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7425 (mp0) outliers start: 23 outliers final: 10 residues processed: 226 average time/residue: 0.1190 time to fit residues: 35.6962 Evaluate side-chains 194 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain L residue 7 MET Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 44 ASN R 258 GLN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 333 GLN B 175 GLN E 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.102171 restraints weight = 13593.518| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.41 r_work: 0.3136 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 9342 Z= 0.177 Angle : 0.597 8.949 12668 Z= 0.307 Chirality : 0.042 0.198 1450 Planarity : 0.004 0.041 1555 Dihedral : 5.901 56.871 1596 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.89 % Allowed : 12.50 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.24), residues: 1123 helix: 0.75 (0.26), residues: 416 sheet: -0.77 (0.31), residues: 244 loop : -1.45 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 218 TYR 0.018 0.002 TYR B 59 PHE 0.012 0.001 PHE B 234 TRP 0.016 0.002 TRP B 211 HIS 0.005 0.001 HIS R 102 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 9339) covalent geometry : angle 0.59623 (12662) SS BOND : bond 0.00389 ( 3) SS BOND : angle 1.40536 ( 6) hydrogen bonds : bond 0.03313 ( 438) hydrogen bonds : angle 5.04410 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7387 (ttm110) cc_final: 0.7114 (ptm160) REVERT: R 71 ASP cc_start: 0.7834 (t70) cc_final: 0.7574 (t70) REVERT: R 90 LYS cc_start: 0.8314 (mttt) cc_final: 0.8018 (mmmm) REVERT: R 161 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7644 (t80) REVERT: R 191 LEU cc_start: 0.7012 (tp) cc_final: 0.6569 (pp) REVERT: R 197 MET cc_start: 0.8150 (tmm) cc_final: 0.7948 (tmm) REVERT: R 300 MET cc_start: 0.8532 (mtt) cc_final: 0.8182 (mtm) REVERT: A 48 THR cc_start: 0.8326 (m) cc_final: 0.8067 (p) REVERT: A 242 ARG cc_start: 0.7545 (mtt-85) cc_final: 0.7159 (mtt-85) REVERT: A 247 MET cc_start: 0.8495 (mmm) cc_final: 0.8192 (mmm) REVERT: A 327 THR cc_start: 0.8028 (p) cc_final: 0.7816 (m) REVERT: B 247 ASP cc_start: 0.7672 (t70) cc_final: 0.6602 (t0) REVERT: B 267 ASP cc_start: 0.8470 (m-30) cc_final: 0.8034 (t0) REVERT: B 291 ASP cc_start: 0.8150 (t70) cc_final: 0.7674 (t70) REVERT: B 297 TRP cc_start: 0.9157 (m100) cc_final: 0.8673 (m100) REVERT: C 13 ARG cc_start: 0.7987 (ptp-110) cc_final: 0.7763 (ttm-80) REVERT: E 6 GLU cc_start: 0.8275 (mp0) cc_final: 0.7910 (mp0) REVERT: E 153 GLU cc_start: 0.8059 (pt0) cc_final: 0.7693 (pm20) REVERT: E 219 LEU cc_start: 0.8749 (mt) cc_final: 0.8447 (mp) outliers start: 38 outliers final: 18 residues processed: 221 average time/residue: 0.1049 time to fit residues: 31.6610 Evaluate side-chains 205 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 308 ASP Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 103 optimal weight: 0.3980 chunk 57 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 88 optimal weight: 0.3980 chunk 75 optimal weight: 0.0030 chunk 24 optimal weight: 0.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN E 13 GLN E 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.145411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.112595 restraints weight = 13542.401| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.54 r_work: 0.3209 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 9342 Z= 0.110 Angle : 0.571 8.901 12668 Z= 0.290 Chirality : 0.041 0.171 1450 Planarity : 0.003 0.044 1555 Dihedral : 5.517 54.461 1596 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.66 % Allowed : 14.45 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.24), residues: 1123 helix: 1.11 (0.26), residues: 420 sheet: -0.66 (0.30), residues: 257 loop : -1.29 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 218 TYR 0.011 0.001 TYR E 190 PHE 0.010 0.001 PHE R 163 