Starting phenix.real_space_refine on Fri Sep 11 12:57:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6omm_20126/09_2026/6omm_20126.cif Found real_map, /net/cci-nas-00/data/ceres_data/6omm_20126/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6omm_20126/09_2026/6omm_20126.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6omm_20126/09_2026/6omm_20126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6omm_20126/09_2026/6omm_20126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6omm_20126/09_2026/6omm_20126.map" model { file = "/net/cci-nas-00/data/ceres_data/6omm_20126/09_2026/6omm_20126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6omm_20126/09_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-2.2.1-6174/lib/python3.11/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: 1.69, per 1000 atoms: 0.19 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: 0.71 Conformation dependent library (CDL) restraints added in 322.7 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: 0.27 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: 1.43 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 5172 15.10 - 30.20: 228 30.20 - 45.30: 73 45.30 - 60.40: 1 60.40 - 75.50: 4 Dihedral angle restraints: 5478 sinusoidal: 2188 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 5475 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: 1.280 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.670 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: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 9.846 75.504 3349 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/Z covalent geometry : bond 0.00523 / 0.24 ( 9339) covalent geometry : angle 0.92817 / 0.48 (12662) SS BOND : bond 0.00268 / 0.14 ( 3) SS BOND : angle 1.85640 / 0.91 ( 6) hydrogen bonds : bond 0.11264 / 6.73 ( 438) hydrogen bonds : angle 6.81575 / 4.96 ( 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 : 0.363 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: 0.1051 time to fit residues: 45.3563 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 : 0.215 ------------------------------------------------------------------------------- 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... ** 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 E 194 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.143934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111455 restraints weight = 13607.222| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.72 r_work: 0.3176 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 9342 Z= 0.140 Angle : 0.612 8.221 12668 Z= 0.314 Chirality : 0.041 0.144 1450 Planarity : 0.004 0.035 1555 Dihedral : 5.791 58.717 1316 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.25 % Allowed : 12.19 % Favored : 85.55 % 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: -1.39 (0.23), residues: 1123 helix: 0.08 (0.25), residues: 417 sheet: -1.14 (0.30), residues: 265 loop : -1.64 (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 B 59 PHE 0.016 0.001 PHE R 96 TRP 0.017 0.002 TRP B 169 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 9339) covalent geometry : angle 0.61033 / 0.31 (12662) SS BOND : bond 0.01038 / 0.65 ( 3) SS BOND : angle 1.94058 / 0.75 ( 6) hydrogen bonds : bond 0.03473 / 2.24 ( 438) hydrogen bonds : angle 5.34573 / 3.88 ( 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 232 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 71 ASP cc_start: 0.7670 (t70) cc_final: 0.7321 (t70) REVERT: R 90 LYS cc_start: 0.8190 (mttt) cc_final: 0.7929 (mmmm) REVERT: R 191 LEU cc_start: 0.6948 (tp) cc_final: 0.6538 (pp) REVERT: R 300 MET cc_start: 0.8470 (mtt) cc_final: 0.8131 (mtm) REVERT: L 7 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6690 (mtp) REVERT: A 48 THR cc_start: 0.8322 (m) cc_final: 