Starting phenix.real_space_refine on Tue Sep 24 13:07:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/09_2024/7xov_33360_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/09_2024/7xov_33360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/09_2024/7xov_33360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/09_2024/7xov_33360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/09_2024/7xov_33360_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/09_2024/7xov_33360_trim.cif" } resolution = 3.0 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: 5 Type Number sf(0) Gaussians S 61 5.16 5 Cl 1 4.86 5 C 5217 2.51 5 N 1427 2.21 5 O 1512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 8218 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1884 Classifications: {'peptide': 227} Incomplete info: {'backbone_only': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 219} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 118} Chain: "R" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2293 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 11, 'TRANS': 276} Chain breaks: 1 Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'IA1': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 5.06, per 1000 atoms: 0.62 Number of scatterers: 8218 At special positions: 0 Unit cell: (90.246, 95.316, 134.862, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 61 16.00 O 1512 8.00 N 1427 7.00 C 5217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 196 " distance=2.04 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: 2.09 Conformation dependent library (CDL) restraints added in 979.8 milliseconds 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 42.1% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.027A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 389 removed outlier: 3.623A pdb=" N ASN A 377 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.920A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 removed outlier: 4.403A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 43 through 69 removed outlier: 3.720A pdb=" N LEU R 47 " --> pdb=" O VAL R 43 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE R 67 " --> pdb=" O ILE R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 95 removed outlier: 3.913A pdb=" N MET R 95 " --> pdb=" O CYS R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 105 removed outlier: 3.551A pdb=" N LEU R 103 " --> pdb=" O LEU R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 145 Processing helix chain 'R' and resid 145 through 153 removed outlier: 4.351A pdb=" N VAL R 151 " --> pdb=" O LEU R 147 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP R 152 " --> pdb=" O GLN R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 173 removed outlier: 4.140A pdb=" N LYS R 160 " --> pdb=" O SER R 156 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR R 171 " --> pdb=" O CYS R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 218 Processing helix chain 'R' and resid 218 through 244 Processing helix chain 'R' and resid 302 through 339 Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 339 through 350 removed outlier: 3.632A pdb=" N GLY R 349 " --> pdb=" O ARG R 345 " (cutoff:3.500A) Processing helix chain 'R' and resid 351 through 361 removed outlier: 3.615A pdb=" N ILE R 355 " --> pdb=" O PRO R 351 " (cutoff:3.500A) Processing helix chain 'R' and resid 361 through 371 Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 378 through 385 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.327A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.870A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.730A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.319A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 152 removed outlier: 3.507A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.607A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.764A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.569A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (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 10 through 11 removed outlier: 5.475A pdb=" N GLN N 120 " --> pdb=" O CYS N 96 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N CYS N 96 " --> pdb=" O GLN N 120 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL N 48 " --> pdb=" O TYR N 60 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR N 60 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP N 50 " --> pdb=" O ILE N 58 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 180 through 182 422 hydrogen bonds defined for protein. 