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS R 102 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9339) covalent geometry : angle 0.57078 (12662) SS BOND : bond 0.00275 ( 3) SS BOND : angle 0.93411 ( 6) hydrogen bonds : bond 0.03018 ( 438) hydrogen bonds : angle 4.76935 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7375 (ttm110) cc_final: 0.7006 (ptp-110) REVERT: R 90 LYS cc_start: 0.8328 (mttt) cc_final: 0.8048 (mmmm) REVERT: R 161 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7600 (t80) REVERT: R 191 LEU cc_start: 0.6935 (tp) cc_final: 0.6603 (pp) REVERT: L 8 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7769 (p) REVERT: A 48 THR cc_start: 0.8282 (m) cc_final: 0.8044 (p) REVERT: A 242 ARG cc_start: 0.7584 (mtt-85) cc_final: 0.7293 (mtt-85) REVERT: A 247 MET cc_start: 0.8334 (mmm) cc_final: 0.7932 (mmm) REVERT: A 287 TYR cc_start: 0.7162 (m-80) cc_final: 0.6941 (m-10) REVERT: A 306 GLN cc_start: 0.8262 (tp40) cc_final: 0.7950 (tp40) REVERT: A 327 THR cc_start: 0.8037 (p) cc_final: 0.7747 (m) REVERT: B 219 ARG cc_start: 0.8751 (mmm-85) cc_final: 0.8451 (mtt-85) REVERT: B 267 ASP cc_start: 0.8143 (m-30) cc_final: 0.7845 (t0) REVERT: B 291 ASP cc_start: 0.7541 (t70) cc_final: 0.7106 (t70) REVERT: B 297 TRP cc_start: 0.8957 (m100) cc_final: 0.8449 (m100) REVERT: B 331 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8506 (t) REVERT: C 13 ARG cc_start: 0.8008 (ptp-110) cc_final: 0.7753 (ttm-80) REVERT: E 161 SER cc_start: 0.8865 (t) cc_final: 0.8415 (t) outliers start: 26 outliers final: 15 residues processed: 204 average time/residue: 0.1061 time to fit residues: 29.4895 Evaluate side-chains 202 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 109 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 67 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 44 ASN R 66 ASN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 175 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 77 ASN E 142 GLN E 186 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.131614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.099154 restraints weight = 13607.223| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.62 r_work: 0.2978 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 9342 Z= 0.381 Angle : 0.772 8.593 12668 Z= 0.392 Chirality : 0.048 0.197 1450 Planarity : 0.005 0.047 1555 Dihedral : 6.757 58.672 1596 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.00 % Allowed : 14.24 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.24), residues: 1123 helix: 0.95 (0.26), residues: 416 sheet: -0.96 (0.30), residues: 271 loop : -1.27 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 205 TYR 0.023 0.003 TYR B 59 PHE 0.015 0.002 PHE R 118 TRP 0.028 0.003 TRP R 95 HIS 0.008 0.002 HIS R 102 Details of bonding type rmsd covalent geometry : bond 0.00889 ( 9339) covalent geometry : angle 0.77190 (12662) SS BOND : bond 0.00193 ( 3) SS BOND : angle 1.52077 ( 6) hydrogen bonds : bond 0.03950 ( 438) hydrogen bonds : angle 5.29775 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7468 (ttm110) cc_final: 0.7079 (ptp-170) REVERT: R 44 ASN cc_start: 0.7809 (m-40) cc_final: 0.7595 (m110) REVERT: R 161 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7971 (t80) REVERT: R 191 LEU cc_start: 0.7224 (tp) cc_final: 0.6793 (pp) REVERT: A 48 THR cc_start: 0.8241 (m) cc_final: 0.7933 (p) REVERT: A 242 ARG cc_start: 0.8003 (mtt-85) cc_final: 0.7751 (mtt-85) REVERT: A 247 MET cc_start: 0.8424 (mmm) cc_final: 0.8103 (mmm) REVERT: A 324 THR cc_start: 0.8287 (p) cc_final: 0.8084 (p) REVERT: B 172 GLU cc_start: 0.7974 (pm20) cc_final: 0.7280 (pm20) REVERT: B 219 ARG cc_start: 0.8902 (mmm-85) cc_final: 0.8580 (mtt-85) REVERT: B 243 THR cc_start: 0.9177 (m) cc_final: 0.8619 (p) REVERT: B 247 ASP cc_start: 0.7412 (t70) cc_final: 0.7148 (t0) REVERT: B 267 ASP cc_start: 0.8511 (m-30) cc_final: 0.8091 (t0) REVERT: B 291 ASP cc_start: 0.8338 (t70) cc_final: 0.7729 (t0) REVERT: C 13 ARG cc_start: 0.8314 (ptp-110) cc_final: 0.8076 (ttm-80) REVERT: C 38 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8488 (mtt) REVERT: C 58 GLN cc_start: 0.7841 (pm20) cc_final: 0.7615 (pm20) REVERT: E 140 MET cc_start: 0.8869 (mmm) cc_final: 0.7849 (mmm) REVERT: E 220 GLU cc_start: 0.7507 (mp0) cc_final: 0.6594 (mp0) outliers start: 39 outliers final: 28 residues processed: 205 average time/residue: 0.0945 time to fit residues: 26.8239 Evaluate side-chains 192 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 308 ASP Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 219 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.138945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101217 restraints weight = 13272.303| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.41 r_work: 0.3126 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9342 Z= 0.144 Angle : 0.608 8.252 12668 Z= 0.309 Chirality : 0.042 0.149 1450 Planarity : 0.003 0.045 1555 Dihedral : 5.834 53.738 1596 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.38 % Allowed : 16.09 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.25), residues: 1123 helix: 1.19 (0.26), residues: 417 sheet: -0.59 (0.31), residues: 252 loop : -1.20 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 24 TYR 0.012 0.001 TYR E 59 PHE 0.009 0.001 PHE R 178 TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS R 102 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9339) covalent geometry : angle 0.60787 (12662) SS BOND : bond 0.00277 ( 3) SS BOND : angle 0.99075 ( 6) hydrogen bonds : bond 0.03254 ( 438) hydrogen bonds : angle 4.92518 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.370 Fit side-chains REVERT: R 26 ARG cc_start: 0.7332 (ttm110) cc_final: 0.7054 (ptp-110) REVERT: R 161 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7916 (t80) REVERT: R 191 LEU cc_start: 0.7192 (tp) cc_final: 0.6783 (pp) REVERT: R 298 ASN cc_start: 0.8463 (m-40) cc_final: 0.8176 (m-40) REVERT: R 300 MET cc_start: 0.8688 (mtt) cc_final: 0.8305 (mtm) REVERT: A 19 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8230 (pt) REVERT: A 48 THR cc_start: 0.8208 (m) cc_final: 0.7909 (p) REVERT: A 247 MET cc_start: 0.8362 (mmm) cc_final: 0.8069 (mmm) REVERT: A 306 GLN cc_start: 0.8416 (tp40) cc_final: 0.8089 (tp40) REVERT: A 316 THR cc_start: 0.7972 (p) cc_final: 0.7589 (t) REVERT: B 101 MET cc_start: 0.8760 (mmm) cc_final: 0.8533 (mmm) REVERT: B 234 PHE cc_start: 0.9469 (OUTLIER) cc_final: 0.9070 (m-80) REVERT: B 243 THR cc_start: 0.9066 (m) cc_final: 0.8538 (p) REVERT: B 267 ASP cc_start: 0.8492 (m-30) cc_final: 0.8018 (t0) REVERT: B 291 ASP cc_start: 0.8021 (t70) cc_final: 0.7583 (t70) REVERT: B 297 TRP cc_start: 0.9242 (m100) cc_final: 0.8841 (m100) REVERT: C 13 ARG cc_start: 0.8275 (ptp-110) cc_final: 0.8053 (ttm-80) REVERT: C 16 VAL cc_start: 0.8941 (t) cc_final: 0.8516 (m) REVERT: C 38 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8466 (mtt) REVERT: E 140 MET cc_start: 0.8864 (mmm) cc_final: 0.7693 (mmm) REVERT: E 161 SER cc_start: 0.9159 (t) cc_final: 0.8528 (t) outliers start: 33 outliers final: 25 residues processed: 203 average time/residue: 0.0982 time to fit residues: 27.4514 Evaluate side-chains 192 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 219 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 84 optimal weight: 0.0000 chunk 20 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 39 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.142085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.109087 restraints weight = 13383.896| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.53 r_work: 0.3157 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9342 Z= 0.125 Angle : 0.592 9.440 12668 Z= 0.300 Chirality : 0.041 0.144 1450 Planarity : 0.004 0.047 1555 Dihedral : 5.274 55.546 1596 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.79 % Allowed : 16.50 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.25), residues: 1123 helix: 1.28 (0.26), residues: 419 sheet: -0.46 (0.31), residues: 269 loop : -1.07 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.011 0.001 TYR E 190 PHE 0.010 0.001 PHE E 32 TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS R 102 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9339) covalent geometry : angle 0.59199 (12662) SS BOND : bond 0.00254 ( 3) SS BOND : angle 0.94260 ( 6) hydrogen bonds : bond 0.03107 ( 438) hydrogen bonds : angle 4.76023 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.346 Fit side-chains REVERT: R 26 ARG cc_start: 0.7221 (ttm110) cc_final: 0.6997 (ptp-110) REVERT: R 161 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7907 (t80) REVERT: R 191 LEU cc_start: 0.6980 (tp) cc_final: 0.6659 (pp) REVERT: A 48 THR cc_start: 0.8027 (m) cc_final: 0.7755 (p) REVERT: A 242 ARG cc_start: 0.7947 (mtt-85) cc_final: 0.7692 (mtt-85) REVERT: A 247 MET cc_start: 0.8236 (mmm) cc_final: 0.7956 (mmm) REVERT: A 306 GLN cc_start: 0.8344 (tp40) cc_final: 0.8034 (tp40) REVERT: A 316 THR cc_start: 0.7748 (p) cc_final: 0.7432 (t) REVERT: B 101 MET cc_start: 0.8504 (mmm) cc_final: 0.8291 (mmm) REVERT: B 207 SER cc_start: 0.8820 (m) cc_final: 0.8470 (p) REVERT: B 217 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7105 (ppp) REVERT: B 234 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.9010 (m-80) REVERT: B 243 THR cc_start: 0.8918 (m) cc_final: 0.8393 (p) REVERT: B 267 ASP cc_start: 0.8279 (m-30) cc_final: 0.7933 (t0) REVERT: B 291 ASP cc_start: 0.7581 (t70) cc_final: 0.7205 (t70) REVERT: B 297 TRP cc_start: 0.9090 (m100) cc_final: 0.8784 (m100) REVERT: C 13 ARG cc_start: 0.8293 (ptp-110) cc_final: 0.8067 (ttm-80) REVERT: C 38 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8526 (mtt) REVERT: E 140 MET cc_start: 0.8688 (mmm) cc_final: 0.7655 (mmm) REVERT: E 161 SER cc_start: 0.8968 (t) cc_final: 0.8627 (p) REVERT: E 183 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8666 (tt0) REVERT: E 220 GLU cc_start: 0.7486 (mp0) cc_final: 0.7275 (mp0) outliers start: 37 outliers final: 24 residues processed: 199 average time/residue: 0.0975 time to fit residues: 27.0158 Evaluate side-chains 194 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain E residue 219 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 0.0770 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN A 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.104210 restraints weight = 13199.118| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.40 r_work: 0.3165 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9342 Z= 0.133 Angle : 0.605 8.902 12668 Z= 0.306 Chirality : 0.041 0.142 1450 Planarity : 0.004 0.048 1555 Dihedral : 5.118 56.584 1596 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.59 % Allowed : 17.62 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.25), residues: 1123 helix: 1.29 (0.26), residues: 421 sheet: -0.46 (0.30), residues: 290 loop : -0.97 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.010 0.001 TYR E 190 PHE 0.010 0.001 PHE E 32 TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS R 102 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9339) covalent geometry : angle 0.60505 (12662) SS BOND : bond 0.00253 ( 3) SS BOND : angle 0.86821 ( 6) hydrogen bonds : bond 0.03058 ( 438) hydrogen bonds : angle 4.71616 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.215 Fit side-chains REVERT: R 26 ARG cc_start: 0.7205 (ttm110) cc_final: 0.6909 (ptp-170) REVERT: R 161 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.8021 (t80) REVERT: R 191 LEU cc_start: 0.6859 (tp) cc_final: 0.6565 (pp) REVERT: A 48 THR cc_start: 0.7962 (m) cc_final: 0.7648 (p) REVERT: A 242 ARG cc_start: 0.7958 (mtt-85) cc_final: 0.7398 (mtt90) REVERT: A 247 MET cc_start: 0.8335 (mmm) cc_final: 0.8016 (mmm) REVERT: A 306 GLN cc_start: 0.8428 (tp40) cc_final: 0.8097 (tp40) REVERT: A 313 ARG cc_start: 0.7997 (ptp90) cc_final: 0.7631 (ptp-170) REVERT: A 316 THR cc_start: 0.7852 (OUTLIER) cc_final: 0.7590 (t) REVERT: B 101 MET cc_start: 0.8656 (mmm) cc_final: 0.8394 (mmm) REVERT: B 207 SER cc_start: 0.8890 (m) cc_final: 0.8650 (p) REVERT: B 217 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.6947 (ppp) REVERT: B 219 ARG cc_start: 0.8817 (mmm-85) cc_final: 0.7824 (mmt-90) REVERT: B 234 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8993 (m-80) REVERT: B 243 THR cc_start: 0.8991 (m) cc_final: 0.8494 (p) REVERT: B 267 ASP cc_start: 0.8471 (m-30) cc_final: 0.8014 (t0) REVERT: B 291 ASP cc_start: 0.7830 (t70) cc_final: 0.7444 (t70) REVERT: B 297 TRP cc_start: 0.9132 (m100) cc_final: 0.8811 (m100) REVERT: C 38 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8541 (mtt) REVERT: E 140 MET cc_start: 0.8871 (mmm) cc_final: 0.7661 (mmm) REVERT: E 161 SER cc_start: 0.9093 (t) cc_final: 0.8733 (p) outliers start: 35 outliers final: 26 residues processed: 199 average time/residue: 0.0934 time to fit residues: 25.7538 Evaluate side-chains 200 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 219 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 76 optimal weight: 0.2980 chunk 89 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN B 75 GLN B 155 ASN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.140692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.108885 restraints weight = 13635.541| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.57 r_work: 0.3141 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 9342 Z= 0.124 Angle : 0.596 8.972 12668 Z= 0.303 Chirality : 0.041 0.146 1450 Planarity : 0.004 0.048 1555 Dihedral : 4.949 56.813 1596 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.18 % Allowed : 18.44 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.25), residues: 1123 helix: 1.45 (0.26), residues: 415 sheet: -0.37 (0.30), residues: 287 loop : -0.97 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.010 0.001 TYR E 190 PHE 0.011 0.001 PHE B 234 TRP 0.023 0.001 TRP R 91 HIS 0.004 0.001 HIS R 102 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9339) covalent geometry : angle 0.59592 (12662) SS BOND : bond 0.00285 ( 3) SS BOND : angle 0.85677 ( 6) hydrogen bonds : bond 0.02990 ( 438) hydrogen bonds : angle 4.62868 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.351 Fit side-chains REVERT: R 26 ARG cc_start: 0.7125 (ttm110) cc_final: 0.6923 (ptm160) REVERT: R 161 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.8024 (t80) REVERT: R 179 ASN cc_start: 0.8086 (t0) cc_final: 0.6804 (m110) REVERT: R 191 LEU cc_start: 0.6847 (tp) cc_final: 0.6604 (pp) REVERT: A 48 THR cc_start: 0.7841 (m) cc_final: 0.7570 (p) REVERT: A 242 ARG cc_start: 0.7936 (mtt-85) cc_final: 0.7427 (mtt90) REVERT: A 306 GLN cc_start: 0.8296 (tp40) cc_final: 0.7984 (tp40) REVERT: A 313 ARG cc_start: 0.7877 (ptp90) cc_final: 0.7576 (ptp-170) REVERT: A 316 THR cc_start: 0.7859 (OUTLIER) cc_final: 0.7590 (t) REVERT: B 101 MET cc_start: 0.8434 (mmm) cc_final: 0.8188 (mmm) REVERT: B 207 SER cc_start: 0.8776 (m) cc_final: 0.8514 (p) REVERT: B 217 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.6892 (ppp) REVERT: B 219 ARG cc_start: 0.8679 (mmm-85) cc_final: 0.7797 (mmt-90) REVERT: B 234 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.8915 (m-80) REVERT: B 243 THR cc_start: 0.8850 (m) cc_final: 0.8343 (p) REVERT: B 267 ASP cc_start: 0.8232 (m-30) cc_final: 0.7916 (t0) REVERT: B 291 ASP cc_start: 0.7597 (t70) cc_final: 0.7236 (t70) REVERT: B 297 TRP cc_start: 0.8946 (m100) cc_final: 0.8668 (m100) REVERT: E 140 MET cc_start: 0.8725 (mmm) cc_final: 0.7559 (mmm) REVERT: E 161 SER cc_start: 0.8918 (t) cc_final: 0.8621 (p) outliers start: 31 outliers final: 22 residues processed: 198 average time/residue: 0.1000 time to fit residues: 