0.8071 (p) REVERT: A 315 ASP cc_start: 0.7207 (p0) cc_final: 0.6965 (p0) REVERT: A 327 THR cc_start: 0.8058 (p) cc_final: 0.7664 (m) REVERT: A 331 ASN cc_start: 0.7893 (m-40) cc_final: 0.7624 (m110) REVERT: A 346 ASN cc_start: 0.8882 (m-40) cc_final: 0.8584 (m110) REVERT: B 101 MET cc_start: 0.8724 (mmm) cc_final: 0.8444 (mmm) REVERT: B 267 ASP cc_start: 0.8150 (m-30) cc_final: 0.7939 (t0) REVERT: B 291 ASP cc_start: 0.7632 (t70) cc_final: 0.7206 (t70) REVERT: B 297 TRP cc_start: 0.8967 (m100) cc_final: 0.8420 (m100) REVERT: C 13 ARG cc_start: 0.7793 (ptp-110) cc_final: 0.7584 (ttm-80) REVERT: E 6 GLU cc_start: 0.8051 (mp0) cc_final: 0.7429 (mp0) REVERT: E 220 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7472 (mp0) outliers start: 22 outliers final: 11 residues processed: 224 average time/residue: 0.1015 time to fit residues: 30.3530 Evaluate side-chains 192 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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: 6.9990 chunk 23 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 99 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 333 GLN B 155 ASN B 175 GLN E 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.142922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109776 restraints weight = 13582.584| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.58 r_work: 0.3178 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 9342 Z= 0.135 Angle : 0.573 8.896 12668 Z= 0.294 Chirality : 0.041 0.202 1450 Planarity : 0.004 0.040 1555 Dihedral : 5.618 58.185 1316 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.79 % Allowed : 12.40 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.24), residues: 1123 helix: 0.82 (0.26), residues: 416 sheet: -0.82 (0.31), residues: 249 loop : -1.43 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 26 TYR 0.014 0.001 TYR B 59 PHE 0.012 0.001 PHE B 234 TRP 0.017 0.002 TRP B 211 HIS 0.004 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 ( 9339) covalent geometry : angle 0.57256 / 0.29 (12662) SS BOND : bond 0.00387 / 0.24 ( 3) SS BOND : angle 1.23497 / 0.48 ( 6) hydrogen bonds : bond 0.03167 / 2.07 ( 438) hydrogen bonds : angle 4.94175 / 3.60 ( 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 234 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7446 (ttm110) cc_final: 0.7168 (ptm160) REVERT: R 90 LYS cc_start: 0.8263 (mttt) cc_final: 0.7989 (mmmm) REVERT: R 191 LEU cc_start: 0.6978 (tp) cc_final: 0.6595 (pp) REVERT: R 300 MET cc_start: 0.8397 (mtt) cc_final: 0.8068 (mtm) REVERT: A 48 THR cc_start: 0.8320 (m) cc_final: 0.8081 (p) REVERT: A 52 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6402 (tt0) REVERT: A 242 ARG cc_start: 0.7458 (mtt-85) cc_final: 0.7258 (mtt-85) REVERT: A 247 MET cc_start: 0.8432 (mmm) cc_final: 0.8110 (mmm) REVERT: A 327 THR cc_start: 0.8128 (p) cc_final: 0.7776 (m) REVERT: A 331 ASN cc_start: 0.7874 (m-40) cc_final: 0.7621 (m110) REVERT: B 267 ASP cc_start: 0.8155 (m-30) cc_final: 0.7862 (t0) REVERT: B 291 ASP cc_start: 0.7693 (t70) cc_final: 0.7260 (t70) REVERT: B 297 TRP cc_start: 0.8994 (m100) cc_final: 0.8497 (m100) REVERT: C 9 ILE cc_start: 0.4742 (OUTLIER) cc_final: 0.4274 (mp) REVERT: C 13 ARG cc_start: 0.7908 (ptp-110) cc_final: 0.7663 (ttm-80) REVERT: C 37 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8232 (tt) REVERT: E 6 GLU cc_start: 0.8151 (mp0) cc_final: 0.7851 (mp0) outliers start: 37 outliers final: 20 residues processed: 219 average time/residue: 0.0925 time to fit residues: 27.9337 Evaluate side-chains 204 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 A residue 324 THR 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 C residue 9 ILE Chi-restraints excluded: chain C residue 37 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 16 optimal weight: 0.0050 chunk 