Starting phenix.real_space_refine on Tue Sep 24 13:07:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcm_32424/09_2024/7wcm_32424.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcm_32424/09_2024/7wcm_32424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcm_32424/09_2024/7wcm_32424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcm_32424/09_2024/7wcm_32424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcm_32424/09_2024/7wcm_32424.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcm_32424/09_2024/7wcm_32424.cif" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 57 5.16 5 C 5222 2.51 5 N 1435 2.21 5 O 1518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8232 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1947 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2240 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 1 Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'8VP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.35, per 1000 atoms: 0.65 Number of scatterers: 8232 At special positions: 0 Unit cell: (81.696, 102.12, 131.054, 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 57 16.00 O 1518 8.00 N 1435 7.00 C 5222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 155 " 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: 2.36 Conformation dependent library (CDL) restraints added in 1.0 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1958 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 45.0% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 9 through 40 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.663A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.749A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.035A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.551A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.572A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 3.550A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 37 Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.577A pdb=" N ILE B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'C' and resid 9 through 23 removed outlier: 3.831A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.646A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 6 through 36 removed outlier: 3.699A pdb=" N VAL R 25 " --> pdb=" O THR R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 60 removed outlier: 3.583A pdb=" N CYS R 42 " --> pdb=" O GLY R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 68 removed outlier: 3.781A pdb=" N SER R 68 " --> pdb=" O ASP R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 109 removed outlier: 3.966A pdb=" N VAL R 85 " --> pdb=" O ARG R 81 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR R 86 " --> pdb=" O MET R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 117 Processing helix chain 'R' and resid 118 through 139 Processing helix chain 'R' and resid 140 through 143 Processing helix chain 'R' and resid 163 through 173 Processing helix chain 'R' and resid 173 through 210 removed outlier: 3.614A pdb=" N ALA R 177 " --> pdb=" O GLY R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 236 Processing helix chain 'R' and resid 238 through 251 Processing helix chain 'R' and resid 255 through 263 removed outlier: 4.182A pdb=" N VAL R 259 " --> pdb=" O HIS R 255 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU R 261 " --> pdb=" O TYR R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 280 removed outlier: 3.723A pdb=" N LEU R 267 " --> pdb=" O TYR R 263 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER R 272 " --> pdb=" O GLY R 268 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU R 273 " --> pdb=" O VAL R 269 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 283 through 300 removed outlier: 3.687A pdb=" N LEU R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY R 296 " --> pdb=" O HIS R 292 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL R 297 " --> pdb=" O MET R 293 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS R 298 " --> pdb=" O ALA R 294 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.449A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 62 removed outlier: 6.798A pdb=" N ILE B 349 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR B 61 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B 347 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 74 removed outlier: 3.637A pdb=" N ALA B 71 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU B 90 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA B 103 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE B 92 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 116 removed outlier: 6.967A pdb=" N GLY B 126 " --> pdb=" O MET B 112 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N CYS B 114 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 124 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYR B 116 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N TYR B 122 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY B 127 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N CYS B 132 " --> pdb=" O GLU B 149 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU B 149 " --> pdb=" O CYS B 132 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 134 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG B 145 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 157 through 162 removed outlier: 6.732A pdb=" N SER B 171 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N CYS B 160 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 169 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N PHE B 162 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLN B 167 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B 168 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP B 181 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLN B 187 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 203 removed outlier: 3.559A pdb=" N SER B 200 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN B 231 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP B 223 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N CYS B 229 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 245 removed outlier: 6.639A pdb=" N CYS B 261 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR B 274 " --> pdb=" O CYS B 261 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU B 263 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 270 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 284 through 289 removed outlier: 3.740A pdb=" N SER B 286 " --> pdb=" O GLY B 299 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASP B 309 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG B 315 " --> pdb=" O ASP B 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.790A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1269 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2690 1.34 - 1.46: 1962 1.46 - 1.58: 3666 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 8400 Sorted by residual: bond pdb=" C20 8VP R 401 " pdb=" N17 8VP R 401 " ideal model delta sigma weight residual 1.357 1.473 -0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C8 8VP R 401 " pdb=" C9 8VP R 401 " ideal model delta sigma weight residual 1.490 1.579 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C9 8VP R 401 " pdb=" N13 8VP R 401 " ideal model delta sigma weight residual 1.378 1.448 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C29 8VP R 401 " pdb=" N28 8VP R 401 " ideal model delta sigma weight residual 1.344 1.401 -0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" C3 8VP R 401 " pdb=" N28 8VP R 401 " ideal model delta sigma weight residual 1.423 1.478 -0.055 2.00e-02 2.50e+03 7.62e+00 ... (remaining 8395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 11151 1.80 - 3.60: 175 3.60 - 5.40: 36 5.40 - 7.20: 4 7.20 - 9.00: 3 Bond angle restraints: 11369 Sorted by residual: angle pdb=" N PHE N 108 " pdb=" CA PHE N 108 " pdb=" C PHE N 108 " ideal model delta sigma weight residual 111.24 115.14 -3.90 1.29e+00 6.01e-01 9.12e+00 angle pdb=" C9 8VP R 401 " pdb=" C8 8VP R 401 " pdb=" O7 8VP R 401 " ideal model delta sigma weight residual 107.91 116.91 -9.00 3.00e+00 1.11e-01 8.99e+00 angle pdb=" C16 8VP R 401 " pdb=" N17 8VP R 401 " pdb=" C18 8VP R 401 " ideal model delta sigma weight residual 116.58 107.78 8.80 3.00e+00 1.11e-01 8.60e+00 angle pdb=" C PRO R 144 " pdb=" N MET R 145 " pdb=" CA MET R 145 " ideal model delta sigma weight residual 121.54 126.54 -5.00 1.91e+00 2.74e-01 6.84e+00 angle pdb=" CA ASP A 310 " pdb=" CB ASP A 310 " pdb=" CG ASP A 310 " ideal model delta sigma weight residual 112.60 115.17 -2.57 1.00e+00 1.00e+00 6.60e+00 ... (remaining 11364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4536 17.93 - 35.85: 399 35.85 - 53.78: 49 53.78 - 71.70: 15 71.70 - 89.63: 13 Dihedral angle restraints: 5012 sinusoidal: 1980 harmonic: 3032 Sorted by residual: dihedral pdb=" CA ASP A 310 " pdb=" C ASP A 310 " pdb=" N TYR A 311 " pdb=" CA TYR A 311 " ideal model delta harmonic sigma weight residual 180.00 152.84 27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA GLN B 86 " pdb=" C GLN B 86 " pdb=" N ASP B 87 " pdb=" CA ASP B 87 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 852 0.036 - 0.072: 303 0.072 - 0.108: 91 0.108 - 0.144: 32 0.144 - 0.180: 2 Chirality restraints: 1280 Sorted by residual: chirality pdb=" CA VAL N 37 " pdb=" N VAL N 37 " pdb=" C VAL N 37 " pdb=" CB VAL N 37 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CA TYR B 70 " pdb=" N TYR B 70 " pdb=" C TYR B 70 " pdb=" CB TYR B 70 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA ASP A 310 " pdb=" N ASP A 310 " pdb=" C ASP A 310 " pdb=" CB ASP A 310 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 