1194 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: 2.41 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1400 1.31 - 1.44: 2275 1.44 - 1.57: 4588 1.57 - 1.70: 29 1.70 - 1.83: 89 Bond restraints: 8381 Sorted by residual: bond pdb=" C19 IA1 R 501 " pdb=" S2 IA1 R 501 " ideal model delta sigma weight residual 1.731 1.520 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C20 IA1 R 501 " pdb=" N8 IA1 R 501 " ideal model delta sigma weight residual 1.372 1.556 -0.184 2.00e-02 2.50e+03 8.44e+01 bond pdb=" C21 IA1 R 501 " pdb=" S2 IA1 R 501 " ideal model delta sigma weight residual 1.727 1.551 0.176 2.00e-02 2.50e+03 7.71e+01 bond pdb=" C25 IA1 R 501 " pdb=" C32 IA1 R 501 " ideal model delta sigma weight residual 1.404 1.565 -0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" C23 IA1 R 501 " pdb=" C30 IA1 R 501 " ideal model delta sigma weight residual 1.414 1.572 -0.158 2.00e-02 2.50e+03 6.26e+01 ... (remaining 8376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.80: 11277 6.80 - 13.59: 64 13.59 - 20.39: 2 20.39 - 27.19: 1 27.19 - 33.99: 2 Bond angle restraints: 11346 Sorted by residual: angle pdb=" C LYS R 187 " pdb=" N ASN R 188 " pdb=" CA ASN R 188 " ideal model delta sigma weight residual 120.72 154.71 -33.99 1.67e+00 3.59e-01 4.14e+02 angle pdb=" C THR N 28 " pdb=" N PHE N 29 " pdb=" CA PHE N 29 " ideal model delta sigma weight residual 122.85 96.53 26.32 1.39e+00 5.18e-01 3.59e+02 angle pdb=" C GLN N 120 " pdb=" N GLY N 121 " pdb=" CA GLY N 121 " ideal model delta sigma weight residual 121.70 151.55 -29.85 1.80e+00 3.09e-01 2.75e+02 angle pdb=" N GLU A 230 " pdb=" CA GLU A 230 " pdb=" C GLU A 230 " ideal model delta sigma weight residual 111.28 123.26 -11.98 1.09e+00 8.42e-01 1.21e+02 angle pdb=" N SER N 30 " pdb=" CA SER N 30 " pdb=" C SER N 30 " ideal model delta sigma weight residual 114.39 100.64 13.75 1.45e+00 4.76e-01 8.99e+01 ... (remaining 11341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 4816 17.11 - 34.22: 148 34.22 - 51.34: 32 51.34 - 68.45: 26 68.45 - 85.56: 6 Dihedral angle restraints: 5028 sinusoidal: 2012 harmonic: 3016 Sorted by residual: dihedral pdb=" CA ASP A 223 " pdb=" C ASP A 223 " pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta harmonic sigma weight residual 180.00 -141.20 -38.80 0 5.00e+00 4.00e-02 6.02e+01 dihedral pdb=" CA ASN N 84 " pdb=" C ASN N 84 " pdb=" N SER N 85 " pdb=" CA SER N 85 " ideal model delta harmonic sigma weight residual -180.00 -145.28 -34.72 0 5.00e+00 4.00e-02 4.82e+01 dihedral pdb=" CB CYS R 114 " pdb=" SG CYS R 114 " pdb=" SG CYS R 196 " pdb=" CB CYS R 196 " ideal model delta sinusoidal sigma weight residual -86.00 -144.12 58.12 1 1.00e+01 1.00e-02 4.53e+01 ... (remaining 5025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 823 0.080 - 0.160: 348 0.160 - 0.239: 95 0.239 - 0.319: 15 0.319 - 0.399: 1 Chirality restraints: 1282 Sorted by residual: chirality pdb=" CA GLU A 230 " pdb=" N GLU A 230 " pdb=" C GLU A 230 " pdb=" CB GLU A 230 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA TYR B 111 " pdb=" N TYR B 111 " pdb=" C TYR B 111 " pdb=" CB TYR B 111 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA ILE B 171 " pdb=" N ILE B 171 " pdb=" C ILE B 171 " pdb=" CB ILE B 171 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1279 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 237 " 0.072 2.00e-02 2.50e+03 1.48e-01 2.19e+02 pdb=" C ASN B 237 " -0.256 2.00e-02 2.50e+03 pdb=" O ASN B 237 " 0.096 2.00e-02 2.50e+03 pdb=" N GLY B 238 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 66 " 0.067 2.00e-02 2.50e+03 1.44e-01 2.08e+02 pdb=" C ASP B 66 " -0.249 