Starting phenix.real_space_refine on Wed Feb 12 16:40:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xov_33360/02_2025/7xov_33360_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xov_33360/02_2025/7xov_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/cci-nas-00/data/ceres_data/7xov_33360/02_2025/7xov_33360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xov_33360/02_2025/7xov_33360.map" model { file = "/net/cci-nas-00/data/ceres_data/7xov_33360/02_2025/7xov_33360_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xov_33360/02_2025/7xov_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.90, per 1000 atoms: 0.60 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: 2.33 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.87 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: 2.66 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: 0.320 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.970 Find NCS groups from input model: 0.080 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:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.080 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.846 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: 1.3220 time to fit residues: 123.6999 Evaluate side-chains 60 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.268708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.229447 restraints weight = 8713.801| |-----------------------------------------------------------------------------| r_work (start): 0.4554 rms_B_bonded: 2.56 r_work: 0.4430 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0678 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 to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: B 188 MET cc_start: 0.2437 (OUTLIER) cc_final: 0.0004 (ttt) REVERT: G 21 MET cc_start: 0.3746 (mtm) cc_final: 0.3482 (ttt) REVERT: R 72 MET cc_start: 0.1362 (mmt) cc_final: 0.0585 (mpp) outliers start: 9 outliers final: 4 residues processed: 66 average time/residue: 1.4334 time to fit residues: 100.6940 Evaluate side-chains 55 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 72 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS B 176 GLN B 230 ASN G 44 HIS N 35 ASN N 74 ASN N 82 GLN ** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 ASN R 131 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5221 r_free = 0.5221 target = 0.324202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.5049 r_free = 0.5049 target = 0.294149 restraints weight = 10222.598| |-----------------------------------------------------------------------------| r_work (start): 0.5008 rms_B_bonded: 2.54 r_work: 0.4915 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4306 moved from start: 1.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.166 8381 Z= 0.609 Angle : 1.385 19.012 11346 Z= 0.726 Chirality : 0.067 0.432 1282 Planarity : 0.011 0.096 1440 Dihedral : 11.295 119.701 1161 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 27.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.70 % Favored : 94.11 % Rotamer: Outliers : 4.48 % Allowed : 7.05 % Favored : 88.47 % 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: -1.86 (0.24), residues: 1018 helix: -0.99 (0.23), residues: 399 sheet: -0.76 (0.35), residues: 204 loop : -1.56 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.005 TRP R 166 HIS 0.019 0.005 HIS A 41 PHE 0.057 0.006 PHE R 198 TYR 0.042 0.005 TYR N 60 ARG 0.019 0.002 ARG B 68 *********************** 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 166 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 HIS cc_start: 0.4226 (OUTLIER) cc_final: 0.3792 (p90) REVERT: B 235 PHE cc_start: 0.3903 (OUTLIER) cc_final: 0.3093 (m-80) REVERT: B 323 ASP cc_start: 0.5980 (p0) cc_final: 0.5757 (p0) REVERT: B 338 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7948 (mt) REVERT: R 166 TRP cc_start: 0.6563 (m100) cc_final: 0.5983 (m100) REVERT: R 195 MET cc_start: 0.3623 (tpt) cc_final: 0.3399 (mtp) REVERT: R 327 MET cc_start: 0.3771 (OUTLIER) cc_final: 0.3235 (mmp) outliers start: 40 outliers final: 7 residues processed: 154 average time/residue: 0.8705 time to fit residues: 145.7045 Evaluate side-chains 90 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 119 TYR Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 327 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 0.0060 chunk 21 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS N 74 ASN ** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 153 GLN R 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5094 r_free = 0.5094 target = 0.304744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.268467 restraints weight = 9846.652| |-----------------------------------------------------------------------------| r_work (start): 0.4847 rms_B_bonded: 2.68 r_work: 0.4743 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4629 moved from start: 1.