77 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109149 restraints weight = 13729.471| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.57 r_work: 0.3161 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 9342 Z= 0.142 Angle : 0.582 8.593 12668 Z= 0.297 Chirality : 0.041 0.165 1450 Planarity : 0.004 0.045 1555 Dihedral : 5.699 59.216 1316 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.28 % Allowed : 13.63 % Favored : 83.09 % 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: -0.38 (0.24), residues: 1123 helix: 1.09 (0.26), residues: 422 sheet: -0.54 (0.31), residues: 252 loop : -1.33 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 218 TYR 0.011 0.001 TYR B 59 PHE 0.010 0.001 PHE B 234 TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 9339) covalent geometry : angle 0.58217 / 0.30 (12662) SS BOND : bond 0.00300 / 0.18 ( 3) SS BOND : angle 1.01710 / 0.39 ( 6) hydrogen bonds : bond 0.03076 / 2.02 ( 438) hydrogen bonds : angle 4.81501 / 3.51 ( 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 217 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7379 (ttm110) cc_final: 0.7045 (ptp-110) REVERT: R 71 ASP cc_start: 0.7731 (t70) cc_final: 0.7098 (t70) REVERT: R 90 LYS cc_start: 0.8307 (mttt) cc_final: 0.8046 (mmmm) REVERT: R 161 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7576 (t80) REVERT: R 191 LEU cc_start: 0.6943 (tp) cc_final: 0.6610 (pp) REVERT: R 300 MET cc_start: 0.8451 (mtt) cc_final: 0.8103 (mtm) REVERT: A 48 THR cc_start: 0.8280 (m) cc_final: 0.8028 (p) REVERT: A 52 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.6378 (tt0) REVERT: A 242 ARG cc_start: 0.7665 (mtt-85) cc_final: 0.7354 (mtt-85) REVERT: A 247 MET cc_start: 0.8332 (mmm) cc_final: 0.7931 (mmm) REVERT: A 327 THR cc_start: 0.8031 (p) cc_final: 0.7660 (m) REVERT: A 331 ASN cc_start: 0.7939 (m-40) cc_final: 0.7635 (m110) REVERT: B 219 ARG cc_start: 0.8736 (mmm-85) cc_final: 0.8391 (mtt-85) REVERT: B 267 ASP cc_start: 0.8182 (m-30) cc_final: 0.7835 (t0) REVERT: B 291 ASP cc_start: 0.7701 (t70) cc_final: 0.7246 (t70) REVERT: B 297 TRP cc_start: 0.9015 (m100) cc_final: 0.8515 (m100) REVERT: C 13 ARG cc_start: 0.7931 (ptp-110) cc_final: 0.7705 (ttm-80) REVERT: C 58 GLN cc_start: 0.7026 (pm20) cc_final: 0.6813 (pm20) REVERT: E 89 GLU cc_start: 0.7479 (tp30) cc_final: 0.7216 (tp30) REVERT: E 140 MET cc_start: 0.8600 (mmm) cc_final: 0.7784 (mmm) REVERT: E 153 GLU cc_start: 0.7754 (pm20) cc_final: 0.7221 (pm20) REVERT: E 161 SER cc_start: 0.8883 (t) cc_final: 0.8271 (t) REVERT: E 218 ARG cc_start: 0.7199 (mmm160) cc_final: 0.6931 (mmp-170) outliers start: 32 outliers final: 20 residues processed: 205 average time/residue: 0.0936 time to fit residues: 26.3286 Evaluate side-chains 200 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 47 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 67 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN E 13 GLN E 77 ASN E 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.139409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102613 restraints weight = 13360.064| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.36 r_work: 0.3151 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9342 Z= 0.148 Angle : 0.575 8.696 12668 Z= 0.296 Chirality : 0.041 0.146 1450 Planarity : 0.004 0.047 1555 Dihedral : 5.508 59.066 1316 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.38 % Allowed : 14.24 % Favored : 82.38 % 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: -0.19 (0.25), residues: 1123 helix: 1.28 (0.26), residues: 420 sheet: -0.44 (0.31), residues: 252 loop : -1.26 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 218 TYR 0.013 0.001 TYR A 296 PHE 0.008 0.001 PHE E 27 TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9339) covalent geometry : angle 0.57503 / 0.30 (12662) SS BOND : bond 0.00242 / 0.14 ( 3) SS BOND : angle 0.96020 / 0.38 ( 6) hydrogen bonds : bond 0.03087 / 2.06 ( 438) hydrogen bonds : angle 4.72101 / 3.45 ( 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 215 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.301 Fit side-chains REVERT: R 26 ARG cc_start: 0.7354 (ttm110) cc_final: 0.6978 (ptp-110) REVERT: R 157 THR cc_start: 0.8006 (m) cc_final: 0.7514 (t) REVERT: R 161 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7762 (t80) REVERT: R 179 ASN cc_start: 0.8022 (t0) cc_final: 0.6731 (m110) REVERT: R 191 LEU cc_start: 0.6885 (tp) cc_final: 0.6526 (pp) REVERT: R 300 MET cc_start: 0.8584 (mtt) cc_final: 0.8272 (mtm) REVERT: A 48 THR cc_start: 0.8222 (m) cc_final: 0.7933 (p) REVERT: A 52 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6527 (tt0) REVERT: A 242 ARG cc_start: 0.7817 (mtt-85) cc_final: 0.7377 (mtt-85) REVERT: A 247 MET cc_start: 0.8388 (mmm) cc_final: 0.8115 (mmm) REVERT: A 306 GLN cc_start: 0.8323 (tp40) cc_final: 0.7976 (tp40) REVERT: A 327 THR cc_start: 0.7949 (p) cc_final: 0.7605 (m) REVERT: A 331 ASN cc_start: 0.8131 (m-40) cc_final: 0.7736 (m110) REVERT: B 118 ASP cc_start: 0.8422 (p0) cc_final: 0.8213 (t0) REVERT: B 170 ASP cc_start: 0.8676 (t0) cc_final: 0.8260 (t70) REVERT: B 234 PHE cc_start: 0.9441 (OUTLIER) cc_final: 0.9036 (m-80) REVERT: B 243 THR cc_start: 0.9009 (m) cc_final: 0.8447 (p) REVERT: B 247 ASP cc_start: 0.7070 (t70) cc_final: 0.6650 (t70) REVERT: B 267 ASP cc_start: 0.8530 (m-30) cc_final: 0.8124 (t0) REVERT: B 291 ASP cc_start: 0.8032 (t70) cc_final: 0.7546 (t70) REVERT: B 297 TRP cc_start: 0.9146 (m100) cc_final: 0.8692 (m100) REVERT: E 89 GLU cc_start: 0.7683 (tp30) cc_final: 0.7404 (tp30) REVERT: E 153 GLU cc_start: 0.7815 (pm20) cc_final: 0.7517 (pm20) REVERT: E 161 SER cc_start: 0.8993 (t) cc_final: 0.8504 (t) outliers start: 33 outliers final: 23 residues processed: 206 average time/residue: 0.0865 time to fit residues: 24.7029 Evaluate side-chains 198 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 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 324 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 234 PHE 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 Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET 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: 2.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 66 ASN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104470 restraints weight = 13425.208| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.70 r_work: 0.3069 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 9342 Z= 0.254 Angle : 0.669 8.910 12668 Z= 0.341 Chirality : 0.044 0.162 1450 Planarity : 0.004 0.048 1555 Dihedral : 6.056 59.665 1316 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.79 % Allowed : 15.78 % Favored : 80.43 % 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: 1.20 (0.26), residues: 417 sheet: -0.61 (0.30), residues: 271 loop : -1.21 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 218 TYR 0.017 0.002 TYR B 59 PHE 0.012 0.002 PHE E 27 TRP 0.026 0.002 TRP R 95 HIS 0.007 0.002 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.25 ( 9339) covalent geometry : angle 0.66857 / 0.34 (12662) SS BOND : bond 0.00130 / 0.08 ( 3) SS BOND : angle 1.20838 / 0.52 ( 6) hydrogen bonds : bond 0.03491 / 2.37 ( 438) hydrogen bonds : angle 5.02397 / 3.70 ( 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 220 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7403 (ttm110) cc_final: 0.7048 (ptp-110) REVERT: R 44 ASN cc_start: 0.7852 (m-40) cc_final: 0.7648 (m110) REVERT: R 161 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7977 (t80) REVERT: R 179 ASN cc_start: 0.7962 (t0) cc_final: 0.6632 (m110) REVERT: R 191 LEU cc_start: 0.7112 (tp) cc_final: 0.6629 (pp) REVERT: R 192 LYS cc_start: 0.7926 (tppp) cc_final: 0.7223 (mttp) REVERT: R 300 MET cc_start: 0.8718 (mtt) cc_final: 0.8400 (mtm) REVERT: A 48 THR cc_start: 0.8178 (m) cc_final: 0.7851 (p) REVERT: A 242 ARG cc_start: 0.8019 (mtt-85) cc_final: 0.7747 (mtt-85) REVERT: A 247 MET cc_start: 0.8366 (mmm) cc_final: 0.8024 (mmm) REVERT: A 306 GLN cc_start: 0.8367 (tp40) cc_final: 0.8022 (tp40) REVERT: A 331 ASN cc_start: 0.8327 (m-40) cc_final: 0.8006 (m110) REVERT: B 118 ASP cc_start: 0.8596 (p0) cc_final: 0.8328 (t70) REVERT: B 170 ASP cc_start: 0.8577 (t0) cc_final: 0.8200 (t0) REVERT: B 219 ARG cc_start: 0.8925 (mmm-85) cc_final: 0.8704 (mmm-85) REVERT: B 243 THR cc_start: 0.9066 (m) cc_final: 0.8543 (p) REVERT: B 267 ASP cc_start: 0.8525 (m-30) cc_final: 0.8095 (t0) REVERT: B 291 ASP cc_start: 0.8157 (t70) cc_final: 0.7740 (t70) REVERT: E 65 LYS cc_start: 0.8558 (tptp) cc_final: 0.8321 (ttpt) REVERT: E 89 GLU cc_start: 0.7869 (tp30) cc_final: 0.7503 (tp30) REVERT: E 140 MET cc_start: 0.8831 (mmm) cc_final: 0.7883 (mmm) REVERT: E 161 SER cc_start: 0.9218 (t) cc_final: 0.8660 (t) REVERT: E 220 GLU cc_start: 0.7517 (mp0) cc_final: 0.7307 (mp0) outliers start: 37 outliers final: 24 residues processed: 211 average time/residue: 0.0965 time to fit residues: 28.0481 Evaluate side-chains 190 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 198 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE 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 324 THR Chi-restraints excluded: chain A residue 337 ASP 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 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 Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 192 MET 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: 0.9990 chunk 64 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 66 ASN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.140015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.107094 restraints weight = 13340.514| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.64 r_work: 0.3127 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9342 Z= 0.143 Angle : 0.589 9.136 12668 Z= 0.301 Chirality : 0.041 0.148 1450 Planarity : 0.004 0.048 1555 Dihedral : 5.693 59.820 1316 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.10 % Allowed : 15.57 % Favored : 80.33 % 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: -0.11 (0.25), residues: 1123 helix: 1.31 (0.26), residues: 419 sheet: -0.51 (0.30), residues: 282 loop : -1.11 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 219 TYR 0.015 0.001 TYR A 296 PHE 0.010 0.001 PHE A 189 TRP 0.017 0.001 TRP R 95 HIS 0.004 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 9339) covalent geometry : angle 0.58916 / 0.30 (12662) SS BOND : bond 0.00285 / 0.16 ( 3) SS BOND : angle 0.93772 / 0.38 ( 6) hydrogen bonds : bond 0.03121 / 2.09 ( 438) hydrogen bonds : angle 4.80020 / 3.50 ( 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 210 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7266 (ttm110) cc_final: 0.6940 (ptp-110) REVERT: R 161 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7864 (t80) REVERT: R 179 ASN cc_start: 0.7980 (t0) cc_final: 0.6632 (m110) REVERT: R 191 LEU cc_start: 0.6913 (tp) cc_final: 0.6585 (pp) REVERT: R 295 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.8477 (t) REVERT: R 298 ASN cc_start: 0.8426 (m-40) cc_final: 0.8154 (m-40) REVERT: R 300 MET cc_start: 0.8647 (mtt) cc_final: 0.8345 (mtm) REVERT: A 48 THR cc_start: 0.8059 (m) cc_final: 0.7756 (p) REVERT: A 247 MET cc_start: 0.8175 (mmm) cc_final: 0.7902 (mmm) REVERT: A 306 GLN cc_start: 0.8293 (tp40) cc_final: 0.7959 (tp40) REVERT: B 101 MET cc_start: 0.8753 (mmm) cc_final: 0.8491 (mmm) REVERT: B 219 ARG cc_start: 0.8811 (mmm-85) cc_final: 0.8580 (mmm-85) REVERT: B 234 PHE cc_start: 