2.00e-02 2.50e+03 pdb=" O ASP B 66 " 0.098 2.00e-02 2.50e+03 pdb=" N SER B 67 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 276 " 0.066 2.00e-02 2.50e+03 1.44e-01 2.07e+02 pdb=" C ILE A 276 " -0.249 2.00e-02 2.50e+03 pdb=" O ILE A 276 " 0.099 2.00e-02 2.50e+03 pdb=" N TRP A 277 " 0.084 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2594 2.84 - 3.35: 7953 3.35 - 3.87: 13738 3.87 - 4.38: 16859 4.38 - 4.90: 27116 Nonbonded interactions: 68260 Sorted by model distance: nonbonded pdb=" O THR N 28 " pdb=" CA PHE N 29 " model vdw 2.322 2.776 nonbonded pdb=" OD2 ASP A 33 " pdb=" NZ LYS B 78 " model vdw 2.342 3.120 nonbonded pdb=" N SER N 30 " pdb=" N ASN N 31 " model vdw 2.344 2.560 nonbonded pdb=" CD1 LEU R 347 " pdb=" C39 IA1 R 501 " model vdw 2.346 3.880 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.352 3.040 ... (remaining 68255 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: 0.370 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.550 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0298 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 : 0.019 0.211 8381 Z= 1.263 Angle : 1.842 33.986 11346 Z= 1.238 Chirality : 0.091 0.399 1282 Planarity : 0.017 0.148 1440 Dihedral : 10.850 85.562 3063 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.86 % Rotamer: Outliers : 0.90 % Allowed : 1.01 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1018 helix: -0.26 (0.23), residues: 388 sheet: 1.46 (0.33), residues: 215 loop : 0.54 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.011 TRP B 99 HIS 0.007 0.003 HIS B 183 PHE 0.050 0.006 PHE N 27 TYR 0.085 0.009 TYR R 179 ARG 0.008 0.001 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.4362 (p0) cc_final: 0.2845 (p0) REVERT: G 21 MET cc_start: 0.3505 (mtm) cc_final: 0.3188 (ttt) outliers start: 8 outliers final: 3 residues processed: 88 average time/residue: 1.2724 time to fit residues: 119.0117 Evaluate side-chains 60 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 119 TYR Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 336 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 0.0470 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 207 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0814 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8381 Z= 0.214 Angle : 0.709 8.248 11346 Z= 0.383 Chirality : 0.046 0.195 1282 Planarity : 0.005 0.078 1440 Dihedral : 7.085 77.682 1163 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.16 % Favored : 97.74 % Rotamer: Outliers : 1.01 % Allowed : 6.61 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.31 (0.26), residues: 1018 helix: 1.67 (0.26), residues: 387 sheet: 1.23 (0.32), residues: 225 loop : -0.05 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 326 HIS 0.006 0.002 HIS B 225 PHE 0.019 0.002 PHE B 278 TYR 0.015 0.002 TYR N 95 ARG 0.006 0.001 ARG R 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: B 188 MET cc_start: 0.2404 (OUTLIER) cc_final: -0.0083 (ttt) REVERT: G 21 MET cc_start: 0.3647 (mtm) cc_final: 0.3402 (ttt) REVERT: R 72 MET cc_start: 0.0861 (mmt) cc_final: 0.0278 (mpp) outliers start: 9 outliers final: 4 residues processed: 66 average time/residue: 1.3580 time to fit residues: 95.6456 Evaluate side-chains 55 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 119 TYR Chi-restraints excluded: chain R residue 336 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 0.0870 chunk 61 optimal weight: 0.4980 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN R 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1435 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8381 Z= 0.218 Angle : 0.676 9.955 11346 Z= 0.356 Chirality : 0.044 0.194 1282 Planarity : 0.005 0.077 1440 Dihedral : 7.071 95.279 1161 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.68 % Allowed : 7.61 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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 (0.27), residues: 1018 helix: 1.80 (0.26), residues: 396 sheet: 0.94 (0.33), residues: 234 loop : 0.06 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP R 326 HIS 0.003 0.001 