1277 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 70 " -0.027 2.00e-02 2.50e+03 2.03e-02 8.28e+00 pdb=" CG TYR B 70 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B 70 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 70 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 70 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 70 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 70 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 70 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 246 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO B 247 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 183 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C PHE R 183 " -0.032 2.00e-02 2.50e+03 pdb=" O PHE R 183 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE R 184 " 0.011 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2044 2.80 - 3.33: 7580 3.33 - 3.85: 13284 3.85 - 4.38: 15798 4.38 - 4.90: 27122 Nonbonded interactions: 65828 Sorted by model distance: nonbonded pdb=" NE2 GLN A 29 " pdb=" OD1 ASP A 33 " model vdw 2.281 3.120 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 197 " model vdw 2.301 3.120 nonbonded pdb=" O GLN R 148 " pdb=" NZ LYS R 152 " model vdw 2.306 3.120 nonbonded pdb=" O TYR B 96 " pdb=" OG1 THR B 97 " model vdw 2.337 3.040 nonbonded pdb=" OD1 ASN A 292 " pdb=" N LYS A 293 " model vdw 2.356 3.120 ... (remaining 65823 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.610 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.003 0.116 8400 Z= 0.236 Angle : 0.607 8.996 11369 Z= 0.329 Chirality : 0.043 0.180 1280 Planarity : 0.004 0.052 1448 Dihedral : 14.074 89.628 3048 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1031 helix: 1.81 (0.27), residues: 411 sheet: 1.03 (0.35), residues: 208 loop : -0.61 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 93 HIS 0.015 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.049 0.002 TYR B 70 ARG 0.002 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.965 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 1.6141 time to fit residues: 221.5849 Evaluate side-chains 120 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 279 ASN R 109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8400 Z= 0.303 Angle : 0.709 10.608 11369 Z= 0.390 Chirality : 0.048 0.191 1280 Planarity : 0.005 0.053 1448 Dihedral : 6.594 71.434 1164 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.14 % Allowed : 6.66 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1031 helix: 1.84 (0.25), residues: 419 sheet: 1.03 (0.35), residues: 210 loop : -0.81 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 234 HIS 0.012 0.002 HIS A 357 PHE 0.017 0.002 PHE B 245 TYR 0.017 0.003 TYR A 339 ARG 0.005 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.984 Fit side-chains REVERT: A 300 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6693 (mtmt) REVERT: A 314 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6659 (mt-10) REVERT: R 261 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.5956 (mm-30) outliers start: 19 outliers final: 10 residues processed: 126 average time/residue: 1.6292 time to fit residues: 215.1822 Evaluate side-chains 128 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN N 3 GLN N 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8400 Z= 0.199 Angle : 0.595 8.972 11369 Z= 0.328 Chirality : 0.044 0.198 1280 Planarity : 0.004 0.053 1448 Dihedral : 6.186 64.905 1164 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.81 % Allowed : 8.92 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1031 helix: 2.20 (0.26), residues: 418 sheet: 1.03 (0.34), residues: 214 loop : -0.79 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.002 PHE A 212 TYR 0.015 0.002 TYR A 339 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.950 Fit side-chains REVERT: A 29 GLN cc_start: 0.8217 (tp40) cc_final: 0.7923 (tp-100) REVERT: A 300 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6697 (mtmt) REVERT: A 314 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6610 (mt-10) REVERT: B 70 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: C 29 LYS cc_start: 0.8286 (mmtm) cc_final: 0.7977 (mtpp) REVERT: R 261 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.5970 (mm-30) outliers start: 16 outliers final: 8 residues processed: 126 average time/residue: 1.6680 time to fit residues: 219.9560 Evaluate side-chains 129 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN N 3 GLN N 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8400 Z= 0.218 Angle : 0.613 8.218 11369 Z= 0.338 Chirality : 0.045 0.196 1280 Planarity : 0.004 0.053 1448 Dihedral : 6.158 61.887 1164 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.60 % Allowed : 9.26 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1031 helix: 2.23 (0.26), residues: 418 sheet: 1.13 (0.35), residues: 208 loop : -0.87 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 234 HIS 0.003 0.001 HIS B 102 PHE 0.015 0.002 PHE A 212 TYR 0.016 0.002 TYR A 339 ARG 0.006 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 1.053 Fit side-chains REVERT: A 29 GLN cc_start: 0.8233 (tp40) cc_final: 0.7948 (tp-100) REVERT: A 300 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6633 (mtmt) REVERT: A 314 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6585 (mt-10) REVERT: B 70 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.7899 (m-80) REVERT: C 29 LYS cc_start: 0.8312 (mmtm) cc_final: 0.8009 (mtpp) REVERT: R 261 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.5939 (mm-30) outliers start: 23 outliers final: 10 residues processed: 128 average time/residue: 1.6553 time to fit residues: 221.7868 Evaluate side-chains 126 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.5980 chunk 87 optimal weight: 0.0870 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN N 3 GLN N 5 GLN R 197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8400 Z= 0.194 Angle : 0.582 7.578 11369 Z= 0.321 Chirality : 0.044 0.196 1280 Planarity : 0.004 0.053 1448 Dihedral : 6.014 59.136 1164 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.82 % Allowed : 9.14 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.26), residues: 1031 helix: 2.43 (0.26), residues: 412 sheet: 1.05 (0.34), residues: 214 loop : -0.80 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.003 0.001 HIS B 102 PHE 0.015 0.002 PHE A 212 TYR 0.015 0.002 TYR A 339 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.902 Fit side-chains REVERT: A 300 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6550 (mtmt) REVERT: A 314 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6570 (mt-10) REVERT: B 26 LYS cc_start: 0.7675 (mttm) cc_final: 0.7377 (mttm) REVERT: B 70 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: C 29 LYS cc_start: 0.8249 (mmtm) cc_final: 0.7943 (mtpp) REVERT: R 261 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.5904 (mm-30) outliers start: 25 outliers final: 11 residues processed: 131 average time/residue: 1.6422 time to fit residues: 225.2123 Evaluate side-chains 129 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.0050 chunk 19 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 overall best weight: 2.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN N 3 GLN N 5 GLN R 197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8400 Z= 0.206 Angle : 0.607 10.875 11369 Z= 0.331 Chirality : 0.044 0.196 1280 Planarity : 0.004 0.053 1448 Dihedral : 6.018 56.967 1164 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.37 % Allowed : 10.61 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 1031 helix: 2.39 (0.26), residues: 413 sheet: 1.13 (0.34), residues: 211 loop : -0.84 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.003 0.001 HIS B 65 PHE 0.015 0.002 PHE A 212 TYR 0.016 0.002 TYR A 339 ARG 0.007 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.031 Fit side-chains REVERT: A 300 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6558 (mtmt) REVERT: A 314 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6599 (mt-10) REVERT: B 26 LYS cc_start: 0.7694 (mttm) cc_final: 0.7385 (mttm) REVERT: B 70 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: C 29 LYS cc_start: 0.8286 (mmtm) cc_final: 0.7978 (mtpp) REVERT: R 261 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.5913 (mm-30) outliers start: 21 outliers final: 13 residues processed: 127 average time/residue: 1.6849 time to fit residues: 224.2451 Evaluate side-chains 130 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN N 3 GLN N 5 GLN R 197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8400 Z= 0.152 Angle : 0.537 9.411 11369 Z= 0.293 Chirality : 0.042 0.197 1280 Planarity : 0.004 0.052 1448 Dihedral : 5.729 54.360 1164 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.26 % Allowed : 11.29 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.26), residues: 1031 helix: 2.68 (0.26), residues: 411 sheet: 1.05 (0.34), residues: 217 loop : -0.73 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.002 0.001 HIS B 102 PHE 0.014 0.001 PHE A 212 TYR 0.014 0.001 TYR A 339 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 0.927 Fit side-chains REVERT: A 300 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6522 (mtmt) REVERT: A 314 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6597 (mt-10) REVERT: B 26 LYS cc_start: 0.7655 (mttm) cc_final: 0.7366 (mttm) REVERT: B 70 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.7723 (m-80) REVERT: C 29 LYS cc_start: 0.8141 (mmtm) cc_final: 0.7827 (mtpp) REVERT: R 115 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7567 (ttpp) REVERT: R 261 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.5860 (mm-30) outliers start: 20 outliers final: 8 