0.9328 (OUTLIER) cc_final: 0.8928 (m-80) REVERT: B 243 THR cc_start: 0.8919 (m) cc_final: 0.8354 (p) REVERT: B 267 ASP cc_start: 0.8249 (m-30) cc_final: 0.7893 (t0) REVERT: B 291 ASP cc_start: 0.7556 (t70) cc_final: 0.7192 (t70) REVERT: B 297 TRP cc_start: 0.9143 (m100) cc_final: 0.8718 (m100) REVERT: E 140 MET cc_start: 0.8697 (mmm) cc_final: 0.7678 (mmm) REVERT: E 161 SER cc_start: 0.8998 (t) cc_final: 0.8664 (p) outliers start: 40 outliers final: 28 residues processed: 197 average time/residue: 0.0898 time to fit residues: 24.5452 Evaluate side-chains 191 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 198 LEU Chi-restraints excluded: chain R residue 295 SER 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 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 337 ASP 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 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 Chi-restraints excluded: chain E residue 192 MET 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: 0.2980 chunk 39 optimal weight: 10.0000 chunk 70 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 66 ASN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.104179 restraints weight = 13521.504| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.34 r_work: 0.3133 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9342 Z= 0.127 Angle : 0.605 11.340 12668 Z= 0.305 Chirality : 0.041 0.150 1450 Planarity : 0.004 0.049 1555 Dihedral : 5.491 59.745 1316 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.59 % Allowed : 16.70 % 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: 0.03 (0.25), residues: 1123 helix: 1.34 (0.26), residues: 419 sheet: -0.37 (0.30), residues: 282 loop : -0.97 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 219 TYR 0.015 0.001 TYR A 296 PHE 0.011 0.001 PHE A 189 TRP 0.022 0.001 TRP R 91 HIS 0.003 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9339) covalent geometry : angle 0.60501 / 0.31 (12662) SS BOND : bond 0.00248 / 0.14 ( 3) SS BOND : angle 0.86594 / 0.35 ( 6) hydrogen bonds : bond 0.03012 / 2.00 ( 438) hydrogen bonds : angle 4.70351 / 3.42 ( 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 : 0.362 Fit side-chains revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7171 (ttm110) cc_final: 0.6835 (ptp-110) REVERT: R 161 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.8023 (t80) REVERT: R 179 ASN cc_start: 0.8065 (t0) cc_final: 0.6647 (m110) REVERT: R 191 LEU cc_start: 0.6867 (tp) cc_final: 0.6556 (pp) REVERT: R 295 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8478 (t) REVERT: R 298 ASN cc_start: 0.8470 (m-40) cc_final: 0.8214 (m-40) REVERT: R 300 MET cc_start: 0.8671 (mtt) cc_final: 0.8352 (mtm) REVERT: A 48 THR cc_start: 0.7827 (m) cc_final: 0.7490 (p) REVERT: A 242 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.7700 (mtt-85) REVERT: A 306 GLN cc_start: 0.8378 (tp40) cc_final: 0.8174 (tp40) REVERT: A 313 ARG cc_start: 0.7944 (ptp90) cc_final: 0.7610 (ptp-170) REVERT: B 15 LYS cc_start: 0.8407 (mtmm) cc_final: 0.7919 (mtmm) REVERT: B 101 MET cc_start: 0.8779 (mmm) cc_final: 0.8528 (mmm) REVERT: B 207 SER cc_start: 0.8815 (m) cc_final: 0.8540 (p) REVERT: B 219 ARG cc_start: 0.8890 (mmm-85) cc_final: 0.8598 (mmm-85) REVERT: B 234 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8927 (m-80) REVERT: B 243 THR cc_start: 0.9037 (m) cc_final: 0.8525 (p) REVERT: B 267 ASP cc_start: 0.8368 (m-30) cc_final: 0.7950 (t0) REVERT: B 291 ASP cc_start: 0.7853 (t70) cc_final: 0.7416 (t70) REVERT: B 297 TRP cc_start: 0.9173 (m100) cc_final: 0.8787 (m100) REVERT: C 32 LYS cc_start: 0.8877 (ptmm) cc_final: 0.8669 (ptmm) REVERT: E 140 MET cc_start: 0.8786 (mmm) cc_final: 0.7681 (mmm) REVERT: E 161 SER cc_start: 0.9053 (t) cc_final: 0.8683 (p) outliers start: 35 outliers final: 24 residues processed: 