HIS G 44 PHE 0.019 0.002 PHE R 198 TYR 0.016 0.002 TYR R 176 ARG 0.016 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: B 188 MET cc_start: 0.3200 (OUTLIER) cc_final: 0.0136 (ttt) REVERT: R 361 THR cc_start: 0.3178 (p) cc_final: 0.2422 (p) outliers start: 15 outliers final: 2 residues processed: 81 average time/residue: 1.0139 time to fit residues: 88.8974 Evaluate side-chains 54 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain R residue 119 TYR Chi-restraints excluded: chain R residue 350 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS G 44 HIS ** R 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2171 moved from start: 0.6452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8381 Z= 0.244 Angle : 0.689 12.223 11346 Z= 0.357 Chirality : 0.044 0.207 1282 Planarity : 0.005 0.072 1440 Dihedral : 6.416 83.246 1157 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.02 % Allowed : 8.40 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1018 helix: 1.33 (0.26), residues: 410 sheet: 0.72 (0.33), residues: 229 loop : -0.25 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.009 0.002 HIS B 91 PHE 0.033 0.002 PHE R 198 TYR 0.014 0.002 TYR R 119 ARG 0.009 0.001 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.3640 (mmt) cc_final: 0.3307 (mtp) REVERT: B 45 MET cc_start: 0.3011 (tpp) cc_final: 0.1674 (mtt) REVERT: B 325 MET cc_start: 0.2415 (ttt) cc_final: 0.2145 (mmt) REVERT: N 83 MET cc_start: 0.0157 (ptm) cc_final: -0.0494 (mmm) outliers start: 18 outliers final: 7 residues processed: 82 average time/residue: 1.0164 time to fit residues: 90.1280 Evaluate side-chains 62 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 119 TYR Chi-restraints excluded: chain R residue 350 THR Chi-restraints excluded: chain R residue 364 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0870 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 82 optimal weight: 0.3980 chunk 66 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2417 moved from start: 0.7245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8381 Z= 0.166 Angle : 0.595 8.288 11346 Z= 0.312 Chirality : 0.043 0.421 1282 Planarity : 0.004 0.070 1440 Dihedral : 5.855 69.078 1157 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.35 % Allowed : 9.74 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 1.08 (0.27), residues: 1018 helix: 1.76 (0.26), residues: 403 sheet: 0.71 (0.34), residues: 222 loop : -0.32 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 335 HIS 0.010 0.001 HIS B 54 PHE 0.023 0.001 PHE R 198 TYR 0.013 0.001 TYR A 360 ARG 0.007 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 307 LYS cc_start: 0.3263 (mmtt) cc_final: 0.2890 (tttm) REVERT: B 45 MET cc_start: 0.2997 (tpp) cc_final: 0.1814 (mtt) REVERT: R 226 MET cc_start: 0.5795 (tpp) cc_final: 0.3725 (ptt) outliers start: 21 outliers final: 9 residues processed: 80 average time/residue: 1.0823 time to fit residues: 93.7616 Evaluate side-chains 62 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 119 TYR Chi-restraints excluded: chain R residue 350 THR Chi-restraints excluded: chain R residue 364 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3906 moved from start: 1.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 8381 Z= 0.316 Angle : 0.858 19.191 11346 Z= 0.435 Chirality : 0.051 0.344 1282 Planarity : 0.006 0.072 1440 Dihedral : 5.762 55.989 1157 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.25 % Allowed : 9.63 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1018 helix: 1.01 (0.26), residues: 402 sheet: 0.42 (0.35), residues: 219 loop : -0.75 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP R 166 HIS 0.007 0.002 HIS B 311 PHE 0.024 0.002 PHE B 235 TYR 0.019 0.002 TYR R 48 ARG 0.011 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.2991 (tpp) cc_final: 0.1743 (tmt) REVERT: B 93 ILE cc_start: 0.4828 (OUTLIER) cc_final: 0.4554 (tp) REVERT: R 121 MET cc_start: 0.5208 (tpt) cc_final: 0.4727 (tpp) REVERT: R 226 MET cc_start: 0.6145 (tpp) cc_final: 0.5591 (ttt) outliers start: 29 outliers final: 9 residues processed: 114 average time/residue: 0.8440 time to fit residues: 104.8858 Evaluate side-chains 82 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 350 THR Chi-restraints excluded: chain R residue 364 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 38 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN N 123 GLN R 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4739 moved from start: 1.