residues processed: 125 average time/residue: 1.6961 time to fit residues: 222.2201 Evaluate side-chains 125 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN N 3 GLN N 5 GLN R 197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8400 Z= 0.271 Angle : 0.669 10.796 11369 Z= 0.364 Chirality : 0.047 0.199 1280 Planarity : 0.004 0.052 1448 Dihedral : 6.096 51.983 1164 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.37 % Allowed : 11.51 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1031 helix: 2.26 (0.26), residues: 413 sheet: 1.16 (0.35), residues: 211 loop : -0.89 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 234 HIS 0.006 0.001 HIS B 65 PHE 0.016 0.002 PHE A 212 TYR 0.016 0.002 TYR A 339 ARG 0.005 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 1.151 Fit side-chains REVERT: A 300 LYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6639 (mtmt) REVERT: A 314 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6608 (mt-10) REVERT: B 70 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: R 145 MET cc_start: 0.5066 (tmm) cc_final: 0.4591 (tmm) REVERT: R 261 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.5916 (mm-30) outliers start: 21 outliers final: 11 residues processed: 124 average time/residue: 1.6976 time to fit residues: 220.1356 Evaluate side-chains 126 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 54 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 58 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN N 3 GLN R 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8400 Z= 0.170 Angle : 0.565 9.325 11369 Z= 0.307 Chirality : 0.043 0.197 1280 Planarity : 0.004 0.052 1448 Dihedral : 5.793 50.482 1164 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.92 % Allowed : 11.96 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1031 helix: 2.55 (0.26), residues: 412 sheet: 1.06 (0.34), residues: 217 loop : -0.80 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.002 0.001 HIS R 204 PHE 0.014 0.001 PHE A 212 TYR 0.014 0.001 TYR A 339 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 0.929 Fit side-chains REVERT: A 300 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6547 (mtmt) REVERT: A 314 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6586 (mt-10) REVERT: B 70 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.7800 (m-80) REVERT: C 29 LYS cc_start: 0.8200 (mmtm) cc_final: 0.7946 (mtpp) REVERT: R 261 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.5937 (mm-30) outliers start: 17 outliers final: 8 residues processed: 123 average time/residue: 1.7084 time to fit residues: 219.6439 Evaluate side-chains 123 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN N 3 GLN R 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8400 Z= 0.194 Angle : 0.599 9.745 11369 Z= 0.324 Chirality : 0.044 0.199 1280 Planarity : 0.004 0.052 1448 Dihedral : 5.853 49.399 1164 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.69 % Allowed : 12.42 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.26), residues: 1031 helix: 2.52 (0.26), residues: 411 sheet: 1.05 (0.34), residues: 217 loop : -0.79 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.003 0.001 HIS B 65 PHE 0.015 0.002 PHE A 212 TYR 0.015 0.002 TYR A 339 ARG 0.005 0.000 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 0.971 Fit side-chains REVERT: A 300 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6564 (mtmt) REVERT: A 314 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6601 (mt-10) REVERT: B 70 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.7861 (m-80) REVERT: R 261 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.5881 (mm-30) outliers start: 15 outliers final: 8 residues processed: 122 average time/residue: 1.6983 time to fit residues: 216.8340 Evaluate side-chains 124 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 115 LYS Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 LYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN N 3 GLN R 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.160692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.112212 restraints weight = 7684.064| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.78 r_work: 0.3028 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8400 Z= 0.185 Angle : 0.586 9.551 11369 Z= 0.318 Chirality : 0.043 0.200 1280 Planarity : 0.004 0.052 1448 Dihedral : 5.824 49.151 1164 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.69 % Allowed : 12.42 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1031 helix: 2.55 (0.26), residues: 411 sheet: 1.07 (0.34), residues: 217 loop : -0.79 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.003 0.001 HIS B 65 PHE 0.015 0.001 PHE A 212 TYR 0.015 0.002 TYR A 339 ARG 0.005 0.000 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3989.60 seconds wall clock time: 70 minutes 15.43 seconds (4215.43 seconds total)