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8381 Z= 0.226 Angle : 0.773 14.339 11346 Z= 0.396 Chirality : 0.046 0.170 1282 Planarity : 0.006 0.073 1440 Dihedral : 7.635 84.666 1157 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.25 % Allowed : 13.21 % Favored : 83.54 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.70 (0.26), residues: 1018 helix: 0.32 (0.25), residues: 409 sheet: -0.22 (0.33), residues: 226 loop : -1.38 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.020 0.002 PHE A 219 TYR 0.018 0.002 TYR R 119 ARG 0.008 0.001 ARG B 219 *********************** 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 120 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 GLN cc_start: 0.3073 (OUTLIER) cc_final: 0.1982 (mp10) REVERT: N 83 MET cc_start: 0.2185 (OUTLIER) cc_final: 0.0495 (mtm) REVERT: R 195 MET cc_start: 0.3403 (tpt) cc_final: 0.3126 (mtp) outliers start: 29 outliers final: 6 residues processed: 109 average time/residue: 0.8546 time to fit residues: 102.0972 Evaluate side-chains 78 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 125 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 78 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5090 r_free = 0.5090 target = 0.302903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.268090 restraints weight = 9708.246| |-----------------------------------------------------------------------------| r_work (start): 0.4809 rms_B_bonded: 2.92 r_work: 0.4657 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4988 moved from start: 1.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8381 Z= 0.211 Angle : 0.709 11.453 11346 Z= 0.360 Chirality : 0.045 0.188 1282 Planarity : 0.005 0.079 1440 Dihedral : 6.344 63.965 1155 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.13 % Allowed : 15.68 % Favored : 82.19 % 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: -0.08 (0.26), residues: 1018 helix: 0.90 (0.26), residues: 412 sheet: 0.03 (0.34), residues: 225 loop : -1.10 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.024 0.002 HIS A 357 PHE 0.012 0.001 PHE A 290 TYR 0.016 0.002 TYR R 119 ARG 0.011 0.001 ARG R 378 *********************** 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 92 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.5400 (mttt) cc_final: 0.5129 (tppt) REVERT: A 227 GLN cc_start: 0.3297 (OUTLIER) cc_final: 0.2339 (mp10) REVERT: R 195 MET cc_start: 0.3475 (tpt) cc_final: 0.3154 (mtp) REVERT: R 372 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6980 (t80) outliers start: 19 outliers final: 8 residues processed: 85 average time/residue: 0.9080 time to fit residues: 84.9715 Evaluate side-chains 78 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 372 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN R 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.284549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.235174 restraints weight = 9326.655| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 2.93 r_work: 0.4455 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5823 moved from start: 1.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8381 Z= 0.289 Angle : 0.839 18.108 11346 Z= 0.427 Chirality : 0.049 0.192 1282 Planarity : 0.006 0.088 1440 Dihedral : 5.949 43.957 1155 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.02 % Allowed : 15.45 % Favored : 81.52 % Cbeta Deviations : 0.10 % 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: -0.08 (0.26), residues: 1018 helix: 0.95 (0.26), residues: 404 sheet: -0.24 (0.34), residues: 235 loop : -0.94 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 339 HIS 0.019 0.003 HIS A 357 PHE 0.031 0.003 PHE B 180 TYR 0.019 0.002 TYR N 60 ARG 0.009 0.001 ARG B 137 *********************** 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 137 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7273 (mm-30) cc_final: 0.7072 (mm-30) REVERT: A 227 GLN cc_start: 0.4023 (OUTLIER) cc_final: 0.3479 (mp10) REVERT: A 389 ARG cc_start: 0.7468 (mtt180) cc_final: 0.7171 (mtt-85) REVERT: B 217 MET cc_start: 0.5079 (tpp) cc_final: 0.3264 (pp-130) REVERT: B 232 ILE cc_start: 0.7100 (mt) cc_final: 0.6882 (mt) REVERT: R 195 MET cc_start: 0.4547 (tpt) cc_final: 0.4193 (ptp) REVERT: R 336 ARG cc_start: 0.4729 (OUTLIER) cc_final: 0.4034 (ttt-90) REVERT: R 338 TYR cc_start: 0.7784 (m-80) cc_final: 0.7531 (m-80) REVERT: R 372 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7148 (t80) REVERT: R 382 MET cc_start: 0.3151 (mmp) cc_final: 0.2801 (mtt) outliers start: 27 outliers final: 3 residues processed: 129 average time/residue: 0.9886 time to fit residues: 137.7926 Evaluate side-chains 88 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain R residue 372 PHE Chi-restraints excluded: chain R residue 377 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 89 optimal weight: 0.0970 chunk 82 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 88 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.276945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.228130 restraints weight = 9017.232| |-----------------------------------------------------------------------------| r_work (start): 0.4541 rms_B_bonded: 2.66 r_work: 0.4412 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 1.6713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8381 Z= 0.198 Angle : 0.703 10.027 11346 Z= 0.358 Chirality : 0.044 0.226 1282 Planarity : 0.004 0.041 1440 Dihedral : 5.376 45.375 1155 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.13 % Allowed : 19.37 % Favored : 78.50 % 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: 0.54 (0.27), residues: 1018 helix: 1.60 (0.27), residues: 400 sheet: -0.09 (0.34), residues: 239 loop : -0.61 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.008 0.001 HIS A 357 PHE 0.023 0.002 PHE A 238 TYR 0.025 0.002 TYR B 264 ARG 0.008 0.001 ARG R 378 *********************** 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 115 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 389 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7425 (mtp85) REVERT: B 197 ARG cc_start: 0.7177 (tmm-80) cc_final: 0.6779 (tpp80) REVERT: B 235 PHE cc_start: 0.6078 (OUTLIER) cc_final: 0.5771 (t80) REVERT: B 325 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8132 (mmp) REVERT: N 83 MET cc_start: 0.4537 (ppp) cc_final: 0.1868 (mmp) REVERT: R 372 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.7366 (m-80) outliers start: 19 outliers final: 9 residues processed: 107 average time/residue: 1.0949 time to fit residues: 126.3865 Evaluate side-chains 93 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 121 MET Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 372 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.276335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.224912 restraints weight = 9373.477| |-----------------------------------------------------------------------------| r_work (start): 0.4502 rms_B_bonded: 2.86 r_work: 0.4382 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 1.7671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8381 Z= 0.223 Angle : 0.702 10.244 11346 Z= 0.361 Chirality : 0.046 0.306 1282 Planarity : 0.005 0.068 1440 Dihedral : 5.460 46.333 1155 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.83 % Favored : 96.07 % Rotamer: Outliers : 2.69 % Allowed : 20.60 % Favored : 76.71 % 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: 0.56 (0.27), residues: 1018 helix: 1.67 (0.27), residues: 400 sheet: -0.14 (0.34), residues: 242 loop : -0.61 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 277 HIS 0.012 0.002 HIS A 357 PHE 0.017 0.002 PHE B 199 TYR 0.014 0.002 TYR N 115 ARG 0.009 0.001 ARG N 98 *********************** 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 112 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.2936 (ttt) cc_final: -0.0163 (mmm) REVERT: A 389 ARG cc_start: 0.7950 (mtt180) cc_final: 0.7488 (mtp85) REVERT: B 99 TRP cc_start: 0.4682 (m100) cc_final: 0.4214 (m100) REVERT: B 121 CYS cc_start: 0.7648 (OUTLIER) cc_final: 0.6974 (t) REVERT: B 217 MET cc_start: 0.5408 (tpt) cc_final: 0.4239 (tmm) REVERT: B 262 MET cc_start: 0.4578 (tpp) cc_final: 0.4122 (mmt) REVERT: N 83 MET cc_start: 0.4658 (ppp) cc_final: 0.2290 (mmm) REVERT: R 137 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7704 (mt) REVERT: R 237 TYR cc_start: 0.6824 (t80) cc_final: 0.6350 (t80) REVERT: R 306 MET cc_start: 0.5572 (mmp) cc_final: 0.5214 (mmm) REVERT: R 327 MET cc_start: 0.7462 (tpt) cc_final: 0.7215 (mmm) REVERT: R 372 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.7430 (m-80) outliers start: 24 outliers final: 10 residues processed: 105 average time/residue: 1.0564 time to fit residues: 119.6977 Evaluate side-chains 93 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 136 SER Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 183 VAL 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 25 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 3 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 77 optimal weight: 0.0030 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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** ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.275807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.224021 restraints weight = 9403.768| |-----------------------------------------------------------------------------| r_work (start): 0.4512 rms_B_bonded: 2.92 r_work: 0.4390 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 1.8129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8381 Z= 0.176 Angle : 0.654 9.741 11346 Z= 0.334 Chirality : 0.043 0.213 1282 Planarity : 0.004 0.054 1440 Dihedral : 5.237 44.955 1155 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.34 % Favored : 96.56 % Rotamer: Outliers : 2.02 % Allowed : 20.94 % Favored : 77.04 % 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: 0.70 (0.27), residues: 1018 helix: 1.75 (0.27), residues: 401 sheet: 0.10 (0.35), residues: 229 loop : -0.62 