27.3219 Evaluate side-chains 195 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 76 optimal weight: 0.0470 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN E 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.103608 restraints weight = 13543.090| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.33 r_work: 0.3160 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9342 Z= 0.134 Angle : 0.621 9.223 12668 Z= 0.315 Chirality : 0.041 0.148 1450 Planarity : 0.004 0.048 1555 Dihedral : 4.894 57.446 1596 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.77 % Allowed : 19.16 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.25), residues: 1123 helix: 1.38 (0.26), residues: 420 sheet: -0.29 (0.30), residues: 285 loop : -1.00 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 13 TYR 0.010 0.001 TYR E 190 PHE 0.011 0.001 PHE B 234 TRP 0.029 0.001 TRP R 91 HIS 0.004 0.001 HIS R 102 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9339) covalent geometry : angle 0.62047 (12662) SS BOND : bond 0.00283 ( 3) SS BOND : angle 0.83408 ( 6) hydrogen bonds : bond 0.03009 ( 438) hydrogen bonds : angle 4.63562 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.358 Fit side-chains REVERT: R 26 ARG cc_start: 0.7148 (ttm110) cc_final: 0.6897 (ptm160) REVERT: R 39 LEU cc_start: 0.9214 (tp) cc_final: 0.8937 (tt) REVERT: R 158 LEU cc_start: 0.7545 (tp) cc_final: 0.7325 (mt) REVERT: R 161 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8023 (t80) REVERT: R 179 ASN cc_start: 0.8123 (t0) cc_final: 0.6776 (m110) REVERT: R 191 LEU cc_start: 0.6847 (tp) cc_final: 0.6588 (pp) REVERT: A 48 THR cc_start: 0.7648 (m) cc_final: 0.7388 (p) REVERT: A 306 GLN cc_start: 0.8366 (tp40) cc_final: 0.8072 (tp40) REVERT: A 313 ARG cc_start: 0.8015 (ptp90) cc_final: 0.7683 (ptp-170) REVERT: A 316 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7590 (t) REVERT: B 101 MET cc_start: 0.8641 (mmm) cc_final: 0.8366 (mmm) REVERT: B 207 SER cc_start: 0.8870 (m) cc_final: 0.8592 (p) REVERT: B 217 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7036 (ppp) REVERT: B 219 ARG cc_start: 0.8758 (mmm-85) cc_final: 0.7818 (mmt-90) REVERT: B 234 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.8969 (m-80) REVERT: B 243 THR cc_start: 0.8975 (m) cc_final: 0.8496 (p) REVERT: B 267 ASP cc_start: 0.8339 (m-30) cc_final: 0.8050 (m-30) REVERT: B 291 ASP cc_start: 0.7832 (t70) cc_final: 0.7464 (t70) REVERT: B 297 TRP cc_start: 0.9037 (m100) cc_final: 0.8754 (m100) REVERT: E 140 MET cc_start: 0.8843 (mmm) cc_final: 0.7558 (mmm) REVERT: E 161 SER cc_start: 0.9025 (t) cc_final: 0.8700 (p) outliers start: 27 outliers final: 22 residues processed: 192 average time/residue: 0.1048 time to fit residues: 27.6056 Evaluate side-chains 189 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.138810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.102982 restraints weight = 13241.992| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.28 r_work: 0.3150 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9342 Z= 0.142 Angle : 0.624 9.084 12668 Z= 0.316 Chirality : 0.041 0.150 1450 Planarity : 0.004 0.048 1555 Dihedral : 4.907 57.742 1596 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.66 % Allowed : 19.16 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.25), residues: 1123 helix: 1.34 (0.26), residues: 421 sheet: -0.26 (0.30), residues: 285 loop : -1.01 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 13 TYR 0.010 0.001 TYR E 190 PHE 0.011 0.001 PHE B 234 TRP 0.025 0.001 TRP R 91 HIS 0.004 0.001 HIS R 102 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9339) covalent geometry : angle 0.62377 (12662) SS BOND : bond 0.00267 ( 3) SS BOND : angle 0.84957 ( 6) hydrogen bonds : bond 0.03061 ( 438) hydrogen bonds : angle 4.64661 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2779.22 seconds wall clock time: 48 minutes 16.47 seconds (2896.47 seconds total)