202 average time/residue: 0.0912 time to fit residues: 25.7256 Evaluate side-chains 193 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 161 PHE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 295 SER 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 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 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 Chi-restraints excluded: chain E residue 192 MET 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: 0.9980 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.142714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.105667 restraints weight = 13302.625| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.37 r_work: 0.3183 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9342 Z= 0.131 Angle : 0.616 11.347 12668 Z= 0.311 Chirality : 0.041 0.157 1450 Planarity : 0.004 0.049 1555 Dihedral : 5.405 59.471 1316 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.07 % Allowed : 17.62 % Favored : 79.30 % 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: 1.37 (0.26), residues: 420 sheet: -0.26 (0.30), residues: 288 loop : -0.97 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 197 TYR 0.015 0.001 TYR A 296 PHE 0.011 0.001 PHE A 189 TRP 0.027 0.001 TRP R 91 HIS 0.004 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 9339) covalent geometry : angle 0.61595 / 0.31 (12662) SS BOND : bond 0.00237 / 0.13 ( 3) SS BOND : angle 0.84599 / 0.34 ( 6) hydrogen bonds : bond 0.02995 / 2.00 ( 438) hydrogen bonds : angle 4.66696 / 3.40 ( 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 203 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7197 (ttm110) cc_final: 0.6851 (ptp-110) REVERT: R 161 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.8068 (t80) REVERT: R 179 ASN cc_start: 0.8129 (t0) cc_final: 0.6670 (m110) REVERT: R 191 LEU cc_start: 0.6842 (tp) cc_final: 0.6562 (pp) REVERT: R 295 SER cc_start: 0.8764 (OUTLIER) cc_final: 0.8449 (t) REVERT: R 298 ASN cc_start: 0.8419 (m-40) cc_final: 0.8165 (m-40) REVERT: R 300 MET cc_start: 0.8597 (mtt) cc_final: 0.8266 (mtm) REVERT: A 48 THR cc_start: 0.7614 (m) cc_final: 0.7280 (p) REVERT: A 242 ARG cc_start: 0.7965 (mtt-85) cc_final: 0.7410 (mtt90) REVERT: A 306 GLN cc_start: 0.8347 (tp40) cc_final: 0.8077 (tp40) REVERT: A 313 ARG cc_start: 0.7957 (ptp90) cc_final: 0.7615 (ptp-170) REVERT: B 101 MET cc_start: 0.8821 (mmm) cc_final: 0.8574 (mmm) REVERT: B 207 SER cc_start: 0.8924 (m) cc_final: 0.8584 (p) REVERT: B 219 ARG cc_start: 0.8863 (mmm-85) cc_final: 0.8566 (mmm-85) REVERT: B 234 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.8991 (m-80) REVERT: B 243 THR cc_start: 0.8977 (m) cc_final: 0.8463 (p) REVERT: B 267 ASP cc_start: 0.8457 (m-30) cc_final: 0.8038 (t0) REVERT: B 291 ASP cc_start: 0.7709 (t70) cc_final: 0.7313 (t70) REVERT: B 297 TRP cc_start: 0.9164 (m100) cc_final: 0.8767 (m100) REVERT: E 140 MET cc_start: 0.8805 (mmm) cc_final: 0.7658 (mmm) REVERT: E 161 SER cc_start: 0.9103 (t) cc_final: 0.8733 (p) outliers start: 30 outliers final: 24 residues processed: 195 average time/residue: 0.0929 time to fit residues: 25.1542 Evaluate side-chains 192 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 161 PHE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 295 SER 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 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 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 Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 0.0370 chunk 76 optimal weight: 0.0870 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.3640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.139337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101846 restraints weight = 13320.405| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.39 r_work: 0.3133 