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 277 HIS 0.009 0.001 HIS A 357 PHE 0.016 0.001 PHE A 290 TYR 0.018 0.002 TYR N 115 ARG 0.010 0.001 ARG N 98 *********************** 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 113 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7437 (tm-30) cc_final: 0.6700 (mm-30) REVERT: A 27 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7203 (tm-30) REVERT: A 60 MET cc_start: 0.2912 (ttt) cc_final: -0.1061 (mmm) REVERT: A 277 TRP cc_start: 0.5265 (m100) cc_final: 0.4978 (t-100) REVERT: A 389 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7594 (mtp85) REVERT: B 99 TRP cc_start: 0.4780 (m100) cc_final: 0.4100 (m100) REVERT: B 121 CYS cc_start: 0.7560 (OUTLIER) cc_final: 0.7115 (t) REVERT: B 262 MET cc_start: 0.5074 (tpp) cc_final: 0.4709 (mmt) REVERT: B 325 MET cc_start: 0.8408 (mmp) cc_final: 0.8114 (mmt) REVERT: N 83 MET cc_start: 0.4712 (ppp) cc_final: 0.2308 (mmm) REVERT: R 137 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7804 (mt) REVERT: R 306 MET cc_start: 0.5680 (mmp) cc_final: 0.5311 (mmm) REVERT: R 327 MET cc_start: 0.7471 (tpt) cc_final: 0.7225 (mmm) REVERT: R 336 ARG cc_start: 0.4588 (OUTLIER) cc_final: 0.4109 (ttt-90) REVERT: R 372 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7425 (OUTLIER) REVERT: R 378 ARG cc_start: 0.6090 (mtm110) cc_final: 0.5546 (ptt90) outliers start: 18 outliers final: 10 residues processed: 106 average time/residue: 1.1295 time to fit residues: 128.2021 Evaluate side-chains 98 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 136 SER Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain R residue 372 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 84 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 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 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.258094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.204930 restraints weight = 8839.526| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 2.75 r_work: 0.4238 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 1.9709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8381 Z= 0.282 Angle : 0.836 11.141 11346 Z= 0.426 Chirality : 0.050 0.460 1282 Planarity : 0.005 0.056 1440 Dihedral : 6.026 53.089 1155 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.13 % Favored : 95.78 % Rotamer: Outliers : 1.79 % Allowed : 21.61 % Favored : 76.60 % 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: 0.18 (0.27), residues: 1018 helix: 1.37 (0.27), residues: 401 sheet: -0.20 (0.35), residues: 217 loop : -0.92 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 281 HIS 0.013 0.002 HIS A 357 PHE 0.030 0.003 PHE A 290 TYR 0.016 0.002 TYR N 115 ARG 0.015 0.001 ARG N 98 ********************** 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 127 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.2718 (ttt) cc_final: -0.0547 (mmm) REVERT: A 389 ARG cc_start: 0.7966 (mtt180) cc_final: 0.7558 (mtp85) REVERT: B 121 CYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7843 (t) REVERT: B 192 LEU cc_start: 0.8271 (mp) cc_final: 0.8057 (mt) REVERT: B 262 MET cc_start: 0.7041 (tpp) cc_final: 0.6454 (tpt) REVERT: B 264 TYR cc_start: 0.8526 (m-80) cc_final: 0.8263 (m-80) REVERT: R 306 MET cc_start: 0.6342 (mmp) cc_final: 0.5882 (mmm) REVERT: R 336 ARG cc_start: 0.4879 (OUTLIER) cc_final: 0.4467 (ttt-90) REVERT: R 379 LEU cc_start: 0.5562 (mp) cc_final: 0.5227 (mp) REVERT: R 382 MET cc_start: 0.4446 (mmp) cc_final: 0.4232 (mtt) outliers start: 16 outliers final: 8 residues processed: 122 average time/residue: 0.9445 time to fit residues: 124.7961 Evaluate side-chains 103 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain R residue 372 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 0.0980 chunk 86 optimal weight: 0.0060 chunk 14 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 390 GLN B 230 ASN N 35 ASN R 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.252622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.202043 restraints weight = 9041.900| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 2.59 r_work: 0.4212 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 2.0001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8381 Z= 0.191 Angle : 0.712 13.070 11346 Z= 0.363 Chirality : 0.045 0.207 1282 Planarity : 0.004 0.038 1440 Dihedral : 5.602 47.633 1155 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.93 % Favored : 95.97 % Rotamer: Outliers : 2.24 % Allowed : 23.29 % Favored : 74.47 % 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: 0.49 (0.27), residues: 1018 helix: 1.74 (0.27), residues: 405 sheet: -0.18 (0.35), residues: 228 loop : -0.84 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 277 HIS 0.009 0.002 HIS A 357 PHE 0.016 0.001 PHE A 290 TYR 0.014 0.002 TYR N 95 ARG 0.008 0.001 ARG N 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5422.02 seconds wall clock time: 96 minutes 29.31 seconds (5789.31 seconds total)