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.154 8381 Z= 0.322 Angle : 0.828 11.852 11346 Z= 0.415 Chirality : 0.047 0.172 1282 Planarity : 0.006 0.075 1440 Dihedral : 5.646 48.828 1155 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.02 % Allowed : 14.67 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 1018 helix: 1.37 (0.26), residues: 402 sheet: 0.24 (0.36), residues: 214 loop : -0.71 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 166 HIS 0.008 0.002 HIS A 362 PHE 0.038 0.003 PHE A 219 TYR 0.026 0.003 TYR B 59 ARG 0.018 0.001 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.5835 (mttt) cc_final: 0.5597 (tppt) REVERT: A 227 GLN cc_start: 0.3410 (OUTLIER) cc_final: 0.2028 (mt0) REVERT: B 45 MET cc_start: 0.5136 (tpp) cc_final: 0.4231 (mtp) REVERT: B 91 HIS cc_start: 0.5305 (OUTLIER) cc_final: 0.5033 (t-170) REVERT: N 123 GLN cc_start: 0.1881 (OUTLIER) cc_final: 0.0591 (mm-40) REVERT: R 182 LEU cc_start: 0.5355 (pt) cc_final: 0.4983 (mm) REVERT: R 195 MET cc_start: 0.2307 (tpt) cc_final: 0.1993 (mtp) outliers start: 18 outliers final: 7 residues processed: 122 average time/residue: 0.8715 time to fit residues: 115.9936 Evaluate side-chains 92 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain N residue 123 GLN Chi-restraints excluded: chain R residue 364 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 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 23 ASN A 239 ASN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 207 GLN R 304 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5246 moved from start: 1.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8381 Z= 0.265 Angle : 0.781 10.751 11346 Z= 0.402 Chirality : 0.047 0.247 1282 Planarity : 0.006 0.084 1440 Dihedral : 5.738 51.603 1155 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.91 % Allowed : 16.69 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.27), residues: 1018 helix: 1.39 (0.27), residues: 398 sheet: -0.05 (0.35), residues: 227 loop : -0.78 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 339 HIS 0.004 0.001 HIS A 220 PHE 0.021 0.002 PHE A 238 TYR 0.039 0.002 TYR R 119 ARG 0.016 0.001 ARG R 378 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 0.806 Fit side-chains REVERT: A 21 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6619 (mm-30) REVERT: A 60 MET cc_start: 0.2138 (OUTLIER) cc_final: 0.1595 (tpt) REVERT: B 45 MET cc_start: 0.5452 (OUTLIER) cc_final: 0.4747 (mtp) REVERT: B 91 HIS cc_start: 0.5543 (OUTLIER) cc_final: 0.5268 (t-90) REVERT: B 199 PHE cc_start: 0.3771 (m-10) cc_final: 0.3522 (m-10) REVERT: B 217 MET cc_start: 0.4902 (tpt) cc_final: 0.3722 (ttm) REVERT: B 239 ASN cc_start: 0.4707 (t0) cc_final: 0.4445 (t0) REVERT: B 318 LEU cc_start: 0.6602 (pt) cc_final: 0.6293 (pp) REVERT: N 123 GLN cc_start: 0.2095 (OUTLIER) cc_final: 0.1211 (tp40) REVERT: R 195 MET cc_start: 0.3121 (tpt) cc_final: 0.2849 (mtp) REVERT: R 237 TYR cc_start: 0.6640 (t80) cc_final: 0.6231 (t80) outliers start: 26 outliers final: 9 residues processed: 119 average time/residue: 0.7607 time to fit residues: 100.0223 Evaluate side-chains 91 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 123 GLN Chi-restraints excluded: chain R residue 364 CYS Chi-restraints excluded: chain R residue 372 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS N 123 GLN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5611 moved from start: 1.7171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 8381 Z= 0.307 Angle : 0.841 14.114 11346 Z= 0.430 Chirality : 0.048 0.199 1282 Planarity : 0.006 0.084 1440 Dihedral : 5.805 50.064 1155 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.44 % Favored : 96.46 % Rotamer: Outliers : 2.24 % Allowed : 