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9342 Z= 0.181 Angle : 0.650 11.629 12668 Z= 0.328 Chirality : 0.042 0.159 1450 Planarity : 0.004 0.049 1555 Dihedral : 5.566 57.745 1316 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.56 % Allowed : 18.24 % Favored : 79.20 % 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: 0.01 (0.25), residues: 1123 helix: 1.28 (0.26), residues: 421 sheet: -0.30 (0.30), residues: 286 loop : -1.00 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 197 TYR 0.018 0.002 TYR A 296 PHE 0.012 0.001 PHE R 163 TRP 0.026 0.002 TRP R 91 HIS 0.005 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 ( 9339) covalent geometry : angle 0.64940 / 0.33 (12662) SS BOND : bond 0.00176 / 0.10 ( 3) SS BOND : angle 0.98410 / 0.41 ( 6) hydrogen bonds : bond 0.03181 / 2.15 ( 438) hydrogen bonds : angle 4.73785 / 3.45 ( 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 194 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7202 (ttm110) cc_final: 0.6866 (ptp-110) REVERT: R 161 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8041 (t80) REVERT: R 179 ASN cc_start: 0.8152 (t0) cc_final: 0.6726 (m110) REVERT: R 191 LEU cc_start: 0.6887 (tp) cc_final: 0.6676 (pp) REVERT: R 295 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8429 (t) REVERT: R 298 ASN cc_start: 0.8454 (m-40) cc_final: 0.8215 (m-40) REVERT: R 300 MET cc_start: 0.8608 (mtt) cc_final: 0.8268 (mtm) REVERT: A 48 THR cc_start: 0.7538 (m) cc_final: 0.7236 (p) REVERT: A 306 GLN cc_start: 0.8375 (tp40) cc_final: 0.8142 (tp40) REVERT: A 313 ARG cc_start: 0.7968 (ptp90) cc_final: 0.7616 (ptp-170) REVERT: B 101 MET cc_start: 0.8955 (mmm) cc_final: 0.8683 (mmm) REVERT: B 207 SER cc_start: 0.8912 (m) cc_final: 0.8589 (p) REVERT: B 234 PHE cc_start: 0.9389 (OUTLIER) cc_final: 0.8964 (m-80) REVERT: B 243 THR cc_start: 0.8982 (m) cc_final: 0.8508 (p) REVERT: B 267 ASP cc_start: 0.8419 (m-30) cc_final: 0.8113 (m-30) REVERT: B 291 ASP cc_start: 0.7861 (t70) cc_final: 0.7486 (t70) REVERT: B 297 TRP cc_start: 0.9242 (m100) cc_final: 0.8839 (m100) REVERT: E 140 MET cc_start: 0.8854 (mmm) cc_final: 0.7740 (mmm) REVERT: E 161 SER cc_start: 0.9155 (t) cc_final: 0.8807 (p) outliers start: 25 outliers final: 21 residues processed: 188 average time/residue: 0.0907 time to fit residues: 24.0685 Evaluate side-chains 185 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 161 PHE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 218 VAL 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 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 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 Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.140550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.103393 restraints weight = 13096.216| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.39 r_work: 0.3153 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9342 Z= 0.153 Angle : 0.635 11.409 12668 Z= 0.321 Chirality : 0.042 0.164 1450 Planarity : 0.004 0.049 1555 Dihedral : 5.523 57.151 1316 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.56 % Allowed : 18.44 % Favored : 79.00 % 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: 0.02 (0.25), residues: 1123 helix: 1.24 (0.26), residues: 421 sheet: -0.29 (0.30), residues: 286 loop : -0.96 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 219 TYR 0.017 0.001 TYR A 296 PHE 0.009 0.001 PHE E 27 TRP 0.023 0.001 TRP R 91 HIS 0.004 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 9339) covalent geometry : angle 0.63451 / 0.32 (12662) SS BOND : bond 0.00217 / 0.12 ( 3) SS BOND : angle 0.91181 / 0.36 ( 6) hydrogen bonds : bond 0.03129 / 2.11 ( 438) hydrogen bonds : angle 4.70740 / 3.43 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2527.83 seconds wall clock time: 44 minutes 3.82 seconds (2643.82 seconds total)