19.04 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.27), residues: 1018 helix: 1.37 (0.27), residues: 401 sheet: -0.04 (0.36), residues: 212 loop : -0.89 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP B 169 HIS 0.004 0.001 HIS A 220 PHE 0.021 0.002 PHE R 198 TYR 0.019 0.003 TYR R 119 ARG 0.012 0.001 ARG R 378 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.2116 (OUTLIER) cc_final: -0.1564 (mmm) REVERT: A 389 ARG cc_start: 0.7770 (mtt180) cc_final: 0.7508 (mmt-90) REVERT: B 45 MET cc_start: 0.5585 (OUTLIER) cc_final: 0.5310 (mtp) REVERT: B 91 HIS cc_start: 0.5780 (OUTLIER) cc_final: 0.5433 (t-90) REVERT: B 197 ARG cc_start: 0.7559 (tmm-80) cc_final: 0.7229 (ttm-80) REVERT: B 217 MET cc_start: 0.5167 (tpt) cc_final: 0.4405 (ttm) REVERT: B 262 MET cc_start: 0.4199 (tpp) cc_final: 0.3829 (mmt) REVERT: R 237 TYR cc_start: 0.6730 (t80) cc_final: 0.6347 (t80) REVERT: R 306 MET cc_start: 0.5637 (mmp) cc_final: 0.5230 (mmm) outliers start: 20 outliers final: 10 residues processed: 112 average time/residue: 0.9439 time to fit residues: 114.6073 Evaluate side-chains 103 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 364 CYS Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.0770 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 0.0670 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5545 moved from start: 1.7402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8381 Z= 0.207 Angle : 0.730 9.586 11346 Z= 0.369 Chirality : 0.045 0.268 1282 Planarity : 0.005 0.084 1440 Dihedral : 5.600 48.572 1155 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.03 % Favored : 95.87 % Rotamer: Outliers : 1.57 % Allowed : 21.61 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 1018 helix: 1.61 (0.27), residues: 404 sheet: -0.22 (0.34), residues: 224 loop : -0.81 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 277 HIS 0.015 0.001 HIS B 91 PHE 0.022 0.002 PHE B 199 TYR 0.020 0.002 TYR R 119 ARG 0.011 0.001 ARG R 378 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7073 (mm-30) REVERT: A 60 MET cc_start: 0.1805 (OUTLIER) cc_final: -0.1333 (mmm) REVERT: A 389 ARG cc_start: 0.7836 (mtt180) cc_final: 0.7472 (mtp85) REVERT: B 99 TRP cc_start: 0.5922 (OUTLIER) cc_final: 0.4588 (t-100) REVERT: B 217 MET cc_start: 0.4925 (tpt) cc_final: 0.4299 (ttm) REVERT: B 228 ASP cc_start: 0.7704 (m-30) cc_final: 0.7467 (m-30) REVERT: B 262 MET cc_start: 0.4715 (tpp) cc_final: 0.4318 (mmt) REVERT: N 34 MET cc_start: 0.3922 (tmm) cc_final: 0.3328 (tpt) REVERT: R 217 LEU cc_start: 0.8273 (tp) cc_final: 0.7996 (mp) REVERT: R 237 TYR cc_start: 0.6606 (t80) cc_final: 0.6250 (t80) REVERT: R 306 MET cc_start: 0.5484 (mmp) cc_final: 0.5136 (mmm) outliers start: 14 outliers final: 8 residues processed: 99 average time/residue: 0.8769 time to fit residues: 94.7340 Evaluate side-chains 94 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 364 CYS Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 377 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS B 230 ASN N 31 ASN ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 366 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.256405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.203001 restraints weight = 8991.689| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 2.76 r_work: 0.4151 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 1.9844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 8381 Z= 0.331 Angle : 0.905 12.026 11346 Z= 0.463 Chirality : 0.051 0.241 1282 Planarity : 0.008 0.171 1440 Dihedral : 6.290 54.260 1155 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.13 % Favored : 95.68 % Rotamer: Outliers : 1.90 % Allowed : 21.61 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1018 helix: 1.16 (0.27), residues: 401 sheet: -0.38 (0.34), residues: 224 loop : -0.97 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 339 HIS 0.007 0.002 HIS B 91 PHE 0.035 0.003 PHE A 238 TYR 0.026 0.003 TYR N 115 ARG 0.023 0.001 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2696.31 seconds wall clock time: 48 minutes 18.71 seconds (2898.71 seconds total)